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
AGRN	375790	broad.mit.edu	37	1	979279	979279	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:979279delC	uc001ack.1	+	10	1925	c.1875delC	c.(1873-1875)CACfs	p.H625fs		NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin precursor	625	Kazal-like 7.				axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1883792	1883793	+	IGR	DEL	AA	-	-	rs111449449		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1883792_1883793delAA								TMEM52 (33052 upstream) : KIAA1751 (959 downstream)																																			---	---	---	---
KIAA1751	85452	broad.mit.edu	37	1	1896381	1896381	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1896381delC	uc001aim.1	-	13	1677	c.1521delG	c.(1519-1521)GGGfs	p.G507fs	KIAA1751_uc009vkz.1_Frame_Shift_Del_p.G507fs	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	507										pancreas(1)	1	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;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	2994603	2994603	+	Intron	DEL	C	-	-	rs34471979		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2994603delC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3300824	3300824	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3300824delC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	1	4025572	4025572	+	IGR	DEL	T	-	-	rs34400281		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4025572delT								LOC100133612 (191695 upstream) : LOC284661 (446539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5349681	5349682	+	IGR	INS	-	ATGG	ATGG	rs145485294	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5349681_5349682insATGG								AJAP1 (505831 upstream) : NPHP4 (573188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5715742	5715743	+	Intron	INS	-	T	T	rs140272906		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5715742_5715743insT	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6173484	6173484	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6173484delA	uc001amb.1	-						CHD5_uc001alz.1_Intron|CHD5_uc001ama.1_Intron	NM_015557	NP_056372			chromodomain helicase DNA binding protein 5						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)														---	---	---	---
NOL9	79707	broad.mit.edu	37	1	6600055	6600055	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6600055delT	uc001ans.2	-						NOL9_uc010nzs.1_Intron	NM_024654	NP_078930			nucleolar protein 9						maturation of 5.8S rRNA	nucleolus	ATP binding|polynucleotide 5'-hydroxyl-kinase activity|RNA binding			skin(1)	1	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7000989	7000989	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7000989delA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7232219	7232219	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7232219delT	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7708452	7708452	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7708452delA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
NMNAT1	64802	broad.mit.edu	37	1	10044970	10044970	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10044970delT	uc001aqp.2	+	5						NM_022787	NP_073624			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	nucleoplasm	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity|protein binding				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10177642	10177642	+	Frame_Shift_Del	DEL	A	-	-	rs143511579	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10177642delA	uc001aqs.3	+	8	2035	c.1322delA	c.(1321-1323)GAAfs	p.E441fs	UBE4B_uc001aqr.3_Frame_Shift_Del_p.E312fs|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_5'UTR	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	441					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10211221	10211221	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10211221delA	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron|UBE4B_uc001aqt.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10376960	10376961	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10376960_10376961insT	uc001aqx.3	+						KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
DFFA	1676	broad.mit.edu	37	1	10527572	10527572	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10527572delT	uc001arj.2	-						DFFA_uc001ark.2_Intron	NM_004401	NP_004392			DNA fragmentation factor, 45kDa, alpha						DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis	cytosol|mitochondrion|nucleoplasm|plasma membrane	deoxyribonuclease activity|identical protein binding				0	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
PEX14	5195	broad.mit.edu	37	1	10550758	10550763	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10550758_10550763delTTTTTT	uc001arn.2	+						PEX14_uc001arm.1_Intron|PEX14_uc009vmu.1_Intron|PEX14_uc009vmv.2_Intron|PEX14_uc010oam.1_Intron|PEX14_uc010oan.1_Intron|PEX14_uc001arl.2_Intron	NM_004565	NP_004556			peroxisomal biogenesis factor 14						negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10781350	10781350	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10781350delA	uc001aro.2	-						CASZ1_uc001arp.1_Intron	NM_001079843	NP_001073312			castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11227303	11227303	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11227303delA	uc001asd.2	-							NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
PTCHD2	57540	broad.mit.edu	37	1	11595512	11595512	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11595512delC	uc001ash.3	+							NM_020780	NP_065831			patched domain containing 2						cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	11599192	11599193	+	IGR	INS	-	AG	AG	rs142115100	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11599192_11599193insAG								PTCHD2 (1553 upstream) : FBXO2 (109257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	11618157	11618157	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11618157delG								PTCHD2 (20518 upstream) : FBXO2 (90293 downstream)																																			---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12198204	12198206	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12198204_12198206delAAA	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron|TNFRSF8_uc001atr.2_Intron|TNFRSF8_uc001ats.2_Intron	NM_001243	NP_001234			tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;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)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12303016	12303016	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12303016delT	uc001atv.2	+						VPS13D_uc001atw.2_Intron	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
FHAD1	114827	broad.mit.edu	37	1	15656201	15656202	+	Intron	DEL	AA	-	-	rs111349324		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15656201_15656202delAA	uc001awb.2	+						FHAD1_uc001awa.1_Intron|uc001awc.1_Intron	NM_052929	NP_443161			forkhead-associated (FHA) phosphopeptide binding											skin(1)	1																		---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15862427	15862427	+	Intron	DEL	T	-	-	rs112722089		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15862427delT	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron	NM_015291	NP_056106			DnaJ (Hsp40) homolog, subfamily C, member 16						cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15873410	15873410	+	Intron	DEL	C	-	-	rs76961003		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15873410delC	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron	NM_015291	NP_056106			DnaJ (Hsp40) homolog, subfamily C, member 16						cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
C1orf64	149563	broad.mit.edu	37	1	16328001	16328002	+	5'Flank	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16328001_16328002delAA	uc001axn.2	+							NM_178840	NP_849162			hypothetical protein LOC149563											breast(2)	2		Colorectal(325;0.000435)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16841472	16841472	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16841472delT								CROCCL2 (22276 upstream) : NBPF1 (48940 downstream)																																			---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17202932	17202932	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17202932delT	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17299013	17299014	+	3'UTR	DEL	CA	-	-	rs6661019	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17299013_17299014delCA	uc001azt.2	+	37					CROCC_uc001azu.2_3'UTR|CROCC_uc001azv.2_3'UTR	NM_014675	NP_055490			ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	17345217	17345217	+	IGR	DEL	T	-	-	rs75557632		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17345217delT								ATP13A2 (6794 upstream) : SDHB (10 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	17631664	17631665	+	IGR	DEL	GA	-	-	rs59625190		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17631664_17631665delGA								PADI3 (20939 upstream) : PADI4 (3025 downstream)																																			---	---	---	---
PADI4	23569	broad.mit.edu	37	1	17680744	17680745	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17680744_17680745delAA	uc001baj.2	+							NM_012387	NP_036519			peptidyl arginine deiminase, type IV						chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)													---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17735793	17735793	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17735793delA	uc001bal.2	-						RCC2_uc001bam.2_Intron	NM_001136204	NP_001129676			regulator of chromosome condensation 2						cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)														---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17748523	17748523	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17748523delA	uc001bal.2	-						RCC2_uc001bam.2_Intron	NM_001136204	NP_001129676			regulator of chromosome condensation 2						cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18912392	18912392	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18912392delG								KLHDC7A (99853 upstream) : PAX7 (45108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	19906566	19906568	+	IGR	DEL	TCT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19906566_19906568delTCT								CAPZB (94574 upstream) : C1orf151 (16899 downstream)																																			---	---	---	---
NBL1	4681	broad.mit.edu	37	1	19949953	19949953	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19949953delT	uc009vpl.1	+						C1orf151_uc001bch.1_Intron|C1orf151_uc001bci.1_Intron	NM_005380	NP_005371			neuroblastoma, suppression of tumorigenicity 1 2							extracellular region				ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00043)|Ovarian(437;0.00373)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.9e-05)|Kidney(64;0.000173)|GBM - Glioblastoma multiforme(114;0.0012)|KIRC - Kidney renal clear cell carcinoma(64;0.0026)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PLA2G2F	64600	broad.mit.edu	37	1	20467902	20467905	+	Intron	DEL	GTGA	-	-	rs10580056		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20467902_20467905delGTGA	uc009vpp.1	+							NM_022819	NP_073730			phospholipase A2, group IIF						lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)														---	---	---	---
HP1BP3	50809	broad.mit.edu	37	1	21097593	21097593	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21097593delT	uc001bdw.1	-						HP1BP3_uc001bdv.1_Intron|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Intron|HP1BP3_uc001bdz.2_Intron|HP1BP3_uc001bea.2_Intron|HP1BP3_uc010odg.1_Intron	NM_016287	NP_057371			HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21307744	21307746	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21307744_21307746delTTT	uc001bec.2	-						EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21560488	21560488	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21560488delT	uc001bek.2	-						ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron|ECE1_uc009vqa.1_Intron	NM_001397	NP_001388			endothelin converting enzyme 1 isoform 1						bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22079458	22079459	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22079458_22079459delAA	uc001bfb.2	-						USP48_uc010odq.1_Intron|USP48_uc009vqc.2_Intron|USP48_uc001bfc.2_Intron|USP48_uc001bfe.1_Intron|USP48_uc001bff.2_Intron	NM_032236	NP_115612			ubiquitin specific protease 48 isoform a						ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22080659	22080659	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22080659delA	uc001bfb.2	-						USP48_uc010odq.1_Intron|USP48_uc009vqc.2_Intron|USP48_uc001bfc.2_Intron|USP48_uc001bfe.1_Intron|USP48_uc001bff.2_Intron	NM_032236	NP_115612			ubiquitin specific protease 48 isoform a						ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
CDC42	998	broad.mit.edu	37	1	22400032	22400032	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22400032delA	uc001bfq.2	+						CDC42_uc009vqg.1_Intron|CDC42_uc001bfp.2_Intron|CDC42_uc001bfr.2_Intron|CDC42_uc010odr.1_Intron|CDC42_uc010ods.1_Intron|CDC42_uc009vqh.2_Intron	NM_001039802	NP_001034891			cell division cycle 42 isoform 1						actin cytoskeleton organization|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|establishment or maintenance of cell polarity|macrophage differentiation|muscle cell differentiation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of protein complex assembly|positive regulation of muscle cell differentiation|positive regulation of pseudopodium assembly|regulation of filopodium assembly|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|filopodium|plasma membrane	GTP binding|GTPase activity|protein binding|thioesterase binding			haematopoietic_and_lymphoid_tissue(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)														---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23125450	23125450	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23125450delG	uc009vqj.1	+						EPHB2_uc001bge.2_Intron|EPHB2_uc001bgf.2_Intron|EPHB2_uc010odu.1_Intron	NM_017449	NP_059145			ephrin receptor EphB2 isoform 1 precursor						axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)										Hereditary_Prostate_Cancer				---	---	---	---
FUCA1	2517	broad.mit.edu	37	1	24175456	24175456	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24175456delT	uc001bie.2	-							NM_000147	NP_000138			fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)														---	---	---	---
IL28RA	163702	broad.mit.edu	37	1	24504774	24504774	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24504774delA	uc001bis.2	-						IL28RA_uc001bir.2_Intron|IL28RA_uc001bit.2_Intron|IL28RA_uc001biu.2_Intron|IL28RA_uc001biv.2_Intron	NM_170743	NP_734464			interleukin 28 receptor, alpha isoform 1						cytokine-mediated signaling pathway|negative regulation of cell proliferation|regulation of defense response to virus by host	interleukin-28 receptor complex	protein binding|receptor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00117)|all_lung(284;0.00151)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.21e-24)|Colorectal(126;6.61e-08)|COAD - Colon adenocarcinoma(152;3.56e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00918)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.185)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	24624424	24624425	+	IGR	INS	-	AGG	AGG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24624424_24624425insAGG								LOC284632 (86244 upstream) : GRHL3 (21456 downstream)																																			---	---	---	---
C1orf201	90529	broad.mit.edu	37	1	24684918	24684918	+	3'UTR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24684918delC	uc001bjc.2	-	9					C1orf201_uc010oej.1_Frame_Shift_Del_p.G160fs|C1orf201_uc001bja.2_3'UTR|C1orf201_uc001bjb.2_3'UTR|C1orf201_uc001bjd.2_3'UTR					RecName: Full=UPF0490 protein C1orf201;											ovary(1)|breast(1)	2		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.0191)|all_lung(284;0.0251)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.056)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.48e-25)|Colorectal(126;7.29e-08)|COAD - Colon adenocarcinoma(152;3.85e-06)|GBM - Glioblastoma multiforme(114;0.000399)|BRCA - Breast invasive adenocarcinoma(304;0.00107)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00393)|READ - Rectum adenocarcinoma(331;0.0672)|Lung(427;0.145)														---	---	---	---
CLIC4	25932	broad.mit.edu	37	1	25167137	25167138	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25167137_25167138insT	uc001bjo.2	+						CLIC4_uc001bjn.2_Intron|CLIC4_uc001bjp.1_Intron	NM_013943	NP_039234			chloride intracellular channel 4						cellular response to calcium ion|establishment or maintenance of apical/basal cell polarity|keratinocyte differentiation|negative regulation of cell migration|regulation of cytoskeleton organization	actin cytoskeleton|apical part of cell|cell surface|cell-cell junction|centrosome|chloride channel complex|cytoplasmic vesicle membrane|cytosol|microvillus|midbody|mitochondrion|nuclear matrix|perinuclear region of cytoplasm|soluble fraction	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	25192416	25192416	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25192416delA								CLIC4 (21601 upstream) : RUNX3 (33587 downstream)																																			---	---	---	---
CCDC21	64793	broad.mit.edu	37	1	26560432	26560432	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26560432delC	uc001bls.1	+						CCDC21_uc001blr.2_5'Flank|CCDC21_uc010ofa.1_5'Flank	NM_022778	NP_073615			coiled-coil domain containing 21							centrosome|nucleolus|spindle pole					0		all_cancers(24;7e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.6e-26)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;9.48e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00917)|READ - Rectum adenocarcinoma(331;0.0649)												OREG0013263	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DHDDS	79947	broad.mit.edu	37	1	26764478	26764481	+	Intron	DEL	AAGT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26764478_26764481delAAGT	uc001bml.2	+						DHDDS_uc001bmk.2_Intron|DHDDS_uc001bmm.2_Intron|DHDDS_uc001bmn.2_Intron|DHDDS_uc010ofd.1_Intron	NM_205861	NP_995583			dehydrodolichyl diphosphate synthase isoform b								protein binding|transferase activity, transferring alkyl or aryl (other than methyl) groups			breast(3)	3		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27105757	27105757	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27105757delT	uc001bmv.1	+	20	5741	c.5368delT	c.(5368-5370)TTTfs	p.F1790fs	ARID1A_uc001bmu.1_Frame_Shift_Del_p.F1573fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.F636fs|ARID1A_uc009vsm.1_Frame_Shift_Del_p.F118fs|ARID1A_uc009vsn.1_Frame_Shift_Del_p.F32fs	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1790					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
C1orf172	126695	broad.mit.edu	37	1	27278443	27278443	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27278443delG	uc001bni.1	-	2	518	c.429delC	c.(427-429)CCCfs	p.P143fs		NM_152365	NP_689578	Q8NAX2	CA172_HUMAN	hypothetical protein LOC126695	143										large_intestine(1)|ovary(1)	2		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	27312253	27312254	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27312253_27312254insT								C1orf172 (25356 upstream) : TRNP1 (7941 downstream)																																			---	---	---	---
PTAFR	5724	broad.mit.edu	37	1	28519149	28519149	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28519149delT	uc001bpm.3	-						PTAFR_uc009vte.2_Intron	NM_000952	NP_000943			platelet-activating factor receptor						chemotaxis|inflammatory response|interferon-gamma-mediated signaling pathway|phosphatidylinositol-mediated signaling	integral to plasma membrane|nucleus	phospholipid binding|platelet activating factor receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28800189	28800190	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28800189_28800190insA	uc001bpw.2	+	7	1229_1230	c.947_948insA	c.(946-948)ACAfs	p.T316fs	PHACTR4_uc001bpv.1_RNA|PHACTR4_uc001bpx.2_Frame_Shift_Ins_p.T300fs|PHACTR4_uc001bpy.2_Frame_Shift_Ins_p.T326fs	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1	316	Pro-rich.						actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28817356	28817357	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817356_28817357delAA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28817970	28817970	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817970delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	29041386	29041387	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29041386_29041387delAA								GMEB1 (1 upstream) : YTHDF2 (21749 downstream)																																			---	---	---	---
YTHDF2	51441	broad.mit.edu	37	1	29070507	29070509	+	Intron	DEL	CTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29070507_29070509delCTT	uc001brc.2	+						YTHDF2_uc001brd.2_Intron|YTHDF2_uc010ofx.1_Intron|YTHDF2_uc001bre.2_Intron	NM_016258	NP_057342			high glucose-regulated protein 8						humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	30380810	30380810	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30380810delT								PTPRU (727495 upstream) : MATN1 (803316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30503947	30503947	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30503947delA	uc001bry.3	-											Homo sapiens cDNA clone IMAGE:4830073.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	30716648	30716648	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30716648delA								None (None upstream) : MATN1 (467478 downstream)																																			---	---	---	---
MATN1	4146	broad.mit.edu	37	1	31194129	31194129	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31194129delC	uc001brz.2	-						uc001bsb.1_Intron|MATN1_uc001bsa.1_5'Flank	NM_002379	NP_002370			matrilin 1, cartilage matrix protein precursor						protein complex assembly	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			central_nervous_system(1)	1		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31791934	31791934	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31791934delT	uc001bsp.1	+						ZCCHC17_uc001bsq.1_Intron|ZCCHC17_uc010ogf.1_Intron|ZCCHC17_uc009vtu.1_Intron|ZCCHC17_uc001bsr.1_Intron|ZCCHC17_uc009vtv.1_Intron	NM_016505	NP_057589			zinc finger, CCHC domain containing 17							nucleolus	RNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31806156	31806156	+	Intron	DEL	A	-	-	rs66508728		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31806156delA	uc001bsp.1	+						ZCCHC17_uc001bsq.1_Intron|ZCCHC17_uc010ogf.1_Intron|ZCCHC17_uc009vtu.1_Intron|ZCCHC17_uc001bsr.1_Intron|ZCCHC17_uc009vtv.1_Intron	NM_016505	NP_057589			zinc finger, CCHC domain containing 17							nucleolus	RNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)														---	---	---	---
TMEM39B	55116	broad.mit.edu	37	1	32568356	32568356	+	3'UTR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32568356delG	uc010ogv.1	+	9					TMEM39B_uc001bue.3_3'UTR|TMEM39B_uc001buf.3_3'UTR|TMEM39B_uc010ogw.1_3'UTR	NM_018056	NP_060526			transmembrane protein 39B							integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
SYNC	81493	broad.mit.edu	37	1	33146114	33146114	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33146114delT	uc001bvt.2	-	5					SYNC_uc010ohl.1_3'UTR|RBBP4_uc001bvr.2_3'UTR|RBBP4_uc001bvs.2_3'UTR|RBBP4_uc010ohj.1_3'UTR|RBBP4_uc010ohk.1_3'UTR	NM_030786	NP_110413			syncoilin, intermediate filament 1 isoform 1							intermediate filament|perinuclear region of cytoplasm	structural molecule activity			ovary(1)	1																		---	---	---	---
S100PBP	64766	broad.mit.edu	37	1	33294811	33294811	+	Intron	DEL	T	-	-	rs11343539		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33294811delT	uc001bvz.2	+						S100PBP_uc001bwa.1_Intron|S100PBP_uc001bwb.1_Intron|S100PBP_uc001bwc.2_Intron|S100PBP_uc001bwd.2_Intron	NM_022753	NP_073590			S100P binding protein isoform a							nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)																---	---	---	---
RNF19B	127544	broad.mit.edu	37	1	33410296	33410296	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33410296delT	uc010oho.1	-						RNF19B_uc001bwm.3_Intron|RNF19B_uc010ohp.1_Intron	NM_153341	NP_699172			ring finger protein 19B isoform a							integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	33460084	33460084	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33460084delG	uc001bwn.2	+											Homo sapiens cDNA clone IMAGE:4825059, with apparent retained intron.																														---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34003276	34003276	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34003276delC	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	35061567	35061568	+	IGR	INS	-	AAT	AAT	rs59497704		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35061567_35061568insAAT								C1orf94 (376838 upstream) : MIR552 (73632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	35119325	35119325	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35119325delA								C1orf94 (434596 upstream) : MIR552 (15875 downstream)																																			---	---	---	---
ZMYM1	79830	broad.mit.edu	37	1	35561402	35561402	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35561402delT	uc001bym.2	+						ZMYM1_uc001byl.1_Intron|ZMYM1_uc009vus.1_Intron|ZMYM1_uc001byn.2_Intron|ZMYM1_uc010ohu.1_Intron|ZMYM1_uc001byo.2_Intron|ZMYM1_uc009vut.2_Intron	NM_024772	NP_079048			zinc finger, MYM domain containing 1							nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C3	192669	broad.mit.edu	37	1	36394061	36394061	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36394061delT	uc001bzp.2	+						EIF2C3_uc001bzn.1_5'Flank|EIF2C3_uc001bzo.2_5'Flank|EIF2C3_uc001bzq.2_5'Flank|uc001bzm.1_RNA	NM_024852	NP_079128			eukaryotic translation initiation factor 2C, 3						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C3	192669	broad.mit.edu	37	1	36474484	36474484	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36474484delT	uc001bzp.2	+						EIF2C3_uc001bzq.2_Intron	NM_024852	NP_079128			eukaryotic translation initiation factor 2C, 3						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	37568561	37568566	+	IGR	DEL	GAAGAA	-	-	rs849947		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37568561_37568566delGAAGAA								GRIK3 (68717 upstream) : ZC3H12A (371553 downstream)																																			---	---	---	---
MEAF6	64769	broad.mit.edu	37	1	37968087	37968087	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37968087delG	uc001cbg.1	-						MEAF6_uc001cbd.1_Intron|MEAF6_uc001cbe.1_Intron|MEAF6_uc009vvd.1_Intron|MEAF6_uc001cbf.1_Intron|MEAF6_uc001cbh.1_Intron	NM_022756	NP_073593			MYST/Esa1-associated factor 6						histone H2A acetylation|histone H3-K14 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|NuA4 histone acetyltransferase complex|nucleolus	protein binding				0																		---	---	---	---
INPP5B	3633	broad.mit.edu	37	1	38369551	38369551	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38369551delA	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001ccf.1_Intron	NM_005540	NP_005531			inositol polyphosphate-5-phosphatase, 75kDa						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
RRAGC	64121	broad.mit.edu	37	1	39306392	39306392	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39306392delA	uc001ccq.2	-						RRAGC_uc010oim.1_Intron|RRAGC_uc001ccr.2_Intron	NM_022157	NP_071440			Ras-related GTP binding C						apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent	lysosome|nucleus	GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
RRAGC	64121	broad.mit.edu	37	1	39322850	39322850	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39322850delA	uc001ccq.2	-						RRAGC_uc010oim.1_Intron|RRAGC_uc001ccr.2_Intron	NM_022157	NP_071440			Ras-related GTP binding C						apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent	lysosome|nucleus	GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
PPT1	5538	broad.mit.edu	37	1	40558364	40558367	+	Intron	DEL	ACTT	-	-	rs72144657		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40558364_40558367delACTT	uc001cfb.2	-						PPT1_uc010ojf.1_5'Flank|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301			palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40597185	40597185	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40597185delT								PPT1 (34043 upstream) : RLF (29856 downstream)																																			---	---	---	---
RIMS3	9783	broad.mit.edu	37	1	41101736	41101736	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41101736delC	uc001cfu.1	-						RIMS3_uc001cfv.1_Intron	NM_014747	NP_055562			regulating synaptic membrane exocytosis 3						neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)															---	---	---	---
CTPS	1503	broad.mit.edu	37	1	41442625	41442627	+	5'Flank	DEL	AGG	-	-	rs10539027		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41442625_41442627delAGG	uc001cgk.3	+						CTPS_uc010ojo.1_5'Flank	NM_001905	NP_001896			CTP synthase						CTP biosynthetic process|glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|response to drug	cytosol	ATP binding|CTP synthase activity|protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)			L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	41847249	41847249	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41847249delC								SCMH1 (139461 upstream) : EDN2 (97200 downstream)																																			---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42028272	42028273	+	Intron	INS	-	TC	TC	rs5020941		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42028272_42028273insTC	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42097264	42097264	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42097264delC	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
YBX1	4904	broad.mit.edu	37	1	43162183	43162184	+	Intron	DEL	CC	-	-	rs113762321		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43162183_43162184delCC	uc001chs.2	+							NM_004559	NP_004550			nuclease sensitive element binding protein 1						CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
PTPRF	5792	broad.mit.edu	37	1	44071012	44071012	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44071012delC	uc001cjr.2	+	18	3627	c.3287delC	c.(3286-3288)GCCfs	p.A1096fs	PTPRF_uc001cjs.2_Frame_Shift_Del_p.A1087fs|PTPRF_uc001cju.2_Frame_Shift_Del_p.A474fs|PTPRF_uc009vwt.2_Frame_Shift_Del_p.A656fs|PTPRF_uc001cjv.2_Frame_Shift_Del_p.A556fs|PTPRF_uc001cjw.2_Frame_Shift_Del_p.A322fs	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1096	Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	44408688	44408689	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44408688_44408689delAA								ARTN (5777 upstream) : IPO13 (3789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	45245946	45245946	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45245946delT								RPS8 (1535 upstream) : BEST4 (3313 downstream)																																			---	---	---	---
ZSWIM5	57643	broad.mit.edu	37	1	45560533	45560534	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45560533_45560534delAA	uc001cnd.2	-							NM_020883	NP_065934			zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
RAD54L	8438	broad.mit.edu	37	1	46728344	46728344	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46728344delT	uc009vye.2	+						RAD54L_uc001cpl.2_Intron|RAD54L_uc001cpm.1_Intron	NM_001142548	NP_001136020			RAD54-like protein						meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)									Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
ATPAF1	64756	broad.mit.edu	37	1	47116483	47116486	+	Intron	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47116483_47116486delAAAA	uc001cqh.2	-						ATPAF1_uc001cqg.2_Intron|ATPAF1_uc009vyk.2_Intron|ATPAF1_uc010omg.1_Intron|ATPAF1_uc001cqi.2_Intron	NM_022745	NP_073582			ATP synthase mitochondrial F1 complex assembly						protein complex assembly	mitochondrion	protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KIAA0494	9813	broad.mit.edu	37	1	47139255	47139255	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47139255delA	uc010omh.1	-							NM_014774	NP_055589			hypothetical protein LOC9813								calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KIAA0494	9813	broad.mit.edu	37	1	47156706	47156706	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47156706delT	uc001cqk.3	-						KIAA0494_uc010omh.1_Intron|KIAA0494_uc010omj.1_Intron|KIAA0494_uc001cql.1_Intron	NM_014774	NP_055589			hypothetical protein LOC9813								calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4X1	260293	broad.mit.edu	37	1	47513264	47513265	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47513264_47513265delTG	uc001cqt.2	+						CYP4X1_uc001cqr.2_Intron|CYP4X1_uc001cqs.2_Intron	NM_178033	NP_828847			cytochrome P450, family 4, subfamily X,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2																		---	---	---	---
CYP4Z1	199974	broad.mit.edu	37	1	47581140	47581140	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47581140delA	uc001cqu.1	+							NM_178134	NP_835235			cytochrome P450 4Z1							endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	48268688	48268688	+	IGR	DEL	A	-	-	rs78678581		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48268688delA								FOXD2 (362326 upstream) : SKINTL (298699 downstream)																																			---	---	---	---
ELAVL4	1996	broad.mit.edu	37	1	50572178	50572178	+	5'Flank	DEL	A	-	-	rs79810783		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50572178delA	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_5'Flank	NM_021952	NP_068771			ELAV-like 4 isoform 1						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	50791851	50791851	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50791851delC								ELAVL4 (124311 upstream) : DMRTA2 (91378 downstream)																																			---	---	---	---
C1orf185	284546	broad.mit.edu	37	1	51592963	51592964	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51592963_51592964delTT	uc001csh.2	+							NM_001136508	NP_001129980			hypothetical protein LOC284546							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	51623572	51623572	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51623572delG								C1orf185 (9820 upstream) : RNF11 (78373 downstream)																																			---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51825423	51825424	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51825423_51825424delAA	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
OSBPL9	114883	broad.mit.edu	37	1	52212231	52212232	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52212231_52212232insA	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron|OSBPL9_uc001csy.2_Intron|OSBPL9_uc001csz.2_Intron|OSBPL9_uc001cta.2_Intron	NM_024586	NP_078862			oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1																		---	---	---	---
RAB3B	5865	broad.mit.edu	37	1	52446560	52446561	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52446560_52446561insA	uc001cth.2	-							NM_002867	NP_002858			RAB3B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52810259	52810259	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52810259delT	uc001cto.2	+						ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52936605	52936606	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52936605_52936606delTC	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron	NM_015269	NP_056084			zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52937901	52937901	+	Intron	DEL	A	-	-	rs78098408		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52937901delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron	NM_015269	NP_056084			zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
C1orf123	54987	broad.mit.edu	37	1	53687489	53687489	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53687489delA	uc001cvd.2	-						C1orf123_uc001cve.2_5'Flank	NM_017887	NP_060357			hypothetical protein LOC54987											pancreas(2)	2																		---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54870482	54870484	+	Intron	DEL	GGG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54870482_54870484delGGG	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron	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																		---	---	---	---
ACOT11	26027	broad.mit.edu	37	1	55052098	55052101	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55052098_55052101delTTTT	uc001cxm.1	+						ACOT11_uc001cxj.1_Intron|ACOT11_uc001cxk.2_Intron|ACOT11_uc001cxl.1_Intron	NM_015547	NP_056362			thioesterase, adipose associated isoform BFIT1						fatty acid metabolic process|intracellular signal transduction|response to cold		acyl-CoA thioesterase activity|carboxylesterase activity			central_nervous_system(1)	1																		---	---	---	---
C1orf175	374977	broad.mit.edu	37	1	55157531	55157532	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55157531_55157532delTC	uc010ooe.1	+						C1orf175_uc001cxq.2_Intron|C1orf175_uc010ooc.1_Intron|C1orf175_uc001cxs.2_Intron|C1orf175_uc010ood.1_Intron|C1orf175_uc010oof.1_Intron|C1orf175_uc001cxr.1_Intron|C1orf175_uc010oog.1_Intron|C1orf175_uc010ooh.1_Intron|C1orf175_uc009vzq.1_Intron|C1orf175_uc001cxt.1_Intron|C1orf175_uc009vzr.1_Intron|C1orf175_uc001cxu.2_Intron	NM_001039464	NP_001034553			hypothetical protein LOC374977							integral to membrane	binding				0																		---	---	---	---
TMEM61	199964	broad.mit.edu	37	1	55453100	55453100	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55453100delT	uc001cyd.2	+							NM_182532	NP_872338			transmembrane protein 61							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	56421958	56421958	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56421958delG								USP24 (741196 upstream) : PPAP2B (538475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56781748	56781748	+	IGR	DEL	G	-	-	rs113364852		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56781748delG								None (None upstream) : PPAP2B (178685 downstream)																																			---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57755566	57755567	+	Intron	INS	-	G	G	rs138474260	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57755566_57755567insG	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58061299	58061299	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58061299delC	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58461497	58461497	+	Intron	DEL	A	-	-	rs76433154		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58461497delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58490727	58490728	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58490727_58490728delTC	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58918071	58918071	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58918071delA	uc001cyt.1	-							NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	59049357	59049358	+	IGR	INS	-	C	C	rs74076870		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59049357_59049358insC								TACSTD2 (6191 upstream) : MYSM1 (76232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	59676814	59676816	+	IGR	DEL	TGA	-	-	rs331632	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59676814_59676816delTGA								LOC729467 (64335 upstream) : FGGY (85809 downstream)																																			---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59978574	59978574	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59978574delT	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron|FGGY_uc001czm.3_5'Flank	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
C1orf87	127795	broad.mit.edu	37	1	60540639	60540639	+	5'Flank	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60540639delG	uc001czs.1	-							NM_152377	NP_689590			hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61904670	61904671	+	Intron	INS	-	AC	AC	rs150021362		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61904670_61904671insAC	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron|NFIA_uc001czx.2_Intron|NFIA_uc009wae.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61907061	61907061	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61907061delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron|NFIA_uc001czx.2_Intron|NFIA_uc009wae.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
TM2D1	83941	broad.mit.edu	37	1	62189461	62189461	+	Intron	DEL	A	-	-	rs147863719		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62189461delA	uc001czz.1	-							NM_032027	NP_114416			beta-amyloid binding protein precursor						apoptosis					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	63231631	63231631	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63231631delT								DOCK7 (77662 upstream) : ATG4C (18172 downstream)																																			---	---	---	---
PGM1	5236	broad.mit.edu	37	1	64117205	64117205	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64117205delT	uc001dbh.2	+						PGM1_uc010ooy.1_Intron|PGM1_uc010ooz.1_Intron	NM_002633	NP_002624			phosphoglucomutase 1						cellular calcium ion homeostasis|galactose catabolic process|glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity			ovary(2)|kidney(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	64139048	64139048	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64139048delT								PGM1 (13134 upstream) : ROR1 (100642 downstream)																																			---	---	---	---
UBE2U	148581	broad.mit.edu	37	1	64686317	64686318	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64686317_64686318insT	uc001dbn.1	+							NM_152489	NP_689702			ubiquitin-conjugating enzyme E2U (putative)								ATP binding|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
LEPR	3953	broad.mit.edu	37	1	65915368	65915368	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65915368delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron	NM_002303	NP_002294			leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67098850	67098850	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67098850delT	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67099769	67099769	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67099769delA	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
IL23R	149233	broad.mit.edu	37	1	67724149	67724149	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67724149delT	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_Intron|IL23R_uc001ddt.2_Intron	NM_144701	NP_653302			interleukin 23 receptor precursor						inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0																		---	---	---	---
SERBP1	26135	broad.mit.edu	37	1	67878790	67878791	+	3'UTR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67878790_67878791delTT	uc001ddv.2	-	8					SERBP1_uc001ddx.2_3'UTR|SERBP1_uc001ddy.2_3'UTR|SERBP1_uc001ddw.2_3'UTR	NM_001018067	NP_001018077			SERPINE1 mRNA binding protein 1 isoform 1						regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68442772	68442772	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68442772delT	uc001deb.1	+						uc001dec.1_Intron					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	69042946	69042946	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69042946delA								DEPDC1 (80147 upstream) : LRRC7 (989922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69779600	69779603	+	IGR	DEL	TTTT	-	-	rs113900358		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69779600_69779603delTTTT								DEPDC1 (816801 upstream) : LRRC7 (253265 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70441578	70441578	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70441578delT	uc001dep.2	+						LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845			leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	70863617	70863617	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70863617delT								HHLA3 (29914 upstream) : CTH (13338 downstream)																																			---	---	---	---
PTGER3	5733	broad.mit.edu	37	1	71437291	71437291	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71437291delA	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron|PTGER3_uc009wbo.2_Intron|PTGER3_uc001dfo.2_Intron|PTGER3_uc001dfp.1_3'UTR	NM_198714	NP_942007			prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	71689185	71689186	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71689185_71689186insT	uc001dfu.1	+											Homo sapiens cDNA clone IMAGE:6592429, partial cds.																														---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72181933	72181933	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72181933delG	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72235270	72235270	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72235270delT	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	73856130	73856130	+	IGR	DEL	T	-	-	rs74765472		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73856130delT								None (None upstream) : LRRIQ3 (635574 downstream)																																			---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74875177	74875181	+	Intron	DEL	TTTTT	-	-	rs150687389		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74875177_74875181delTTTTT	uc001dgf.1	+						TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062			TNNI3 interacting kinase isoform b							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
CRYZ	1429	broad.mit.edu	37	1	75182069	75182069	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75182069delG	uc001dgk.2	-						CRYZ_uc001dgj.2_Intron|CRYZ_uc001dgl.2_Intron|CRYZ_uc001dgm.2_Intron	NM_001130042	NP_001123514			crystallin, zeta isoform a						protein homotetramerization|visual perception|xenobiotic catabolic process	cytosol|Golgi apparatus	mRNA 3'-UTR binding|NADPH binding|NADPH:quinone reductase activity|zinc ion binding				0					Dicumarol(DB00266)													---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75669626	75669627	+	Intron	INS	-	TG	TG	rs34350348		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75669626_75669627insTG	uc010oqz.1	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron	NM_001130058	NP_001123530			solute carrier family 44, member 5 isoform B							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76779471	76779471	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76779471delT	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541			sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78162897	78162897	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78162897delA	uc001dht.2	-	25					USP33_uc009wca.1_RNA|USP33_uc001dhs.2_3'UTR|USP33_uc001dhu.2_3'UTR	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78188044	78188044	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78188044delA	uc001dht.2	-						USP33_uc001dhs.2_Intron|USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78338833	78338833	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78338833delT	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	79132403	79132405	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79132403_79132405delAAA								IFI44 (2642 upstream) : ELTD1 (223046 downstream)																																			---	---	---	---
ELTD1	64123	broad.mit.edu	37	1	79387214	79387214	+	Intron	DEL	A	-	-	rs74948984		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79387214delA	uc001diq.3	-							NM_022159	NP_071442			EGF, latrophilin and seven transmembrane domain						neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	79847320	79847321	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79847320_79847321delAC								ELTD1 (374825 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79869643	79869643	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79869643delT								ELTD1 (397148 upstream) : None (None downstream)																																			---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82187977	82187977	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82187977delA	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	82936575	82936575	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82936575delA								LPHN2 (478469 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83826812	83826812	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83826812delA								None (None upstream) : TTLL7 (508247 downstream)																																			---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85624415	85624415	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85624415delA	uc009wcm.2	-	7						NM_032184	NP_115560			synapse defective 1, Rho GTPase, homolog 2						activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	86801733	86801733	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86801733delG								COL24A1 (179287 upstream) : ODF2L (12679 downstream)																																			---	---	---	---
ODF2L	57489	broad.mit.edu	37	1	86820549	86820550	+	Intron	INS	-	A	A	rs76785175		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86820549_86820550insA	uc001dll.1	-						ODF2L_uc001dlm.1_Intron|ODF2L_uc001dln.2_Intron|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Intron|ODF2L_uc010osg.1_Intron	NM_020729	NP_065780			outer dense fiber of sperm tails 2-like isoform							centrosome				ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87772559	87772559	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87772559delT								LOC339524 (137675 upstream) : LMO4 (21592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	87847429	87847429	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87847429delT								LMO4 (32826 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	87900378	87900378	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87900378delA								LMO4 (85775 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	90421639	90421639	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90421639delT								LRRC8D (19652 upstream) : GEMIN8P4 (37187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	92086210	92086210	+	IGR	DEL	C	-	-	rs995551	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92086210delC								CDC7 (94890 upstream) : HSP90B3P (14358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	92388629	92388629	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92388629delA								TGFBR3 (17070 upstream) : BRDT (26299 downstream)																																			---	---	---	---
EPHX4	253152	broad.mit.edu	37	1	92510850	92510850	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92510850delT	uc001don.2	+							NM_173567	NP_775838			abhydrolase domain containing 7							integral to membrane	hydrolase activity			central_nervous_system(1)	1																		---	---	---	---
GLMN	11146	broad.mit.edu	37	1	92728825	92728825	+	Intron	DEL	A	-	-	rs77876761		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92728825delA	uc001dor.2	-						GLMN_uc009wdg.2_Intron|GLMN_uc001dos.2_Intron	NM_053274	NP_444504			glomulin						muscle cell differentiation|negative regulation of T cell proliferation|positive regulation of cytokine secretion|positive regulation of interleukin-2 biosynthetic process|positive regulation of phosphorylation|regulation of gene expression, epigenetic|vasculogenesis	intracellular	hepatocyte growth factor receptor binding			skin(1)	1		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)										Multiple_Glomus_Tumors_(of_the_Skin)_Familial				---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93022375	93022376	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93022375_93022376insT	uc001dox.2	-						EVI5_uc010otf.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93094476	93094476	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93094476delA	uc001dox.2	-						EVI5_uc010otf.1_Intron|EVI5_uc001doy.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93560579	93560579	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93560579delT	uc009wdj.2	+						MTF2_uc001dph.2_Intron|MTF2_uc010oth.1_Intron|MTF2_uc009wdk.2_Intron|MTF2_uc001dpi.3_Intron|MTF2_uc010oti.1_Intron|MTF2_uc001dpj.3_Intron	NM_007358	NP_031384			metal response element binding transcription							nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	94451294	94451294	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94451294delG								GCLM (76282 upstream) : ABCA4 (7102 downstream)																																			---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94568424	94568424	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94568424delT	uc001dqh.2	-						ABCA4_uc010otn.1_Intron	NM_000350	NP_000341			ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94643144	94643144	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94643144delT	uc001dqj.3	-						ARHGAP29_uc009wdq.1_Intron|ARHGAP29_uc001dqk.2_3'UTR	NM_004815	NP_004806			PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
ABCD3	5825	broad.mit.edu	37	1	94982583	94982583	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94982583delT	uc001dqn.3	+						ABCD3_uc010oto.1_Intron|ABCD3_uc010otp.1_Intron|ABCD3_uc009wdr.2_Intron|ABCD3_uc001dqo.3_Intron	NM_002858	NP_002849			ATP-binding cassette, sub-family D, member 3						peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)														---	---	---	---
SLC44A3	126969	broad.mit.edu	37	1	95346854	95346855	+	Intron	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95346854_95346855insC	uc001dqv.3	+						SLC44A3_uc001dqx.3_Intron|SLC44A3_uc010otq.1_Intron|SLC44A3_uc010otr.1_Intron|SLC44A3_uc001dqw.3_Intron|SLC44A3_uc010ots.1_Intron|SLC44A3_uc009wds.2_Intron|SLC44A3_uc010ott.1_Intron|SLC44A3_uc010otu.1_Intron	NM_001114106	NP_001107578			solute carrier family 44, member 3 isoform 1							integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)													---	---	---	---
SLC44A3	126969	broad.mit.edu	37	1	95349242	95349242	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95349242delA	uc001dqv.3	+						SLC44A3_uc001dqx.3_Intron|SLC44A3_uc010otq.1_Intron|SLC44A3_uc010otr.1_Intron|SLC44A3_uc001dqw.3_Intron|SLC44A3_uc010ots.1_Intron|SLC44A3_uc009wds.2_Intron|SLC44A3_uc010ott.1_Intron|SLC44A3_uc010otu.1_Intron	NM_001114106	NP_001107578			solute carrier family 44, member 3 isoform 1							integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97700330	97700330	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97700330delT	uc001drv.2	-							NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	100278306	100278306	+	IGR	DEL	A	-	-	rs75586580		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100278306delA								FRRS1 (46957 upstream) : AGL (37334 downstream)																																			---	---	---	---
CDC14A	8556	broad.mit.edu	37	1	100950184	100950186	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100950184_100950186delAAA	uc001dtg.3	+						CDC14A_uc009web.2_Intron|CDC14A_uc010oui.1_Intron|CDC14A_uc001dte.3_3'UTR|CDC14A_uc001dtf.2_Intron|CDC14A_uc009wed.1_Intron|CDC14A_uc009wee.2_Intron	NM_003672	NP_003663			CDC14 homolog A isoform 1						cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)														---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102358807	102358807	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102358807delA	uc001dug.2	-						OLFM3_uc001duh.2_Intron|OLFM3_uc001dui.2_Intron|OLFM3_uc001duj.2_Intron	NM_058170	NP_477518			olfactomedin 3							extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103355904	103355904	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103355904delT	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	104660522	104660522	+	IGR	DEL	A	-	-	rs34492476		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104660522delA								AMY1A (453350 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105092984	105092984	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105092984delA								AMY1A (885812 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106735794	106735794	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106735794delG								None (None upstream) : PRMT6 (863473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106777206	106777206	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106777206delT								None (None upstream) : PRMT6 (822061 downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107954211	107954212	+	Intron	INS	-	T	T	rs77314833	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107954211_107954212insT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvi.2_Intron|NTNG1_uc001dve.2_Intron|NTNG1_uc009wek.2_Intron|NTNG1_uc001dvg.2_Intron|NTNG1_uc009wem.2_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
STXBP3	6814	broad.mit.edu	37	1	109302590	109302590	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109302590delT	uc001dvy.2	+						STXBP3_uc001dvz.2_Intron	NM_007269	NP_009200			syntaxin binding protein 3						negative regulation of calcium ion-dependent exocytosis|neutrophil degranulation|platelet aggregation|protein transport|vesicle docking involved in exocytosis	cytosol|nucleus|platelet alpha granule|specific granule|tertiary granule	syntaxin-2 binding			ovary(3)|central_nervous_system(1)	4		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)														---	---	---	---
AKNAD1	254268	broad.mit.edu	37	1	109369062	109369062	+	Intron	DEL	A	-	-	rs34954897		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109369062delA	uc001dwa.2	-						AKNAD1_uc010ovb.1_Intron|AKNAD1_uc001dwb.2_Intron	NM_152763	NP_689976			hypothetical protein LOC254268											ovary(3)	3																		---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109518994	109518995	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109518994_109518995delAA	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023			WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
CELSR2	1952	broad.mit.edu	37	1	109795396	109795396	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109795396delC	uc001dxa.3	+	1	2756	c.2695delC	c.(2695-2697)CCCfs	p.P899fs		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	899	Extracellular (Potential).|Cadherin 7.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)														---	---	---	---
CELSR2	1952	broad.mit.edu	37	1	109816863	109816864	+	3'UTR	INS	-	C	C	rs145508961	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109816863_109816864insC	uc001dxa.3	+	34						NM_001408	NP_001399			cadherin EGF LAG seven-pass G-type receptor 2						dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110506497	110506499	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110506497_110506499delAAA								CSF1 (34143 upstream) : AHCYL1 (20809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	113323462	113323462	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113323462delT								FAM19A3 (53608 upstream) : SLC16A1 (131010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	113776421	113776421	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113776421delT								LRIG2 (109079 upstream) : MAGI3 (157054 downstream)																																			---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114214310	114214310	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114214310delT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron|MAGI3_uc001edj.2_Intron	NM_001142782	NP_001136254			membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114301137	114301139	+	Intron	DEL	TTT	-	-	rs74861360		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114301137_114301139delTTT	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron|PHTF1_uc001edp.2_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114377352	114377352	+	Intron	DEL	A	-	-	rs79608028		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114377352delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
AP4B1	10717	broad.mit.edu	37	1	114444144	114444145	+	Intron	INS	-	A	A	rs79534272		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114444144_114444145insA	uc001eeb.2	-						AP4B1_uc001eec.2_Intron|AP4B1_uc001eed.2_Intron|AP4B1_uc010owp.1_Intron|AP4B1_uc001eea.1_5'Flank|AP4B1_uc010owq.1_Intron	NM_006594	NP_006585			adaptor-related protein complex 4, beta 1						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			ovary(3)|central_nervous_system(1)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115279333	115279333	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115279333delA	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
SLC22A15	55356	broad.mit.edu	37	1	116570251	116570251	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116570251delT	uc001egb.3	+						SLC22A15_uc001ega.2_Intron	NM_018420	NP_060890			solute carrier family 22, member 15						ion transport	integral to membrane	transmembrane transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116623205	116623205	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116623205delA								SLC22A15 (10533 upstream) : C1orf161 (31171 downstream)																																			---	---	---	---
CD58	965	broad.mit.edu	37	1	117078855	117078855	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117078855delA	uc001egm.2	-						CD58_uc001egn.2_Intron|CD58_uc010owy.1_Intron|CD58_uc001ego.1_Intron|CD58_uc001egp.3_Intron	NM_001779	NP_001770			CD58 molecule isoform 1						blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)														---	---	---	---
CD101	9398	broad.mit.edu	37	1	117555876	117555877	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117555876_117555877insT	uc010oxb.1	+						CD101_uc009whd.2_Intron|CD101_uc010oxc.1_Intron|CD101_uc010oxd.1_Intron	NM_004258	NP_004249			immunoglobulin superfamily, member 2 precursor						cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	118837855	118837855	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118837855delA								SPAG17 (110007 upstream) : TBX15 (587811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119172440	119172440	+	IGR	DEL	G	-	-	rs1742836	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119172440delG								SPAG17 (444592 upstream) : TBX15 (253226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119289663	119289663	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119289663delA								SPAG17 (561815 upstream) : TBX15 (136003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	120149764	120149764	+	IGR	DEL	A	-	-	rs79524356		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120149764delA								HSD3B1 (92083 upstream) : ZNF697 (12236 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120542541	120542544	+	Intron	DEL	AGAA	-	-	rs71775604		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120542541_120542544delAGAA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719			notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	120858691	120858691	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120858691delT								FAM72B (3011 upstream) : HIST2H2BA (47343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142599487	142599488	+	IGR	DEL	AC	-	-	rs148300367		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142599487_142599488delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142613168	142613169	+	IGR	INS	-	TT	TT	rs138101758	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142613168_142613169insTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142621835	142621835	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142621835delG	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142647217	142647217	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142647217delA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142804874	142804874	+	Intron	DEL	T	-	-	rs140820497		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142804874delT	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142935799	142935800	+	Intron	INS	-	T	T	rs144309001		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142935799_142935800insT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143174793	143174793	+	Intron	DEL	G	-	-	rs111919200		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143174793delG	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143261370	143261371	+	IGR	INS	-	A	A	rs145912009		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143261370_143261371insA								None (None upstream) : LOC100286793 (386268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143283418	143283420	+	IGR	DEL	CCG	-	-	rs145714630		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143283418_143283420delCCG								None (None upstream) : LOC100286793 (364219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143538859	143538860	+	IGR	INS	-	C	C	rs143502487	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143538859_143538860insC								None (None upstream) : LOC100286793 (108779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	144028377	144028377	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144028377delA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144519342	144519343	+	Intron	INS	-	A	A	rs151085852	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144519342_144519343insA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|LOC728875_uc001eky.3_Intron|LOC728875_uc001ela.3_Intron|LOC728875_uc001ekz.3_Intron|uc001elb.3_RNA	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144825139	144825140	+	Intron	DEL	CT	-	-	rs33954645		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144825139_144825140delCT	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144891756	144891756	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144891756delC	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_3'UTR|PDE4DIP_uc001emd.1_3'UTR|PDE4DIP_uc001elv.3_Intron|PDE4DIP_uc001emb.1_3'UTR	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144911285	144911286	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144911285_144911286delAA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001eme.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144928113	144928113	+	Intron	DEL	A	-	-	rs67719372		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144928113delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145044047	145044048	+	Intron	INS	-	AAT	AAT	rs112979449	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145044047_145044048insAAT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145077026	145077027	+	Intron	DEL	TT	-	-	rs144410779		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145077026_145077027delTT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_5'Flank|PDE4DIP_uc001emh.2_5'Flank|PDE4DIP_uc001emk.2_5'Flank					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145722370	145722370	+	Intron	DEL	T	-	-	rs111649778		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145722370delT	uc001emp.3	+							NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	146471954	146471954	+	IGR	DEL	A	-	-	rs67168403		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146471954delA								NBPF10 (47859 upstream) : LOC728989 (18941 downstream)																																			---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148252244	148252244	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148252244delA	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron|uc010pah.1_Intron|uc010pai.1_Intron|uc001eqz.2_Intron|uc001erb.2_Intron|uc001erd.3_Intron|uc001erc.3_Intron|uc010paj.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	148538313	148538314	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148538313_148538314insT								NBPF14 (191522 upstream) : NBPF15 (19955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149182627	149182627	+	IGR	DEL	C	-	-	rs71584682		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149182627delC								LOC645166 (229573 upstream) : LOC388692 (96849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149244913	149244914	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149244913_149244914delAA								LOC645166 (291859 upstream) : LOC388692 (34562 downstream)																																			---	---	---	---
VPS45	11311	broad.mit.edu	37	1	150082514	150082515	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150082514_150082515delAA	uc001etp.2	+						VPS45_uc010pbp.1_Intron|VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron	NM_007259	NP_009190			vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
CTSS	1520	broad.mit.edu	37	1	150730530	150730530	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150730530delT	uc001evn.2	-						CTSS_uc010pcj.1_Intron|CTSS_uc001evo.1_Intron	NM_004079	NP_004070			cathepsin S preproprotein						immune response|proteolysis	extracellular region|lysosome	cysteine-type endopeptidase activity				0	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
CTSK	1513	broad.mit.edu	37	1	150778115	150778121	+	Intron	DEL	AAAAAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150778115_150778121delAAAAAAA	uc001evp.1	-						CTSK_uc001evq.1_Intron	NM_000396	NP_000387			cathepsin K preproprotein						proteolysis	lysosome	cysteine-type endopeptidase activity|protein binding			skin(1)	1	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150932978	150932978	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150932978delA	uc001evu.2	+						SETDB1_uc001evv.2_Intron|SETDB1_uc009wmg.1_Intron	NM_001145415	NP_001138887			SET domain, bifurcated 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
GABPB2	126626	broad.mit.edu	37	1	151076447	151076447	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151076447delT	uc001ewr.2	+						GABPB2_uc001ews.2_Intron|GABPB2_uc001ewt.2_Intron	NM_144618	NP_653219			GA repeat binding protein, beta 2						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	protein heterodimerization activity|transcription regulatory region DNA binding				0				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)														---	---	---	---
GABPB2	126626	broad.mit.edu	37	1	151079397	151079397	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151079397delT	uc001ewr.2	+						GABPB2_uc001ews.2_Intron|GABPB2_uc001ewt.2_Intron	NM_144618	NP_653219			GA repeat binding protein, beta 2						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	protein heterodimerization activity|transcription regulatory region DNA binding				0				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)														---	---	---	---
TDRKH	11022	broad.mit.edu	37	1	151755246	151755246	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151755246delA	uc009wnb.1	-						TDRKH_uc001eyy.2_Intron|TDRKH_uc001ezb.3_Intron|TDRKH_uc001ezc.3_Intron|TDRKH_uc001eza.3_Intron|TDRKH_uc001ezd.3_Intron|TDRKH_uc010pdn.1_Intron	NM_006862	NP_006853			tudor and KH domain containing isoform a								RNA binding			ovary(1)|pancreas(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	151832701	151832702	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151832701_151832702delGT								THEM5 (6528 upstream) : THEM4 (13358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152616994	152616994	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152616994delC								LCE3A (21415 upstream) : LCE2D (18878 downstream)																																			---	---	---	---
SPRR2D	6703	broad.mit.edu	37	1	153017226	153017226	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153017226delT	uc009wnz.2	-											Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
SNAPIN	23557	broad.mit.edu	37	1	153631381	153631381	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153631381delG	uc001fcq.2	+							NM_012437	NP_036569			SNAP-associated protein						intracellular protein transport|synaptic vesicle exocytosis	BLOC-1 complex|cell junction|perinuclear region of cytoplasm|synaptic vesicle membrane|synaptosome	SNARE binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153800932	153800939	+	Intron	DEL	ACACACAC	-	-	rs71677766		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153800932_153800939delACACACAC	uc001fdb.3	-							NM_020699	NP_065750			GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153973260	153973260	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153973260delG	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154207835	154207835	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154207835delT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc001fen.1_Intron|UBAP2L_uc010pen.1_Intron	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154212785	154212785	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154212785delT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc010pen.1_Intron	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
DCST2	127579	broad.mit.edu	37	1	155002866	155002866	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155002866delC	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)															---	---	---	---
RUSC1	23623	broad.mit.edu	37	1	155298397	155298397	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155298397delT	uc001fkj.2	+						RAG1AP1_uc010pey.1_Intron|RUSC1_uc001fkk.2_Intron|RUSC1_uc009wqn.1_Intron|RUSC1_uc009wqo.1_Intron|RUSC1_uc001fkl.2_Intron|RUSC1_uc001fkp.2_Intron|RUSC1_uc001fkq.2_Intron|RUSC1_uc010pgb.1_Intron|RUSC1_uc009wqp.1_Intron|RUSC1_uc001fkn.2_Intron|RUSC1_uc001fko.2_Intron|RUSC1_uc001fkr.2_Intron|RUSC1_uc001fks.2_Intron	NM_001105203	NP_001098673			RUN and SH3 domain containing 1 isoform a							cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155444501	155444501	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155444501delA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155590826	155590828	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155590826_155590828delTTT								MSTO1 (6069 upstream) : YY1AP1 (38406 downstream)																																			---	---	---	---
DAP3	7818	broad.mit.edu	37	1	155701653	155701653	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155701653delA	uc001flq.2	+						DAP3_uc001flr.2_Intron|DAP3_uc001fls.2_Intron|DAP3_uc010pgl.1_Intron|DAP3_uc001flt.2_Intron|DAP3_uc001flu.2_Intron|DAP3_uc010pgm.1_Intron	NM_033657	NP_387506			death-associated protein 3						induction of apoptosis by extracellular signals	mitochondrial ribosome|nucleolus|small ribosomal subunit	protein binding			ovary(1)	1	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)																	---	---	---	---
KIAA0907	22889	broad.mit.edu	37	1	155886695	155886695	+	Intron	DEL	T	-	-	rs113079820		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155886695delT	uc001fmi.1	-						KIAA0907_uc001fmj.1_Intron|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_Intron	NM_014949	NP_055764			hypothetical protein LOC22889												0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)															---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156138347	156138347	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156138347delT	uc001fnl.2	+						SEMA4A_uc009wrq.2_Intron|SEMA4A_uc001fnm.2_Intron|SEMA4A_uc001fnn.2_Intron|SEMA4A_uc001fno.2_Intron	NM_022367	NP_071762			semaphorin B precursor						axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156704329	156704331	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156704329_156704331delTTT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	157000479	157000479	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157000479delA	uc001fqo.2	-						ARHGEF11_uc001fqn.2_Intron	NM_014784	NP_055599			Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	157133709	157133709	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157133709delG								ETV3 (25326 upstream) : FCRL5 (349459 downstream)																																	OREG0013896	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FCRL5	83416	broad.mit.edu	37	1	157519226	157519226	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157519226delA	uc001fqu.2	-						FCRL5_uc009wsm.2_Intron|FCRL5_uc010phv.1_Intron|FCRL5_uc010phw.1_Intron|FCRL5_uc001fqv.1_Intron|FCRL5_uc010phx.1_Intron	NM_031281	NP_112571			Fc receptor-like 5							integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)																---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158582498	158582498	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158582498delA	uc001fst.1	-							NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
IFI16	3428	broad.mit.edu	37	1	158984476	158984476	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158984476delA	uc001ftf.1	+	3	613	c.6delA	c.(4-6)GGAfs	p.G2fs	IFI16_uc001ftg.2_Frame_Shift_Del_p.G2fs|IFI16_uc010pis.1_Frame_Shift_Del_p.G2fs	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	2	DAPIN.|Lys-rich.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	159396383	159396383	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159396383delT	uc001fts.3	-											Homo sapiens, clone IMAGE:3917623, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	162021701	162021701	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162021701delT								OLFML2B (28057 upstream) : NOS1AP (17880 downstream)																																			---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162324764	162324764	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162324764delT	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512			nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)															---	---	---	---
HSD17B7	51478	broad.mit.edu	37	1	162782018	162782018	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162782018delT	uc001gci.2	+						HSD17B7_uc009wuv.2_Intron	NM_016371	NP_057455			hydroxysteroid (17-beta) dehydrogenase 7						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	3-keto sterol reductase activity|estradiol 17-beta-dehydrogenase activity			ovary(1)	1	all_hematologic(112;0.115)				NADH(DB00157)													---	---	---	---
RGS5	8490	broad.mit.edu	37	1	163137887	163137887	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163137887delA	uc001gcn.2	-						RGS5_uc009wvb.2_Intron	NM_003617	NP_003608			regulator of G-protein signalling 5						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)															---	---	---	---
NUF2	83540	broad.mit.edu	37	1	163313696	163313697	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163313696_163313697delAA	uc001gcq.1	+						NUF2_uc001gcp.2_Intron|NUF2_uc001gcr.1_Intron|NUF2_uc009wvc.1_Intron	NM_145697	NP_663735			NUF2, NDC80 kinetochore complex component						cell division|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			ovary(3)|skin(1)	4	all_hematologic(923;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	164007340	164007340	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164007340delT								NUF2 (681787 upstream) : PBX1 (521462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164283081	164283081	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164283081delG								NUF2 (957528 upstream) : PBX1 (245721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	165167347	165167348	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165167347_165167348delAC								PBX1 (313047 upstream) : LMX1A (3757 downstream)																																			---	---	---	---
LMX1A	4009	broad.mit.edu	37	1	165174252	165174252	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165174252delA	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron|LMX1A_uc001gcw.1_Intron|LMX1A_uc001gcx.1_Intron	NM_177398	NP_796372			LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	166804814	166804815	+	IGR	INS	-	CTT	CTT	rs143374707	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166804814_166804815insCTT								FMO9P (210343 upstream) : POGK (3909 downstream)																																			---	---	---	---
ADCY10	55811	broad.mit.edu	37	1	167811407	167811407	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167811407delT	uc001ger.2	-						ADCY10_uc009wvk.2_Intron|ADCY10_uc010plj.1_Intron	NM_018417	NP_060887			adenylate cyclase 10						intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169366387	169366387	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169366387delT	uc001gga.1	-						C1orf114_uc001gfz.1_Intron|C1orf114_uc009wvq.1_Intron	NM_021179	NP_067002			hypothetical protein LOC57821												0	all_hematologic(923;0.208)																	---	---	---	---
SELE	6401	broad.mit.edu	37	1	169698253	169698253	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169698253delT	uc001ggm.3	-						C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441			selectin E precursor						actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	169884558	169884558	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169884558delC								SCYL3 (21482 upstream) : KIFAP3 (5914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	171324275	171324276	+	IGR	INS	-	GTGTGCGC	GTGTGCGC	rs6688215	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171324275_171324276insGTGTGCGC								FMO4 (13053 upstream) : BAT2L2 (130390 downstream)																																			---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171505457	171505457	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171505457delT	uc010pmg.1	+							NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171536062	171536062	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171536062delT	uc010pmg.1	+						BAT2L2_uc010pmh.1_Intron|BAT2L2_uc010pmi.1_Intron	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171807851	171807851	+	5'Flank	DEL	A	-	-	rs112821060		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171807851delA	uc001gie.2	+						DNM3_uc001gid.3_5'Flank|DNM3_uc009wwb.2_5'Flank|DNM3_uc001gif.2_5'Flank	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	172036093	172036096	+	Intron	DEL	TGTG	-	-	rs67844258		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172036093_172036096delTGTG	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
SERPINC1	462	broad.mit.edu	37	1	173879823	173879823	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173879823delA	uc001gjt.2	-							NM_000488	NP_000479			serpin peptidase inhibitor, clade C, member 1						blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)													---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173930736	173930736	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173930736delA	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068			roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173962217	173962217	+	5'Flank	DEL	T	-	-	rs77490215		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173962217delT	uc001gju.3	-						RC3H1_uc010pms.1_5'Flank|RC3H1_uc001gjv.2_5'Flank|RC3H1_uc010pmt.1_5'Flank	NM_172071	NP_742068			roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
MRPS14	63931	broad.mit.edu	37	1	174993551	174993551	+	5'Flank	DEL	A	-	-	rs10710388		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174993551delA	uc001gkk.2	-						MRPS14_uc009wwr.2_5'Flank	NM_022100	NP_071383			mitochondrial ribosomal protein S14						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
TNR	7143	broad.mit.edu	37	1	175365823	175365823	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175365823delC	uc001gkp.1	-	3	1178	c.1097delG	c.(1096-1098)GGCfs	p.G366fs	TNR_uc009wwu.1_Frame_Shift_Del_p.G366fs|TNR_uc010pmz.1_Frame_Shift_Del_p.G331fs	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	366	Fibronectin type-III 1.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	175788763	175788764	+	IGR	INS	-	CA	CA	rs145355757	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175788763_175788764insCA								TNR (76011 upstream) : RFWD2 (125203 downstream)																																			---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176554420	176554420	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176554420delT	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|PAPPA2_uc009www.2_Intron	NM_020318	NP_064714			pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	177497327	177497328	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177497327_177497328delAA								FAM5B (245770 upstream) : SEC16B (400161 downstream)																																			---	---	---	---
C1orf49	84066	broad.mit.edu	37	1	178488083	178488083	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178488083delA	uc001glt.1	+						C1orf49_uc001glu.1_Intron|C1orf49_uc001glv.1_Intron|C1orf49_uc001glw.1_Intron	NM_032126	NP_115502			hypothetical protein LOC84066							microtubule cytoskeleton					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	178682326	178682327	+	IGR	INS	-	AG	AG	rs138482742	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178682326_178682327insAG								C1orf220 (164302 upstream) : RALGPS2 (11973 downstream)																																			---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178790728	178790728	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178790728delT	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876			Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0																		---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179503820	179503820	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179503820delT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	179800992	179800992	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179800992delC								FAM163A (15666 upstream) : TOR1AIP2 (12962 downstream)																																			---	---	---	---
CEP350	9857	broad.mit.edu	37	1	179961369	179961369	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179961369delA	uc001gnt.2	+						CEP350_uc001gnr.1_Intron|CEP350_uc009wxl.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180519246	180519248	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180519246_180519248delAAA								ACBD6 (47224 upstream) : XPR1 (81898 downstream)																																			---	---	---	---
C1orf14	81626	broad.mit.edu	37	1	182920666	182920668	+	Intron	DEL	TTT	-	-	rs77465244		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182920666_182920668delTTT	uc001gpu.2	-						C1orf14_uc001gpv.2_Intron|C1orf14_uc010pnz.1_Intron|C1orf14_uc001gpw.2_Intron	NM_030933	NP_112195			chromosome 1 open reading frame 14												0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)														---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	183925875	183925875	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183925875delA	uc001gqr.2	-						GLT25D2_uc010poj.1_Intron|GLT25D2_uc001gqq.2_Intron|GLT25D2_uc001gqs.2_Intron	NM_015101	NP_055916			glycosyltransferase 25 domain containing 2						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184767655	184767655	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184767655delT	uc001gra.2	-						FAM129A_uc001grb.1_Intron	NM_052966	NP_443198			niban protein isoform 2						negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	189283632	189283632	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189283632delA								None (None upstream) : FAM5C (783165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191067484	191067484	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191067484delA								FAM5C (620725 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192117934	192117934	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192117934delA								None (None upstream) : RGS18 (9658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192819319	192819319	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192819319delA								RGS2 (37913 upstream) : UCHL5 (165581 downstream)																																			---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193091320	193091320	+	5'UTR	DEL	G	-	-	rs80356643		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193091320delG	uc001gtb.2	+	1						NM_024529	NP_078805			parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome		OREG0014058	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	194175195	194175197	+	IGR	DEL	TTA	-	-	rs71139403		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194175195_194175197delTTA								CDC73 (951255 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195351916	195351916	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195351916delA								None (None upstream) : KCNT2 (842997 downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196399923	196399923	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196399923delA	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196438097	196438097	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196438097delT	uc001gtd.1	-						KCNT2_uc009wyt.1_5'Flank|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196642337	196642337	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196642337delA	uc001gtj.3	+						CFH_uc001gti.3_Intron|CFH_uc009wyw.2_Intron|CFH_uc009wyx.2_Intron	NM_000186	NP_000177			complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CFHR3	10878	broad.mit.edu	37	1	196748278	196748278	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196748278delT	uc001gtl.2	+						CFHR3_uc001gtk.2_Intron|CFHR3_uc010poy.1_Intron|CFHR1_uc001gtm.2_5'Flank	NM_021023	NP_066303			complement factor H-related 3 precursor							extracellular space					0																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197328480	197328480	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197328480delT	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppc.1_Intron|CRB1_uc010ppd.1_5'Flank	NM_201253	NP_957705			crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197330613	197330614	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197330613_197330614insT	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppc.1_Intron|CRB1_uc010ppd.1_Intron	NM_201253	NP_957705			crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	199168186	199168187	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199168186_199168187delAC								MIR181A1 (339904 upstream) : NR5A2 (828583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199641660	199641660	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199641660delT								MIR181A1 (813378 upstream) : NR5A2 (355110 downstream)																																			---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200712716	200712717	+	Intron	DEL	AA	-	-	rs80312862		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200712716_200712717delAA	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200817150	200817150	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200817150delT	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201081047	201081049	+	Intron	DEL	TCC	-	-	rs71843679		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201081047_201081049delTCC	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201821197	201821197	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201821197delT	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202269786	202269789	+	Intron	DEL	AAAA	-	-	rs111707317		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202269786_202269789delAAAA	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron|LGR6_uc001gxw.2_Intron|LGR6_uc009xac.1_Intron	NM_001017403	NP_001017403			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10																		---	---	---	---
UBE2T	29089	broad.mit.edu	37	1	202300886	202300886	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202300886delA	uc001gxx.3	-	7						NM_014176	NP_054895			ubiquitin-conjugating enzyme E2T						DNA repair|protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination	nucleoplasm	ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	203498808	203498808	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203498808delT								OPTC (20731 upstream) : ATP2B4 (97120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203713640	203713640	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203713640delA								ATP2B4 (433 upstream) : LAX1 (20644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	204363980	204363980	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204363980delA								LOC127841 (25133 upstream) : PPP1R15B (8514 downstream)																																			---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204931027	204931027	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204931027delT	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbk.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204935633	204935634	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204935633_204935634insT	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbk.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
RBBP5	5929	broad.mit.edu	37	1	205060063	205060064	+	Intron	DEL	AA	-	-	rs72199877		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205060063_205060064delAA	uc001hbu.1	-						RBBP5_uc010prd.1_Intron|RBBP5_uc001hbv.1_Intron|RBBP5_uc010pre.1_Intron	NM_005057	NP_005048			retinoblastoma binding protein 5						histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	methylated histone residue binding|transcription regulatory region DNA binding			lung(1)	1	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)															---	---	---	---
TMCC2	9911	broad.mit.edu	37	1	205224011	205224014	+	Intron	DEL	CTTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205224011_205224014delCTTC	uc001hbz.1	+						TMCC2_uc010prf.1_Intron|TMCC2_uc001hca.2_Intron|TMCC2_uc001hcb.1_5'Flank|TMCC2_uc001hcc.1_5'Flank	NM_014858	NP_055673			transmembrane and coiled-coil domain family 2							integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	205469110	205469111	+	IGR	INS	-	GT	GT	rs150373388	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205469110_205469111insGT								MIR135B (51584 upstream) : CDK18 (4616 downstream)																																			---	---	---	---
RASSF5	83593	broad.mit.edu	37	1	206709018	206709019	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206709018_206709019delGT	uc001hed.2	+						RASSF5_uc001hec.1_Intron|RASSF5_uc001hee.2_Intron	NM_182663	NP_872604			Ras association (RalGDS/AF-6) domain family 5						apoptosis|intracellular signal transduction	cytoplasm|microtubule	metal ion binding|protein binding			ovary(1)	1	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
DYRK3	8444	broad.mit.edu	37	1	206835220	206835220	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206835220delT	uc001hek.2	+											Homo sapiens regulatory erythroid kinase long form (RED) mRNA, alternatively spliced product, complete cds.						erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
IL19	29949	broad.mit.edu	37	1	206978726	206978727	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206978726_206978727insA	uc001heo.2	+							NM_153758	NP_715639			interleukin 19 isoform 1 precursor						apoptosis|immune response|signal transduction	extracellular space	cytokine activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(75;0.211)															---	---	---	---
FAIM3	9214	broad.mit.edu	37	1	207077073	207077073	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207077073delT	uc001hey.2	-	8					FAIM3_uc010prz.1_3'UTR|FAIM3_uc010psa.1_3'UTR|FAIM3_uc010psb.1_3'UTR|IL24_uc001hes.1_3'UTR|IL24_uc001het.1_3'UTR|IL24_uc001heu.1_3'UTR|IL24_uc001hev.1_RNA|IL24_uc001hew.1_3'UTR	NM_005449	NP_005440			Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	209378245	209378246	+	IGR	INS	-	GT	GT	rs55645218		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209378245_209378246insGT								PLXNA2 (960580 upstream) : LOC642587 (223922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209386727	209386727	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209386727delT								PLXNA2 (969062 upstream) : LOC642587 (215441 downstream)																																			---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210866012	210866012	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210866012delA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210992946	210992947	+	Intron	INS	-	A	A	rs144386324	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210992946_210992947insA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
C1orf97	84791	broad.mit.edu	37	1	211553523	211553523	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211553523delA	uc010psz.1	+						C1orf97_uc001hil.3_5'Flank					SubName: Full=Putative uncharacterized protein C1orf97;												0																		---	---	---	---
INTS7	25896	broad.mit.edu	37	1	212138528	212138528	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212138528delA	uc001hiw.1	-						INTS7_uc009xdb.1_Intron|INTS7_uc001hix.1_Intron|INTS7_uc001hiy.1_Intron|INTS7_uc010pta.1_Intron	NM_015434	NP_056249			integrator complex subunit 7						snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)														---	---	---	---
NSL1	25936	broad.mit.edu	37	1	212957845	212957845	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212957845delA	uc001hjn.2	-						NSL1_uc001hjm.2_Intron|NSL1_uc010pti.1_Intron	NM_015471	NP_056286			NSL1, MIND kinetochore complex component isoform						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214955662	214955663	+	IGR	INS	-	AT	AT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214955662_214955663insAT								CENPF (117750 upstream) : KCNK2 (223222 downstream)																																			---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215753428	215753428	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215753428delT	uc001hks.2	+						KCTD3_uc001hkt.2_Intron|KCTD3_uc010pub.1_Intron|KCTD3_uc009xdn.2_Intron	NM_016121	NP_057205			potassium channel tetramerisation domain							voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(3)	3				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)														---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215777330	215777330	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215777330delT	uc001hks.2	+						KCTD3_uc001hkt.2_Intron|KCTD3_uc010pub.1_Intron|KCTD3_uc009xdn.2_Intron	NM_016121	NP_057205			potassium channel tetramerisation domain							voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(3)	3				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216241261	216241261	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216241261delA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216248799	216248800	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216248799_216248800insA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216819494	216819494	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216819494delT	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429			estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	218128526	218128527	+	IGR	DEL	AC	-	-	rs59995377		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218128526_218128527delAC								SPATA17 (88024 upstream) : RRP15 (330102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218264861	218264861	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218264861delA								SPATA17 (224359 upstream) : RRP15 (193768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219073244	219073244	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219073244delA								TGFB2 (455285 upstream) : LYPLAL1 (273948 downstream)																																			---	---	---	---
IARS2	55699	broad.mit.edu	37	1	220273700	220273700	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220273700delA	uc001hmc.2	+							NM_018060	NP_060530			mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)													---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220379362	220379362	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220379362delA	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	220537302	220537307	+	IGR	DEL	GTGTGA	-	-	rs60748016	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220537302_220537307delGTGTGA								RAB3GAP2 (91459 upstream) : MARK1 (164261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	224528554	224528554	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224528554delT								NVL (10682 upstream) : CNIH4 (16041 downstream)																																			---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225211067	225211067	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225211067delT	uc001how.2	+						DNAH14_uc001hou.3_Intron|DNAH14_uc001hot.3_Intron	NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225692583	225692583	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225692583delA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron|ENAH_uc001hpb.1_Intron	NM_001008493	NP_001008493			enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	227017494	227017495	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227017494_227017495delTT								ITPKB (90618 upstream) : PSEN2 (40778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	227551712	227551712	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227551712delA								CDC42BPA (45886 upstream) : ZNF678 (199532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229301120	229301124	+	IGR	DEL	AATTA	-	-	rs67342974		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229301120_229301124delAATTA								RHOU (418711 upstream) : RAB4A (105755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229557097	229557098	+	IGR	DEL	TT	-	-	rs72451515		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229557097_229557098delTT								C1orf96 (78409 upstream) : ACTA1 (9897 downstream)																																			---	---	---	---
NUP133	55746	broad.mit.edu	37	1	229618857	229618857	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229618857delT	uc001htn.2	-							NM_018230	NP_060700			nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	229709540	229709541	+	IGR	INS	-	T	T	rs111656965		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229709540_229709541insT								ABCB10 (15098 upstream) : TAF5L (19327 downstream)																																			---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230493045	230493045	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230493045delG	uc010pwb.1	-	2	147	c.147delC	c.(145-147)CCCfs	p.P49fs	PGBD5_uc001htv.2_Frame_Shift_Del_p.P148fs	NM_024554	NP_078830	Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	49						integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)														---	---	---	---
COG2	22796	broad.mit.edu	37	1	230828972	230828972	+	Intron	DEL	T	-	-	rs111313789		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230828972delT	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383			component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
TTC13	79573	broad.mit.edu	37	1	231048935	231048936	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231048935_231048936insA	uc001huf.3	-						TTC13_uc009xfi.2_Intron|TTC13_uc009xfj.2_Intron|TTC13_uc001hug.3_Intron|TTC13_uc009xfk.1_Intron	NM_024525	NP_078801			tetratricopeptide repeat domain 13 isoform a								binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	231219563	231219564	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231219563_231219564insA								FAM89A (43568 upstream) : TRIM67 (79110 downstream)																																			---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233231269	233231269	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233231269delA	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235427309	235427310	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235427309_235427310delAA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron	NM_016374	NP_057458			AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)															---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235634147	235634147	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235634147delA	uc001hxc.2	-						B3GALNT2_uc001hxd.1_Intron	NM_152490	NP_689703			beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)															---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235657414	235657414	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235657414delA	uc001hxc.2	-						B3GALNT2_uc001hxd.1_Intron	NM_152490	NP_689703			beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)															---	---	---	---
LYST	1130	broad.mit.edu	37	1	235993743	235993743	+	Intron	DEL	A	-	-	rs72106995		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235993743delA	uc001hxj.2	-						LYST_uc009xgb.1_Intron|LYST_uc010pxs.1_Intron|LYST_uc001hxl.1_Intron|LYST_uc001hxm.2_Intron|LYST_uc001hxn.1_Intron	NM_000081	NP_000072			lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236926030	236926030	+	3'UTR	DEL	A	-	-	rs1051251	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236926030delA	uc001hyf.2	+	21					ACTN2_uc001hyg.2_3'UTR|ACTN2_uc009xgi.1_3'UTR|ACTN2_uc010pxu.1_3'UTR|ACTN2_uc001hyh.2_3'UTR	NM_001103	NP_001094			actinin, alpha 2						focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237534413	237534413	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237534413delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	238555365	238555366	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238555365_238555366delGT								LOC100130331 (463748 upstream) : LOC339535 (88320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238816051	238816051	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238816051delA								LOC339535 (166734 upstream) : CHRM3 (733814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238929519	238929520	+	IGR	INS	-	G	G	rs148340278	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238929519_238929520insG								LOC339535 (280202 upstream) : CHRM3 (620345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239241566	239241566	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239241566delT								LOC339535 (592249 upstream) : CHRM3 (308299 downstream)																																			---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241033240	241033241	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241033240_241033241insA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc001hyt.2_5'Flank	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241033423	241033423	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241033423delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc001hyt.2_5'Flank	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241838535	241838541	+	Intron	DEL	CCTCCTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241838535_241838541delCCTCCTT	uc001hze.1	+											RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
CEP170	9859	broad.mit.edu	37	1	243395267	243395267	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243395267delT	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron	NM_014812	NP_055627			centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)															---	---	---	---
C1orf101	257044	broad.mit.edu	37	1	244662208	244662208	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244662208delA	uc001iam.2	+						C1orf101_uc001iak.1_Intron|C1orf101_uc001ial.2_Intron|C1orf101_uc010pym.1_Intron|C1orf101_uc010pyn.1_Intron	NM_001130957	NP_001124429			hypothetical protein LOC257044 isoform 1							integral to membrane				ovary(1)|breast(1)	2	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	244993309	244993310	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244993309_244993310delTT								PPPDE1 (120977 upstream) : FAM36A (5329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	245031708	245031709	+	IGR	DEL	AA	-	-	rs77549315		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245031708_245031709delAA								HNRNPU (3881 upstream) : EFCAB2 (101462 downstream)																																			---	---	---	---
EFCAB2	84288	broad.mit.edu	37	1	245215216	245215217	+	Intron	INS	-	T	T	rs149692525	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245215216_245215217insT	uc001ibd.2	+						EFCAB2_uc001ibc.2_Intron|EFCAB2_uc010pyo.1_Intron|EFCAB2_uc010pyp.1_Intron|EFCAB2_uc001ibe.2_Intron	NR_026586				RecName: Full=EF-hand calcium-binding domain-containing protein 2;								calcium ion binding				0	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)															---	---	---	---
EFCAB2	84288	broad.mit.edu	37	1	245228131	245228132	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245228131_245228132delTT	uc001ibd.2	+						EFCAB2_uc001ibc.2_Intron|EFCAB2_uc010pyo.1_Intron|EFCAB2_uc010pyp.1_Intron|EFCAB2_uc001ibe.2_Intron	NR_026586				RecName: Full=EF-hand calcium-binding domain-containing protein 2;								calcium ion binding				0	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	247108314	247108314	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247108314delT								AHCTF1 (13591 upstream) : ZNF695 (540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248596259	248596259	+	IGR	DEL	T	-	-	rs67286515		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248596259delT								OR2T1 (25855 upstream) : OR2T2 (19840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248607635	248607636	+	IGR	INS	-	T	T	rs144008193	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248607635_248607636insT								OR2T1 (37231 upstream) : OR2T2 (8463 downstream)																																			---	---	---	---
ZNF692	55657	broad.mit.edu	37	1	249150856	249150856	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249150856delT	uc001ifc.1	-						ZNF692_uc001iez.1_5'Flank|ZNF692_uc001ifa.1_Intron|ZNF692_uc001ifb.1_Intron|ZNF692_uc001ifd.1_Intron|ZNF692_uc001ife.1_Intron|ZNF692_uc001iff.1_Intron|ZNF692_uc010pzr.1_Intron	NM_017865	NP_060335			zinc finger protein 692 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)															---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1285097	1285098	+	Intron	DEL	GT	-	-	rs142654588		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1285097_1285098delGT	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1815000	1815000	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1815000delG	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewk.2_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	2852432	2852433	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2852432_2852433delCT								MYT1L (517387 upstream) : TSSC1 (340308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2856164	2856165	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2856164_2856165delAC								MYT1L (521119 upstream) : TSSC1 (336576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2956267	2956282	+	Intron	DEL	ACACACACACACACAT	-	-	rs66864747		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2956267_2956282delACACACACACACACAT	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																														---	---	---	---
ADI1	55256	broad.mit.edu	37	2	3509186	3509186	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3509186delA	uc002qxp.3	-						ADI1_uc010yiq.1_Intron	NM_018269	NP_060739			acireductone dioxygenase 1						L-methionine salvage from methylthioadenosine	cytoplasm|nucleus|plasma membrane	acireductone dioxygenase (Ni2+-requiring) activity|metal ion binding|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	3883427	3883427	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3883427delG								ALLC (133169 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4140642	4140643	+	IGR	INS	-	GT	GT	rs145162041	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4140642_4140643insGT								ALLC (390384 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4956617	4956617	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4956617delA								None (None upstream) : SOX11 (876182 downstream)																																			---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001234_7001235delCG	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198			UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9397422	9397423	+	Intron	INS	-	GGG	GGG	rs144820582	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9397422_9397423insGGG	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0																		---	---	---	---
TAF1B	9014	broad.mit.edu	37	2	10025873	10025873	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10025873delC	uc002qzz.2	+						TAF1B_uc010exc.2_Intron|TAF1B_uc002qzy.3_Intron|TAF1B_uc010yja.1_Intron|TAF1B_uc010exd.2_Intron	NM_005680	NP_005671			TBP-associated factor 1B						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PDIA6	10130	broad.mit.edu	37	2	10964759	10964759	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10964759delC	uc002rav.2	-						PDIA6_uc010yjh.1_Intron|PDIA6_uc002raw.2_Intron	NM_005742	NP_005733			protein disulfide isomerase A6 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding	endoplasmic reticulum lumen|ER-Golgi intermediate compartment|melanosome|plasma membrane	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	11998202	11998203	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11998202_11998203insG								LPIN1 (30671 upstream) : TRIB2 (858795 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15467387	15467387	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15467387delT	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	16133132	16133133	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16133132_16133133delGA								MYCN (46004 upstream) : FAM49A (600768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16270725	16270726	+	IGR	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16270725_16270726insAC								MYCN (183597 upstream) : FAM49A (463175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16934264	16934264	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16934264delT								FAM49A (87168 upstream) : RAD51AP2 (757722 downstream)																																			---	---	---	---
RAD51AP2	729475	broad.mit.edu	37	2	17697824	17697824	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17697824delT	uc002rcl.1	-	1	1883	c.1859delA	c.(1858-1860)AATfs	p.N620fs	RAD51AP2_uc010exn.1_Frame_Shift_Del_p.N611fs	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	620										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17898356	17898356	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17898356delT	uc002rco.2	-	13	1476	c.1180delA	c.(1180-1182)AGTfs	p.S394fs	SMC6_uc010exo.2_Frame_Shift_Del_p.S394fs|SMC6_uc002rcn.2_Frame_Shift_Del_p.S394fs|SMC6_uc002rcp.1_Frame_Shift_Del_p.S420fs|SMC6_uc002rcq.2_Frame_Shift_Del_p.S420fs|SMC6_uc002rcr.1_Frame_Shift_Del_p.S394fs	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	394	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17906640	17906640	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17906640delA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron|SMC6_uc002rcp.1_Intron|SMC6_uc002rcq.2_Intron|SMC6_uc002rcr.1_Intron	NM_001142286	NP_001135758			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	19525493	19525494	+	IGR	INS	-	AC	AC	rs138624916	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19525493_19525494insAC								NT5C1B (754655 upstream) : OSR1 (25753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19838687	19838687	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19838687delA								OSR1 (280315 upstream) : TTC32 (257831 downstream)																																			---	---	---	---
C2orf43	60526	broad.mit.edu	37	2	20939618	20939618	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20939618delA	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744			hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	22103335	22103335	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22103335delT								APOB (836390 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22255723	22255724	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22255723_22255724insT								APOB (988778 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22556148	22556149	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22556148_22556149insT								None (None upstream) : None (None downstream)																																			---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24469543	24469543	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24469543delT	uc002rfe.2	-						ITSN2_uc002rff.2_Intron|ITSN2_uc002rfg.2_Intron|ITSN2_uc002rfh.1_Intron	NM_006277	NP_006268			intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24533442	24533442	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24533442delG	uc002rfe.2	-	6	730	c.472delC	c.(472-474)CTAfs	p.L158fs	ITSN2_uc002rff.2_Frame_Shift_Del_p.L158fs|ITSN2_uc002rfg.2_Frame_Shift_Del_p.L158fs|ITSN2_uc010eyd.2_Frame_Shift_Del_p.L158fs	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	158					endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	24701943	24701943	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24701943delT								ITSN2 (118546 upstream) : NCOA1 (85236 downstream)																																			---	---	---	---
CENPO	79172	broad.mit.edu	37	2	25039086	25039086	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25039086delA	uc002rfo.1	+						CENPO_uc002rfn.2_3'UTR|CENPO_uc002rfp.1_Intron|CENPO_uc002rfq.1_Intron	NM_024322	NP_077298			centromere protein O						cell division|CenH3-containing nucleosome assembly at centromere|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26175011	26175011	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26175011delA	uc002rgu.2	-						KIF3C_uc010eyj.1_Intron|KIF3C_uc010ykr.1_Intron	NM_002254	NP_002245			kinesin family member 3C						blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf39	92749	broad.mit.edu	37	2	26663214	26663215	+	Intron	DEL	TA	-	-	rs58723978		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26663214_26663215delTA	uc002rhg.2	+						C2orf39_uc010eym.1_Intron	NM_145038	NP_659475			hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	27417685	27417688	+	IGR	DEL	AAAT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27417685_27417688delAAAT								TCF23 (41952 upstream) : SLC5A6 (4771 downstream)																																			---	---	---	---
BRE	9577	broad.mit.edu	37	2	28464370	28464370	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28464370delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31231391	31231391	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31231391delC	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848			N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31358385	31358385	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31358385delA	uc002rnr.2	-						GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848			N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SRD5A2	6716	broad.mit.edu	37	2	31756599	31756600	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31756599_31756600insT	uc002rnw.1	-							NM_000348	NP_000339			3-oxo-5 alpha-steroid 4-dehydrogenase 2						androgen biosynthetic process|cell differentiation|cell-cell signaling|male gonad development	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|sterol 5-alpha reductase activity				0	Acute lymphoblastic leukemia(172;0.155)				Azelaic Acid(DB00548)|Dutasteride(DB01126)													---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32690110	32690110	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32690110delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32706268	32706268	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32706268delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33301609	33301610	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33301609_33301610delTT	uc002ros.2	+							NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	33859911	33859912	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33859911_33859912delTT								FAM98A (35549 upstream) : MYADML (91220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	33875314	33875314	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33875314delT								FAM98A (50952 upstream) : MYADML (75818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	33918875	33918876	+	IGR	INS	-	TCT	TCT	rs144498363	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33918875_33918876insTCT								FAM98A (94513 upstream) : MYADML (32256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36526516	36526516	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36526516delT								None (None upstream) : CRIM1 (56881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36779350	36779350	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36779350delA								CRIM1 (1073 upstream) : FEZ2 (54 downstream)																																			---	---	---	---
VIT	5212	broad.mit.edu	37	2	37000464	37000465	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37000464_37000465delTT	uc002rpl.2	+						VIT_uc010ynf.1_Intron|VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506			vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)																---	---	---	---
STRN	6801	broad.mit.edu	37	2	37090336	37090336	+	Intron	DEL	T	-	-	rs76909810		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37090336delT	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153			striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37229751	37229751	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37229751delA	uc002rpp.1	-						HEATR5B_uc002rpo.1_5'Flank|HEATR5B_uc010ezy.1_Intron	NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
FAM82A1	151393	broad.mit.edu	37	2	38178340	38178340	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38178340delT	uc002rql.2	+						FAM82A1_uc002rqn.1_Intron|FAM82A1_uc002rqk.1_Intron|FAM82A1_uc002rqm.2_Intron	NM_144713	NP_653314			family with sequence similarity 82, member A1							cytoplasm|integral to membrane|microtubule|spindle pole	binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	38421588	38421588	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38421588delT								C2orf58 (12597 upstream) : ATL2 (100443 downstream)																																			---	---	---	---
ATL2	64225	broad.mit.edu	37	2	38605001	38605001	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38605001delC	uc002rqq.2	-						ATL2_uc010ynm.1_5'Flank|ATL2_uc010ynn.1_5'Flank|ATL2_uc010yno.1_5'Flank|ATL2_uc002rqs.2_5'Flank|ATL2_uc002rqr.2_5'Flank	NM_001135673	NP_001129145			atlastin GTPase 2 isoform 2						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
SFRS7	6432	broad.mit.edu	37	2	38973132	38973132	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38973132delA	uc002rqz.2	-						SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron	NM_001031684	NP_001026854			splicing factor, arginine/serine-rich 7						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)																---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39262296	39262297	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39262296_39262297insA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron|SOS1_uc002rrj.3_Intron|SOS1_uc002rrl.2_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40402646	40402647	+	Intron	INS	-	TG	TG	rs146364894	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40402646_40402647insTG	uc002rrx.2	-						uc002rrw.2_Intron|SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_Intron	NM_021097	NP_066920			solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	40784876	40784877	+	IGR	DEL	AC	-	-	rs35754385		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40784876_40784877delAC								SLC8A1 (45301 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41906483	41906483	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41906483delT								None (None upstream) : PKDCC (368678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42654577	42654578	+	IGR	INS	-	CTA	CTA	rs147020276	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42654577_42654578insCTA								COX7A2L (58427 upstream) : KCNG3 (14581 downstream)																																			---	---	---	---
THADA	63892	broad.mit.edu	37	2	43768234	43768234	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43768234delA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
LRPPRC	10128	broad.mit.edu	37	2	44145165	44145165	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44145165delT	uc002rtr.2	-	29	3205	c.3147delA	c.(3145-3147)AAAfs	p.K1049fs	LRPPRC_uc010yob.1_Frame_Shift_Del_p.K949fs	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein	1049	PPR 15.				mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46401838	46401838	+	Intron	DEL	T	-	-	rs142366817	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46401838delT	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
EPAS1	2034	broad.mit.edu	37	2	46603177	46603177	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46603177delT	uc002ruv.2	+							NM_001430	NP_001421			endothelial PAS domain protein 1						angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	48477935	48477938	+	IGR	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48477935_48477938delAAAA								FBXO11 (345121 upstream) : FOXN2 (63857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48513440	48513441	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48513440_48513441delTT								FBXO11 (380626 upstream) : FOXN2 (28354 downstream)																																			---	---	---	---
KLRAQ1	129285	broad.mit.edu	37	2	48738837	48738838	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48738837_48738838insA	uc002rwm.2	+						KLRAQ1_uc002rwl.2_Intron|KLRAQ1_uc002rwk.2_Intron|KLRAQ1_uc010yok.1_Intron	NM_001135629	NP_001129101			KLRAQ motif containing 1 isoform 1											ovary(1)	1																		---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49206571	49206571	+	Intron	DEL	C	-	-	rs1558607	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49206571delC	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50729390	50729390	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50729390delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50940463	50940464	+	Intron	DEL	AG	-	-	rs59624350		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50940463_50940464delAG	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	53345560	53345560	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53345560delT								None (None upstream) : ASB3 (551558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53783481	53783481	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53783481delT								None (None upstream) : ASB3 (113637 downstream)																																			---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54126955	54126955	+	Intron	DEL	A	-	-	rs71408744		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54126955delA	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54167140	54167140	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54167140delG	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54192240	54192241	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54192240_54192241delAC	uc002rxp.2	-						PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54893033	54893033	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54893033delT	uc002rxu.2	+						SPTBN1_uc010you.1_Intron	NM_003128	NP_003119			spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
EML6	400954	broad.mit.edu	37	2	55140381	55140383	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55140381_55140383delTTT	uc002ryb.3	+							NM_001039753	NP_001034842			echinoderm microtubule associated protein like							cytoplasm|microtubule					0																		---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58362161	58362161	+	Intron	DEL	G	-	-	rs11678320	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58362161delG	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	59362172	59362172	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59362172delA								FANCL (893657 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59786648	59786648	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59786648delT								None (None upstream) : BCL11A (891655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60534988	60534988	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60534988delC								None (None upstream) : BCL11A (143315 downstream)																																			---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61312652	61312652	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61312652delT	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron|KIAA1841_uc002sav.3_Intron	NM_001129993	NP_001123465			KIAA1841 protein isoform a												0			Epithelial(17;0.193)															---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61336316	61336316	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61336316delT	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron	NM_001129993	NP_001123465			KIAA1841 protein isoform a												0			Epithelial(17;0.193)															---	---	---	---
AHSA2	130872	broad.mit.edu	37	2	61413739	61413739	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61413739delT	uc002sbc.1	+						AHSA2_uc002sbb.1_Intron	NM_152392	NP_689605			AHA1, activator of heat shock 90kDa protein						response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61517102	61517102	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61517102delG	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61552412	61552412	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61552412delA	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
CCT4	10575	broad.mit.edu	37	2	62110688	62110688	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62110688delA	uc002sbo.2	-						CCT4_uc010ypp.1_Intron|CCT4_uc010ypq.1_Intron|CCT4_uc010ypr.1_Intron|CCT4_uc010yps.1_Intron	NM_006430	NP_006421			chaperonin containing TCP1, subunit 4 (delta)						'de novo' posttranslational protein folding	melanosome|microtubule organizing center|nucleus	ATP binding|unfolded protein binding			ovary(2)	2	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)															---	---	---	---
COMMD1	150684	broad.mit.edu	37	2	62181999	62181999	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62181999delG	uc002sbp.2	+							NM_152516	NP_689729			MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)															---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	62990358	62990358	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62990358delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron|EHBP1_uc002sca.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63059574	63059575	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63059574_63059575delTT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63664885	63664886	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63664885_63664886insT	uc002sch.2	-						C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron|C2orf86_uc002sci.1_Intron|C2orf86_uc010fcr.1_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63713749	63713749	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63713749delA	uc002sch.2	-						C2orf86_uc002sci.1_Intron|C2orf86_uc010fcr.1_5'Flank	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64392643	64392643	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64392643delA								PELI1 (21038 upstream) : HSPC159 (288684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64493050	64493051	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64493050_64493051delAC								PELI1 (121445 upstream) : HSPC159 (188276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64574342	64574342	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64574342delT								PELI1 (202737 upstream) : HSPC159 (106985 downstream)																																			---	---	---	---
SERTAD2	9792	broad.mit.edu	37	2	64864067	64864067	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64864067delA	uc002sde.1	-							NM_014755	NP_055570			SERTA domain containing 2						negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0																		---	---	---	---
SPRED2	200734	broad.mit.edu	37	2	65581156	65581156	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65581156delA	uc002sdr.3	-						SPRED2_uc010fcw.2_Intron|SPRED2_uc010fcx.1_Intron	NM_181784	NP_861449			sprouty-related protein with EVH-1 domain 2						inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	65668218	65668218	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65668218delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65858549	65858550	+	Intron	INS	-	A	A	rs79105847		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65858549_65858550insA	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	68149071	68149071	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68149071delT								ETAA1 (511538 upstream) : C1D (120262 downstream)																																			---	---	---	---
SNRPG	6637	broad.mit.edu	37	2	70516451	70516451	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70516451delA	uc002sgp.2	-						SNRPG_uc002sgo.2_Intron	NM_003096	NP_003087			small nuclear ribonucleoprotein polypeptide G						histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	72075414	72075415	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72075414_72075415delGA								DYSF (161522 upstream) : CYP26B1 (280952 downstream)																																			---	---	---	---
SMYD5	10322	broad.mit.edu	37	2	73450866	73450866	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73450866delG	uc002siw.2	+						SMYD5_uc010yre.1_Intron|SMYD5_uc002six.1_Intron	NM_006062	NP_006053			SMYD family member 5								metal ion binding				0																		---	---	---	---
C2orf7	84279	broad.mit.edu	37	2	73456259	73456259	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73456259delT	uc002siy.2	-							NM_032319	NP_115695			chromosome 2 open reading frame 7 precursor							extracellular region					0																		---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73830582	73830582	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73830582delA	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjh.1_3'UTR	NM_015120	NP_055935			Alstrom syndrome 1						G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
TET3	200424	broad.mit.edu	37	2	74313507	74313507	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74313507delA	uc002skb.3	+							NM_144993	NP_659430			tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
SLC4A5	57835	broad.mit.edu	37	2	74526002	74526003	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74526002_74526003insA	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019			sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75081242	75081245	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75081242_75081245delTTTT	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	75561136	75561136	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75561136delT								TACR1 (134491 upstream) : FAM176A (158308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76647891	76647891	+	IGR	DEL	T	-	-	rs72182376		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76647891delT								C2orf3 (709780 upstream) : LRRTM4 (326967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76742136	76742137	+	IGR	DEL	AT	-	-	rs146382469		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76742136_76742137delAT								C2orf3 (804025 upstream) : LRRTM4 (232721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76937479	76937480	+	IGR	INS	-	T	T	rs141310669	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76937479_76937480insT								C2orf3 (999368 upstream) : LRRTM4 (37378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	77996992	77996994	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77996992_77996994delAAA								LRRTM4 (247490 upstream) : SNAR-H (185039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	78713514	78713514	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78713514delT	uc002snv.3	-											Homo sapiens cytochrome c, somatic pseudogene 6, mRNA (cDNA clone IMAGE:4815768).																														---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79754418	79754418	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79754418delA	uc010yse.1	+						CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79853703	79853704	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79853703_79853704delGT	uc010yse.1	+						CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80009956	80009956	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80009956delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	81995275	81995275	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81995275delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83444096	83444096	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83444096delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84180666	84180666	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84180666delA								None (None upstream) : FUNDC2P2 (337140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84692630	84692630	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84692630delA								SUCLG1 (6044 upstream) : DNAH6 (50949 downstream)																																			---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84912421	84912421	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84912421delT	uc010fgb.2	+						DNAH6_uc002sor.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
IMMT	10989	broad.mit.edu	37	2	86385684	86385684	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86385684delA	uc002sqz.3	-						IMMT_uc002sqy.3_Intron|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002src.1_Intron|IMMT_uc002srd.2_3'UTR	NM_006839	NP_006830			inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86855699	86855700	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86855699_86855700delTT	uc010ytl.1	-							NM_001005753	NP_001005753			vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87051115	87051116	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87051115_87051116delTG	uc002srs.3	+						CD8B_uc002srw.2_Intron|CD8B_uc002srx.2_Intron|CD8B_uc002sry.2_Intron|CD8B_uc010fgt.2_Intron					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87578349	87578349	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87578349delA	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RGPD1	400966	broad.mit.edu	37	2	88118145	88118145	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88118145delA	uc010fhc.1	-							NM_001024457	NP_001019628			RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	90372485	90372486	+	Intron	INS	-	T	T	rs145778132	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90372485_90372486insT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90417154	90417155	+	Intron	INS	-	ATG	ATG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90417154_90417155insATG	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96517688	96517690	+	IGR	DEL	TTG	-	-	rs67460523		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96517688_96517690delTTG								TRIM43 (252221 upstream) : LOC729234 (158609 downstream)																																			---	---	---	---
DUSP2	1844	broad.mit.edu	37	2	96809473	96809474	+	3'UTR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96809473_96809474insT	uc002svk.3	-	4						NM_004418	NP_004409			dual specificity phosphatase 2						endoderm formation|inactivation of MAPK activity|regulation of apoptosis	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity			breast(1)	1		Ovarian(717;0.0228)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	96913477	96913477	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96913477delA								LOC285033 (5776 upstream) : TMEM127 (2837 downstream)																																			---	---	---	---
ITPRIPL1	150771	broad.mit.edu	37	2	96994051	96994051	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96994051delA	uc002svx.2	+	3					ITPRIPL1_uc010yuk.1_3'UTR|ITPRIPL1_uc002svy.2_3'UTR|ITPRIPL1_uc010yul.1_3'UTR	NM_001008949	NP_001008949			inositol 1,4,5-triphosphate receptor interacting							integral to membrane				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
NCAPH	23397	broad.mit.edu	37	2	97020221	97020221	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97020221delT	uc002svz.1	+						NCAPH_uc010fhu.1_Intron|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156			non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	97140809	97140809	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97140809delA								NCAPH (99535 upstream) : NEURL3 (22576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	99577231	99577231	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99577231delT								C2orf55 (24547 upstream) : TSGA10 (36494 downstream)																																			---	---	---	---
MRPL30	51263	broad.mit.edu	37	2	99811772	99811772	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99811772delT	uc002szu.2	+						MRPL30_uc002szl.1_Intron|MRPL30_uc002szt.1_Intron|MRPL30_uc002szv.2_Intron	NM_145213	NP_660214			RecName: Full=39S ribosomal protein L30, mitochondrial;          Short=L30mt; AltName: Full=MRP-L30; AltName: Full=MRP-L28; Flags: Precursor;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	100126637	100126638	+	IGR	DEL	TT	-	-	rs79664989		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100126637_100126638delTT								REV1 (20157 upstream) : AFF3 (37080 downstream)																																			---	---	---	---
RFX8	731220	broad.mit.edu	37	2	102047580	102047595	+	Intron	DEL	CCATCCATCCAACCAA	-	-	rs149825288		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102047580_102047595delCCATCCATCCAACCAA	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136			regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102180416	102180421	+	IGR	DEL	AAGGAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102180416_102180421delAAGGAG								RFX8 (89251 upstream) : MAP4K4 (134067 downstream)																																			---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102835403	102835404	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102835403_102835404delTT	uc002tbs.2	+						IL1RL2_uc002tbt.2_Intron	NM_003854	NP_003845			interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103200345	103200345	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103200345delT								SLC9A4 (49915 upstream) : SLC9A2 (35821 downstream)																																			---	---	---	---
TMEM182	130827	broad.mit.edu	37	2	103413337	103413338	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103413337_103413338insA	uc010fjb.2	+						TMEM182_uc002tcc.3_Intron|TMEM182_uc002tcd.3_Intron|TMEM182_uc010ywe.1_5'Flank	NM_144632	NP_653233			transmembrane protein 182 precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	105275284	105275285	+	IGR	INS	-	TT	TT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105275284_105275285insTT								LOC150568 (146070 upstream) : POU3F3 (196684 downstream)																																			---	---	---	---
FHL2	2274	broad.mit.edu	37	2	106056977	106056978	+	5'Flank	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106056977_106056978insA	uc002tdd.2	-						FHL2_uc002tdc.2_5'Flank	NM_201557	NP_963851			four and a half LIM domains 2						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent	actin cytoskeleton|focal adhesion|nucleus	androgen receptor binding|identical protein binding|transcription coactivator activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	106201686	106201687	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106201686_106201687delAA								FHL2 (146456 upstream) : NCK2 (159667 downstream)																																			---	---	---	---
UXS1	80146	broad.mit.edu	37	2	106717579	106717579	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106717579delA	uc002tdm.2	-						UXS1_uc002tdl.2_Intron|UXS1_uc002tdn.2_Intron|UXS1_uc002tdo.2_Intron|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352			UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	107234772	107234773	+	IGR	INS	-	T	T	rs151062839	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107234772_107234773insT								RGPD3 (149971 upstream) : ST6GAL2 (183285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107315190	107315190	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107315190delA								RGPD3 (230389 upstream) : ST6GAL2 (102868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107345912	107345913	+	IGR	INS	-	CTATGGA	CTATGGA	rs138133575	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107345912_107345913insCTATGGA								RGPD3 (261111 upstream) : ST6GAL2 (72145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107701026	107701026	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107701026delA								ST6GAL2 (197463 upstream) : LOC729121 (738494 downstream)																																			---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109300314	109300314	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109300314delT	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron|LIMS1_uc002tej.2_Intron|LIMS1_uc002tek.3_Intron|uc002tel.2_5'Flank	NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	109954193	109954193	+	Intron	DEL	T	-	-	rs111316139		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109954193delT	uc010ywt.1	+							NM_001099289	NP_001092759			SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	110065874	110065874	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110065874delC	uc010ywt.1	+	8	2077	c.2077delC	c.(2077-2079)CCCfs	p.P693fs		NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	693							zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	110271059	110271061	+	IGR	DEL	CAC	-	-	rs146833536	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110271059_110271061delCAC								SH3RF3 (8852 upstream) : SEPT10 (29313 downstream)																																			---	---	---	---
SEPT10	151011	broad.mit.edu	37	2	110325591	110325591	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110325591delT	uc002tew.2	-						SEPT10_uc010ywu.1_Intron|SEPT10_uc002tex.2_Intron|SEPT10_uc002tey.2_Intron|SEPT10_uc010ywv.1_Intron|SEPT10_uc002tev.1_Intron|SEPT10_uc010fjo.2_Intron|SEPT10_uc002tez.1_5'Flank	NM_144710	NP_653311			septin 10 isoform 1						cell cycle|cell division	septin complex	GTP binding				0																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111515320	111515320	+	Intron	DEL	T	-	-	rs60916256		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111515320delT	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986			acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112610713	112610713	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112610713delT	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
TMEM87B	84910	broad.mit.edu	37	2	112854564	112854565	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112854564_112854565delTT	uc002thm.2	+							NM_032824	NP_116213			transmembrane protein 87B precursor							integral to membrane					0																		---	---	---	---
FBLN7	129804	broad.mit.edu	37	2	112905467	112905467	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112905467delG	uc002tho.1	+						FBLN7_uc002thn.2_Intron|FBLN7_uc010fki.1_Intron|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946			fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RGPD5	84220	broad.mit.edu	37	2	113127926	113127926	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113127926delG	uc002ths.1	-						RGPD8_uc010fkk.1_Intron	NM_005054	NP_005045			RANBP2-like and GRIP domain containing 5 isoform						intracellular transport	cytoplasm	binding				0																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115583234	115583234	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115583234delC	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115951807	115951807	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115951807delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	119093282	119093282	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119093282delT								INSIG2 (225686 upstream) : EN1 (506466 downstream)																																			---	---	---	---
C2orf76	130355	broad.mit.edu	37	2	120071591	120071601	+	Intron	DEL	TTTTTTTTTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120071591_120071601delTTTTTTTTTTT	uc002tls.2	-						C2orf76_uc010flf.1_Intron|C2orf76_uc010yyg.1_Intron|C2orf76_uc002tlt.2_Intron|C2orf76_uc002tlu.2_Intron	NM_001017927	NP_001017927			hypothetical protein LOC130355												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	120420566	120420566	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120420566delC								PCDP1 (6330 upstream) : TMEM177 (16177 downstream)																																			---	---	---	---
TSN	7247	broad.mit.edu	37	2	122516421	122516421	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122516421delA	uc002tnl.2	+						TSN_uc002tnm.2_Intron|TSN_uc010yze.1_Intron|TSN_uc010flt.2_Intron	NM_004622	NP_004613			translin						DNA recombination	cytoplasm|nucleus	sequence-specific DNA binding			breast(2)|large_intestine(1)	3		Ovarian(717;0.0563)|Prostate(154;0.116)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	123960729	123960730	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123960729_123960730delTG								None (None upstream) : CNTNAP5 (822134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124273127	124273127	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124273127delT								None (None upstream) : CNTNAP5 (509737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126494314	126494314	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126494314delA								CNTNAP5 (821453 upstream) : GYPC (919370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127296775	127296775	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127296775delA								None (None upstream) : GYPC (116909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127569008	127569008	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127569008delT								GYPC (114763 upstream) : BIN1 (236599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	128232256	128232256	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128232256delC								PROC (45440 upstream) : IWS1 (6127 downstream)																																			---	---	---	---
AMMECR1L	83607	broad.mit.edu	37	2	128628050	128628050	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128628050delA	uc002tpl.2	-						AMMECR1L_uc002tpm.2_Intron	NM_031445	NP_113633			AMME chromosomal region gene 1-like											central_nervous_system(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)														---	---	---	---
SAP130	79595	broad.mit.edu	37	2	128781893	128781893	+	Intron	DEL	A	-	-	rs67915956		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128781893delA	uc002tpp.2	-						SAP130_uc010fmd.2_Intron|SAP130_uc002tpq.1_Intron	NM_024545	NP_078821			Sin3A-associated protein, 130kDa isoform b						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)														---	---	---	---
HS6ST1	9394	broad.mit.edu	37	2	129059384	129059384	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129059384delC	uc002tpt.3	-							NM_004807	NP_004798			heparan sulfate 6-O-sulfotransferase 1						heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	129304100	129304100	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129304100delC								HS6ST1 (227929 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130625145	130625145	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130625145delT								None (None upstream) : LOC389033 (55290 downstream)																																			---	---	---	---
POTEF	728378	broad.mit.edu	37	2	130832989	130832989	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130832989delT	uc010fmh.2	-	17	2456	c.2056delA	c.(2056-2058)AGGfs	p.R686fs		NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on	686	Potential.					cell cortex	ATP binding			skin(3)|ovary(2)	5																		---	---	---	---
ARHGEF4	50649	broad.mit.edu	37	2	131752804	131752807	+	Intron	DEL	TCTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131752804_131752807delTCTG	uc002tsa.1	+						ARHGEF4_uc010fmw.1_Intron|ARHGEF4_uc002tsb.1_Intron|ARHGEF4_uc010fmx.1_Intron	NM_015320	NP_056135			Rho guanine nucleotide exchange factor 4 isoform						apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132333922	132333922	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132333922delT								CCDC74A (42685 upstream) : C2orf27A (146142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132383788	132383788	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132383788delC								CCDC74A (92551 upstream) : C2orf27A (96276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132788552	132788553	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132788552_132788553insA								C2orf27B (229318 upstream) : NCRNA00164 (116611 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133006337	133006337	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133006337delT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	133028130	133028131	+	IGR	DEL	AC	-	-	rs145524384		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133028130_133028131delAC								NCRNA00164 (12588 upstream) : GPR39 (146016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134460114	134460115	+	IGR	DEL	TG	-	-	rs113508993		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134460114_134460115delTG								NCKAP5 (134083 upstream) : MGAT5 (551715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134489079	134489080	+	IGR	INS	-	A	A	rs140796443	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134489079_134489080insA								NCKAP5 (163048 upstream) : MGAT5 (522750 downstream)																																			---	---	---	---
MGAT5	4249	broad.mit.edu	37	2	135044010	135044010	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135044010delT	uc002ttv.1	+							NM_002410	NP_002401			N-acetylglucosaminyltransferase V						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)														---	---	---	---
MGAT5	4249	broad.mit.edu	37	2	135158663	135158663	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135158663delT	uc002ttv.1	+							NM_002410	NP_002401			N-acetylglucosaminyltransferase V						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)														---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135870711	135870711	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135870711delT	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_Intron|RAB3GAP1_uc010fnh.1_Intron	NM_012233	NP_036365			RAB3 GTPase-activating protein							centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139063376	139063376	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139063376delT								HNMT (289443 upstream) : SPOPL (195974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139376090	139376090	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139376090delT								SPOPL (45287 upstream) : NXPH2 (50639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140368300	140368302	+	IGR	DEL	CTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140368300_140368302delCTG								NXPH2 (830489 upstream) : LRP1B (620694 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141773495	141773495	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141773495delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	142929934	142929934	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142929934delT								LRP1B (40664 upstream) : KYNU (705261 downstream)																																			---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144276716	144276716	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144276716delA	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145992128	145992129	+	IGR	INS	-	TG	TG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145992128_145992129insTG								ZEB2 (714197 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146477778	146477779	+	IGR	INS	-	T	T	rs145119748	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146477778_146477779insT								None (None upstream) : PABPC1P2 (866846 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148683686delA	uc002twg.2	+	11	1572	c.1303delA	c.(1303-1305)AAAfs	p.K435fs	ACVR2A_uc010zbn.1_Frame_Shift_Del_p.K327fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.K435fs	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	435	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149622682	149622682	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149622682delT								EPC2 (77547 upstream) : KIF5C (10137 downstream)																																			---	---	---	---
LYPD6B	130576	broad.mit.edu	37	2	149919528	149919529	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149919528_149919529delCT	uc002twv.1	+						LYPD6B_uc002tww.1_Intron	NM_177964	NP_808879			LY6/PLAUR domain containing 6B							anchored to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	151606292	151606294	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151606292_151606294delAAA								RND3 (262112 upstream) : RBM43 (498435 downstream)																																			---	---	---	---
NEB	4703	broad.mit.edu	37	2	152353795	152353796	+	Intron	INS	-	T	T	rs76662961		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152353795_152353796insT	uc010fnx.2	-						NEB_uc002txr.2_Intron|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Intron|NEB_uc002txq.2_Intron|NEB_uc010zca.1_Intron|NEB_uc010zcb.1_Intron	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152426974	152426974	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152426974delA	uc010fnx.2	-						NEB_uc002txr.2_Intron	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152695482	152695482	+	3'UTR	DEL	T	-	-	rs111950042		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152695482delT	uc002tya.2	-	14					CACNB4_uc002txy.2_3'UTR|CACNB4_uc002txz.2_3'UTR|CACNB4_uc010fnz.2_3'UTR	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	153660465	153660465	+	IGR	DEL	A	-	-	rs111343980		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153660465delA								ARL6IP6 (42698 upstream) : RPRM (673387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154237820	154237820	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154237820delT								ARL6IP6 (620053 upstream) : RPRM (96032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156683480	156683480	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156683480delT								KCNJ3 (970466 upstream) : NR4A2 (497466 downstream)																																			---	---	---	---
NR4A2	4929	broad.mit.edu	37	2	157185074	157185074	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157185074delT	uc002tyz.3	-						NR4A2_uc002tyx.3_Intron|NR4A2_uc010zcf.1_Intron|NR4A2_uc010zcg.1_5'Flank	NM_006186	NP_006177			nuclear receptor subfamily 4, group A, member 2						cellular response to extracellular stimulus|dopaminergic neuron differentiation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus	nucleoplasm	sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158390653	158390653	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158390653delT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159903701	159903701	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159903701delC	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
MARCH7	64844	broad.mit.edu	37	2	160605489	160605489	+	Intron	DEL	C	-	-	rs72017785		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160605489delC	uc002uax.2	+						MARCH7_uc010foq.2_Intron|MARCH7_uc010zcn.1_Intron|MARCH7_uc010for.2_Intron|MARCH7_uc002uay.2_Intron	NM_022826	NP_073737			axotrophin								ligase activity|zinc ion binding				0																		---	---	---	---
LY75	4065	broad.mit.edu	37	2	160728864	160728864	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160728864delT	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron|LY75_uc010fot.1_3'UTR	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162922761	162922762	+	Intron	DEL	TT	-	-	rs3216640		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162922761_162922762delTT	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_Intron|DPP4_uc002ucb.1_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163510668	163510668	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163510668delA	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	163716917	163716917	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163716917delA								KCNH7 (21677 upstream) : FIGN (747201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164938218	164938218	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164938218delT								FIGN (345705 upstream) : GRB14 (411115 downstream)																																			---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165551296	165551296	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165551296delA	uc010zcw.1	-	15	3045	c.2921delT	c.(2920-2922)TTGfs	p.L974fs	COBLL1_uc002ucp.2_Frame_Shift_Del_p.L907fs|COBLL1_uc002ucq.2_Frame_Shift_Del_p.L869fs|COBLL1_uc010zcx.1_Frame_Shift_Del_p.L915fs|COBLL1_uc002ucn.2_Frame_Shift_Del_p.L335fs|COBLL1_uc002uco.2_Frame_Shift_Del_p.L638fs	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	945										ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165889135	165889137	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165889135_165889137delTTT								SLC38A11 (77100 upstream) : SCN3A (54895 downstream)																																			---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165971884	165971884	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165971884delT	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Intron|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166771641	166771641	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166771641delA	uc002udk.2	-							NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	167583208	167583208	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167583208delT								SCN7A (232491 upstream) : XIRP2 (161789 downstream)																																			---	---	---	---
ABCB11	8647	broad.mit.edu	37	2	169873316	169873317	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169873316_169873317insA	uc002ueo.1	-							NM_003742	NP_003733			ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)													---	---	---	---
PPIG	9360	broad.mit.edu	37	2	170463802	170463802	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170463802delA	uc002uez.2	+						PPIG_uc010fpx.2_Intron|PPIG_uc010fpy.2_Intron|PPIG_uc002ufa.2_Intron|PPIG_uc002ufb.2_Intron|PPIG_uc002ufc.1_Intron|PPIG_uc002ufd.2_Intron	NM_004792	NP_004783			peptidylprolyl isomerase G						protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)													---	---	---	---
C2orf77	129881	broad.mit.edu	37	2	170513507	170513507	+	Intron	DEL	A	-	-	rs71006017		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170513507delA	uc002ufe.2	-							NM_001085447	NP_001078916			hypothetical protein LOC129881												0																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171259144	171259144	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171259144delA	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482			myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	171516018	171516018	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171516018delA	uc002ugc.1	-											Homo sapiens cDNA FLJ25833 fis, clone TST08193.																														---	---	---	---
GAD1	2571	broad.mit.edu	37	2	171700448	171700448	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171700448delT	uc002ugi.2	+							NM_000817	NP_000808			glutamate decarboxylase 1 isoform GAD67						glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171916563	171916563	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171916563delA	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc002ugq.2_Intron|TLK1_uc010zdn.1_Intron	NM_012290	NP_036422			tousled-like kinase 1 isoform 1						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
DYNC1I2	1781	broad.mit.edu	37	2	172563690	172563690	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172563690delT	uc002uha.1	+						DYNC1I2_uc002uhc.2_Intron|DYNC1I2_uc002uhb.1_Intron|DYNC1I2_uc010zds.1_Intron|DYNC1I2_uc002uhd.1_Intron|DYNC1I2_uc002uhe.1_Intron|DYNC1I2_uc002uhf.1_Intron|DYNC1I2_uc010zdt.1_Intron|DYNC1I2_uc002uhg.1_5'UTR	NM_001378	NP_001369			dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)															---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172847964	172847964	+	Intron	DEL	A	-	-	rs78900975		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172847964delA	uc002uhi.2	+						HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174123373	174123373	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174123373delA	uc002uhz.2	+						uc002uib.2_Intron	NM_016653	NP_057737			MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174414005	174414005	+	IGR	DEL	T	-	-	rs112517738		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174414005delT								CDCA7 (180287 upstream) : SP3 (359254 downstream)																																			---	---	---	---
WIPF1	7456	broad.mit.edu	37	2	175439682	175439682	+	Intron	DEL	A	-	-	rs68082019		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175439682delA	uc002uiy.2	-						uc002uiw.2_Intron|uc002uix.1_Intron|WIPF1_uc002uja.2_Intron|WIPF1_uc010fqt.1_Intron|WIPF1_uc002ujc.1_Intron|WIPF1_uc002uiz.2_Intron|WIPF1_uc002ujb.1_Intron|WIPF1_uc010zep.1_Intron	NM_003387	NP_003378			WAS/WASL interacting protein family, member 1						actin polymerization or depolymerization|protein complex assembly	cytoplasmic membrane-bounded vesicle	actin binding|profilin binding			ovary(1)|skin(1)	2																		---	---	---	---
ATF2	1386	broad.mit.edu	37	2	175978513	175978513	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175978513delA	uc002ujl.2	-						ATF2_uc010fqv.2_Intron|ATF2_uc002ujv.2_Intron|ATF2_uc002ujm.2_Intron|ATF2_uc002ujn.2_Intron|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Intron|ATF2_uc002ujq.2_Intron|ATF2_uc002ujr.2_Intron|ATF2_uc010fqu.2_Intron|ATF2_uc002ujs.2_Intron|ATF2_uc002ujt.2_Intron|ATF2_uc002uju.2_Intron|ATF2_uc002ujw.1_Intron|ATF2_uc002ujx.1_Intron	NM_001880	NP_001871			activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	176507734	176507735	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176507734_176507735insA								ATP5G3 (461244 upstream) : KIAA1715 (282675 downstream)																																			---	---	---	---
HOXD11	3237	broad.mit.edu	37	2	176973387	176973388	+	Intron	INS	-	TGTG	TGTG	rs71874941		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176973387_176973388insTGTG	uc002uki.2	+						HOXD11_uc010fqx.2_Intron	NM_021192	NP_067015			homeobox D11							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)				T	NUP98	AML								---	---	---	---
MTX2	10651	broad.mit.edu	37	2	177184976	177184976	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177184976delA	uc002ukx.2	+						MTX2_uc002ukw.2_Intron	NM_006554	NP_006545			metaxin 2						protein targeting to mitochondrion	mitochondrial outer membrane				ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)															---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178357853	178357853	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178357853delT	uc002ull.2	+						AGPS_uc010zfb.1_Intron	NM_003659	NP_003650			alkyldihydroxyacetone phosphate synthase						ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)															---	---	---	---
PDE11A	50940	broad.mit.edu	37	2	178898906	178898906	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178898906delA	uc002ulq.2	-						PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649			phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)											Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	2	179040564	179040564	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179040564delA								RBM45 (46184 upstream) : OSBPL6 (18810 downstream)																																			---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179248597	179248597	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179248597delT	uc002ulx.2	+						OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_Intron|OSBPL6_uc002uma.2_Intron	NM_032523	NP_115912			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179442178	179442178	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179442178delC	uc010zfg.1	-	273	61404	c.61180delG	c.(61180-61182)GATfs	p.D20394fs	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.D14089fs|TTN_uc010zfi.1_Frame_Shift_Del_p.D14022fs|TTN_uc010zfj.1_Frame_Shift_Del_p.D13897fs|uc002umv.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	21321							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	181185156	181185156	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181185156delA								CWC22 (313316 upstream) : UBE2E3 (659956 downstream)																																			---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181925322	181925322	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181925322delT	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619			ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	186544550	186544550	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186544550delA								ZNF804A (740338 upstream) : ZC3H15 (806335 downstream)																																			---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187618917	187618917	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187618917delT	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237			KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	187784391	187784391	+	IGR	DEL	T	-	-	rs5837007		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187784391delT								ZSWIM2 (70494 upstream) : CALCRL (423460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187900179	187900179	+	IGR	DEL	A	-	-	rs71396901		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187900179delA								ZSWIM2 (186282 upstream) : CALCRL (307672 downstream)																																			---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189169632	189169632	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189169632delT	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189176925	189176925	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189176925delA	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189334022	189334023	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189334022_189334023insG	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
COL5A2	1290	broad.mit.edu	37	2	189943836	189943836	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189943836delA	uc002uqk.2	-						COL5A2_uc010frx.2_Intron	NM_000393	NP_000384			alpha 2 type V collagen preproprotein						axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)															---	---	---	---
COL5A2	1290	broad.mit.edu	37	2	189945892	189945893	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189945892_189945893insA	uc002uqk.2	-						COL5A2_uc010frx.2_Intron	NM_000393	NP_000384			alpha 2 type V collagen preproprotein						axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)															---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191152424	191152424	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191152424delA	uc002uru.2	-						HIBCH_uc002urv.2_Intron	NM_014362	NP_055177			3-hydroxyisobutyryl-Coenzyme A hydrolase isoform						branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	192482466	192482466	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192482466delA								MYO1B (192351 upstream) : OBFC2A (60332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193453094	193453094	+	IGR	DEL	A	-	-	rs112860893		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193453094delA								TMEFF2 (393450 upstream) : PCGEM1 (161477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194121352	194121353	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194121352_194121353insT								PCGEM1 (479731 upstream) : None (None downstream)																																			---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196741292	196741292	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196741292delA	uc002utj.3	-	37	6194	c.6093delT	c.(6091-6093)TTTfs	p.F2031fs		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2031	AAA 3 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196857099	196857099	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196857099delT	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197136016	197136017	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197136016_197136017insA	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
CCDC150	284992	broad.mit.edu	37	2	197584401	197584401	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197584401delT	uc002utp.1	+						CCDC150_uc010zgs.1_Intron|CCDC150_uc010zgt.1_Intron|CCDC150_uc002utq.1_Intron|CCDC150_uc002utr.1_Intron	NM_001080539	NP_001074008			coiled-coil domain containing 150												0																		---	---	---	---
SF3B1	23451	broad.mit.edu	37	2	198257295	198257296	+	Intron	DEL	GG	-	-	rs72167899		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198257295_198257296delGG	uc002uue.2	-							NM_012433	NP_036565			splicing factor 3b, subunit 1 isoform 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
SF3B1	23451	broad.mit.edu	37	2	198258180	198258182	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198258180_198258182delTTT	uc002uue.2	-							NM_012433	NP_036565			splicing factor 3b, subunit 1 isoform 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
COQ10B	80219	broad.mit.edu	37	2	198324935	198324937	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198324935_198324937delTTT	uc002uuh.1	+						COQ10B_uc010fsl.1_Intron	NM_025147	NP_079423			coenzyme Q10 homolog B precursor							mitochondrial inner membrane					0			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
HSPD1	3329	broad.mit.edu	37	2	198359954	198359954	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198359954delA	uc002uui.2	-						HSPD1_uc002uuj.2_Intron|HSPD1_uc010zgx.1_Intron|HSPD1_uc010fsm.2_5'UTR|HSPD1_uc002uuk.2_Intron	NM_002156	NP_002147			chaperonin						'de novo' protein folding|activation of caspase activity|B cell cytokine production|B cell proliferation|chaperone-mediated protein complex assembly|interspecies interaction between organisms|isotype switching to IgG isotypes|MyD88-dependent toll-like receptor signaling pathway|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of interferon-alpha production|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of macrophage activation|positive regulation of T cell activation|positive regulation of T cell mediated immune response to tumor cell|protein maturation|protein refolding|protein stabilization|response to unfolded protein|T cell activation	cell surface|coated pit|coated vesicle|cytosol|early endosome|extracellular space|lipopolysaccharide receptor complex|mitochondrial inner membrane|mitochondrial matrix|stored secretory granule	ATP binding|ATPase activity|cell surface binding|chaperone binding|DNA replication origin binding|lipopolysaccharide binding|p53 binding|single-stranded DNA binding				0			Epithelial(96;0.225)															---	---	---	---
RFTN2	130132	broad.mit.edu	37	2	198511140	198511140	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198511140delT	uc002uuo.3	-							NM_144629	NP_653230			raftlin family member 2							plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	199989661	199989662	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199989661_199989662insA								PLCL1 (975055 upstream) : SATB2 (144562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200684250	200684253	+	Intron	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200684250_200684253delAAAA	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	200704623	200704624	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200704623_200704624insT	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																														---	---	---	---
AOX1	316	broad.mit.edu	37	2	201478784	201478785	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201478784_201478785insA	uc002uvx.2	+						AOX1_uc010zhf.1_Intron|AOX1_uc010fsu.2_Intron	NM_001159	NP_001150			aldehyde oxidase 1						inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)													---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201886732	201886733	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201886732_201886733insA	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_Intron	NM_173822	NP_776183			hypothetical protein LOC285172							intracellular				ovary(1)	1																		---	---	---	---
TRAK2	66008	broad.mit.edu	37	2	202306406	202306407	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202306406_202306407delTT	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron	NM_015049	NP_055864			trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0																		---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202360781	202360781	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202360781delA	uc002uye.2	-						ALS2CR11_uc002uyf.2_Intron|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202484550	202484550	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202484550delT	uc002uye.2	-						ALS2CR11_uc002uyf.2_5'Flank|ALS2CR11_uc010fti.2_5'Flank	NM_152525	NP_689738			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	203487592	203487593	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203487592_203487593insT								BMPR2 (55119 upstream) : FAM117B (12308 downstream)																																			---	---	---	---
ALS2CR8	79800	broad.mit.edu	37	2	203820371	203820372	+	Intron	INS	-	TA	TA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203820371_203820372insTA	uc002uzo.2	+						ALS2CR8_uc002uzn.2_Intron|ALS2CR8_uc002uzm.2_Intron|ALS2CR8_uc010zhy.1_Intron|ALS2CR8_uc010zhz.1_Intron|ALS2CR8_uc010ftu.1_Intron|ALS2CR8_uc010zia.1_Intron|ALS2CR8_uc010zib.1_Intron|ALS2CR8_uc010zic.1_Intron|ALS2CR8_uc002uzp.2_Intron	NM_001104586	NP_001098056			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)	2																		---	---	---	---
NBEAL1	65065	broad.mit.edu	37	2	204066451	204066451	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204066451delT	uc002uzt.3	+						NBEAL1_uc002uzs.3_Intron	NM_001114132	NP_001107604			neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204265919	204265919	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204265919delT	uc002vaa.2	+						ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_Intron|ABI2_uc010zik.1_Intron|ABI2_uc010zil.1_Intron|ABI2_uc010zim.1_Intron|ABI2_uc002vac.2_Intron|ABI2_uc010zin.1_Intron	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
RAPH1	65059	broad.mit.edu	37	2	204305757	204305757	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204305757delG	uc002vad.2	-	14	2381	c.2156delC	c.(2155-2157)CCAfs	p.P719fs		NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	719					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	205139531	205139532	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205139531_205139532delTT								ICOS (313235 upstream) : PARD3B (270984 downstream)																																			---	---	---	---
MDH1B	130752	broad.mit.edu	37	2	207619560	207619560	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207619560delA	uc002vbs.2	-						MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Intron|MDH1B_uc010fuj.2_Intron|MDH1B_uc002vbt.2_Intron	NM_001039845	NP_001034934			malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	207907027	207907027	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207907027delA								CPO (72829 upstream) : KLF7 (38502 downstream)																																			---	---	---	---
CREB1	1385	broad.mit.edu	37	2	208425770	208425770	+	Intron	DEL	A	-	-	rs35728983		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208425770delA	uc002vcc.2	+						CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_Intron|CREB1_uc010zja.1_Intron	NM_134442	NP_604391			cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								---	---	---	---
CRYGA	1418	broad.mit.edu	37	2	209028422	209028422	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209028422delT	uc002vcq.3	-							NM_014617	NP_055432			crystallin, gamma A						visual perception		structural constituent of eye lens				0				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210504485	210504485	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210504485delT	uc002vde.1	+						MAP2_uc002vdc.1_Intron|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212336714	212336714	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212336714delA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron	NM_005235	NP_005226			v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214174682	214174682	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214174682delA	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron|SPAG16_uc002veo.2_Intron|SPAG16_uc002vep.1_Intron|SPAG16_uc002ves.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	215504076	215504076	+	IGR	DEL	G	-	-	rs149203917		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215504076delG								VWC2L (63423 upstream) : BARD1 (89199 downstream)																																			---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215890372	215890372	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215890372delT	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099			ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216249704	216249704	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216249704delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron|FN1_uc010fvc.1_5'Flank|FN1_uc010fvd.1_5'Flank	NM_212482	NP_997647			fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	216323813	216323813	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216323813delG								FN1 (23022 upstream) : MREG (483502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	216357476	216357476	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216357476delC								FN1 (56685 upstream) : MREG (449839 downstream)																																			---	---	---	---
PECR	55825	broad.mit.edu	37	2	216939217	216939224	+	Intron	DEL	AAGGAAGG	-	-	rs72274918		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216939217_216939224delAAGGAAGG	uc002vft.2	-						PECR_uc010zjq.1_Intron|PECR_uc002vfu.1_Intron	NM_018441	NP_060911			peroxisomal trans-2-enoyl-CoA reductase						fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	217250668	217250669	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217250668_217250669delGT								MARCH4 (13918 upstream) : SMARCAL1 (26468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217638429	217638429	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217638429delA								IGFBP5 (78157 upstream) : TNP1 (85755 downstream)																																			---	---	---	---
USP37	57695	broad.mit.edu	37	2	219352921	219352921	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219352921delG	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986			ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)														---	---	---	---
SLC4A3	6508	broad.mit.edu	37	2	220504282	220504282	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220504282delG	uc002vmp.3	+	20	3371	c.3102delG	c.(3100-3102)CTGfs	p.L1034fs	SLC4A3_uc002vmo.3_Frame_Shift_Del_p.L1061fs|SLC4A3_uc010fwm.2_Frame_Shift_Del_p.L584fs	NM_005070	NP_005061	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member	1034	Helical; (Potential).|Membrane (anion exchange).				bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	5		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	222012928	222012928	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222012928delT								None (None upstream) : EPHA4 (269821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222964245	222964245	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222964245delT								EPHA4 (525323 upstream) : PAX3 (100362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	223433230	223433231	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223433230_223433231insA								SGPP2 (9614 upstream) : FARSB (2931 downstream)																																			---	---	---	---
FARSB	10056	broad.mit.edu	37	2	223505480	223505480	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223505480delA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678			phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)													---	---	---	---
SERPINE2	5270	broad.mit.edu	37	2	224891903	224891903	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224891903delC	uc002vnu.2	-						SERPINE2_uc002vnt.2_Intron|SERPINE2_uc010zlr.1_Intron|SERPINE2_uc002vnv.2_Intron	NM_006216	NP_006207			plasminogen activator inhibitor type 1, member 2						negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	225146429	225146431	+	IGR	DEL	AAA	-	-	rs34096129		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225146429_225146431delAAA								SERPINE2 (242393 upstream) : FAM124B (96985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	227533231	227533231	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227533231delA								KIAA1486 (937760 upstream) : IRS1 (62803 downstream)																																			---	---	---	---
RHBDD1	84236	broad.mit.edu	37	2	227859815	227859815	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227859815delA	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652			rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)														---	---	---	---
AGFG1	3267	broad.mit.edu	37	2	228388444	228388444	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228388444delT	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495			HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	229763282	229763282	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229763282delT								SPHKAP (716921 upstream) : PID1 (125408 downstream)																																			---	---	---	---
DNER	92737	broad.mit.edu	37	2	230423814	230423815	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230423814_230423815insG	uc002vpv.2	-						DNER_uc010zly.1_Intron	NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
DNER	92737	broad.mit.edu	37	2	230580209	230580209	+	5'Flank	DEL	G	-	-	rs113855041		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230580209delG	uc002vpv.2	-							NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230652431	230652431	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230652431delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron	NM_004238	NP_004229			thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
FBXO36	130888	broad.mit.edu	37	2	230798122	230798123	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230798122_230798123delAC	uc002vqa.2	+						FBXO36_uc002vpz.2_Intron|FBXO36_uc002vqb.2_Intron|FBXO36_uc010fxi.1_Intron|FBXO36_uc002vqc.2_Intron	NM_174899	NP_777559			F-box protein 36											ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
FBXO36	130888	broad.mit.edu	37	2	230863841	230863844	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230863841_230863844delTTTT	uc002vqa.2	+						FBXO36_uc002vqb.2_Intron|FBXO36_uc010fxi.1_Intron|FBXO36_uc002vqc.2_Intron	NM_174899	NP_777559			F-box protein 36											ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	230949286	230949286	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230949286delA								FBXO36 (1270 upstream) : SP110 (84359 downstream)																																			---	---	---	---
SP110	3431	broad.mit.edu	37	2	231065504	231065504	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231065504delA	uc002vqh.3	-						SP110_uc002vqg.3_Intron|SP110_uc002vqi.3_Intron|SP110_uc010fxk.2_Intron|SP110_uc010fxj.2_Intron	NM_004509	NP_004500			SP110 nuclear body protein isoform a						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)														---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232156528	232156528	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232156528delA	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron|ARMC9_uc002vrr.1_Intron	NM_025139	NP_079415			armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232884268	232884270	+	Intron	DEL	TTT	-	-	rs11301026		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232884268_232884270delTTT	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_Intron	NM_152383	NP_689596			DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233627732	233627732	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233627732delA	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_5'Flank	NM_015575	NP_056390			GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233635585	233635585	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233635585delT	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtn.2_Intron|KCNJ13_uc002vto.2_Intron|KCNJ13_uc002vtp.2_Intron	NM_015575	NP_056390			GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233747763	233747764	+	Intron	DEL	AC	-	-	rs66854547		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233747763_233747764delAC	uc002vts.2	-						NGEF_uc010zmm.1_Intron|NGEF_uc010fyg.1_Intron	NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233784152	233784152	+	Intron	DEL	T	-	-	rs77154555		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233784152delT	uc002vts.2	-						NGEF_uc010fyg.1_Intron|NGEF_uc002vtt.2_Intron	NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	233939333	233939333	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233939333delT	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
HJURP	55355	broad.mit.edu	37	2	234754664	234754665	+	Intron	INS	-	AC	AC	rs147320613	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234754664_234754665insAC	uc002vvg.2	-						HJURP_uc010znd.1_Intron|HJURP_uc010zne.1_Intron	NM_018410	NP_060880			Holliday junction recognition protein						cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)														---	---	---	---
SH3BP4	23677	broad.mit.edu	37	2	235931166	235931166	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235931166delA	uc002vvp.2	+						SH3BP4_uc010fym.2_Intron|SH3BP4_uc002vvq.2_Intron	NM_014521	NP_055336			SH3-domain binding protein 4						endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			skin(3)|ovary(1)	4		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)														---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236773374	236773374	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236773374delA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236776180	236776181	+	Intron	INS	-	GTGTGT	GTGTGT	rs71400787		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236776180_236776181insGTGTGT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
MLPH	79083	broad.mit.edu	37	2	238418403	238418403	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238418403delC	uc002vwt.2	+						MLPH_uc002vws.2_Intron|MLPH_uc010fyt.1_Intron|MLPH_uc002vwu.2_Intron|MLPH_uc002vwv.2_Intron|MLPH_uc002vww.2_5'Flank	NM_024101	NP_077006			melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)														---	---	---	---
RAB17	64284	broad.mit.edu	37	2	238497864	238497864	+	Intron	DEL	A	-	-	rs78861711		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238497864delA	uc002vwz.1	-						RAB17_uc002vxa.1_Intron|RAB17_uc002vxb.1_Intron	NM_022449	NP_071894			RAB17, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|protein binding				0		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239186719	239186720	+	Intron	INS	-	TCTCTCTG	TCTCTCTG	rs149341285	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239186719_239186720insTCTCTCTG	uc002vyc.2	-						PER2_uc010znv.1_Intron|PER2_uc010znw.1_Intron|PER2_uc010fyx.1_5'Flank	NM_022817	NP_073728			period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
TRAF3IP1	26146	broad.mit.edu	37	2	239262394	239262394	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239262394delT	uc002vye.2	+						TRAF3IP1_uc002vyf.2_Intron	NM_015650	NP_056465			TNF receptor-associated factor 3 interacting							cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	239326245	239326245	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239326245delT								TRAF3IP1 (16706 upstream) : ASB1 (9381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241248687	241248688	+	IGR	DEL	TA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241248687_241248688delTA								OTOS (168614 upstream) : GPC1 (126427 downstream)																																			---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241473136	241473137	+	Intron	DEL	AC	-	-	rs148729272		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241473136_241473137delAC	uc002vyz.1	-						ANKMY1_uc002vza.1_Intron|ANKMY1_uc010fzd.1_Intron|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron|ANKMY1_uc010fze.1_Intron|ANKMY1_uc002vze.2_Intron	NM_016552	NP_057636			ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	241570957	241570957	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241570957delG								GPR35 (282 upstream) : AQP12B (44879 downstream)																																			---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241683337	241683337	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241683337delC	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312			axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241724608	241724608	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241724608delG	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312			axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242229373	242229374	+	Intron	DEL	AA	-	-	rs112233392		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242229373_242229374delAA	uc002wba.2	-							NM_005336	NP_005327			high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
STK25	10494	broad.mit.edu	37	2	242440350	242440351	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242440350_242440351delCT	uc002wbm.2	-						STK25_uc002wbk.2_5'Flank|STK25_uc002wbl.2_5'Flank|STK25_uc002wbn.2_Intron|STK25_uc002wbo.2_Intron|STK25_uc010zos.1_Intron|STK25_uc010zot.1_Intron|STK25_uc002wbp.2_Intron|STK25_uc010fzo.2_Intron|STK25_uc010zou.1_Intron|STK25_uc010zov.1_Intron|STK25_uc010zow.1_Intron	NM_006374	NP_006365			serine/threonine kinase 25						response to oxidative stress|signal transduction	Golgi apparatus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	1751943	1751944	+	IGR	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1751943_1751944delAT								CNTN6 (306666 upstream) : CNTN4 (388606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	1877419	1877420	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1877419_1877420delTT								CNTN6 (432142 upstream) : CNTN4 (263130 downstream)																																			---	---	---	---
IL5RA	3568	broad.mit.edu	37	3	3117289	3117289	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3117289delT	uc011ask.1	-						IL5RA_uc010hbq.2_Intron|IL5RA_uc010hbr.2_Intron|IL5RA_uc010hbs.2_Intron|IL5RA_uc011asl.1_Intron|IL5RA_uc010hbp.2_Intron	NM_000564	NP_000555			interleukin 5 receptor, alpha isoform 1						cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)														---	---	---	---
IL5RA	3568	broad.mit.edu	37	3	3154475	3154475	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3154475delT	uc011ask.1	-						IL5RA_uc010hbs.2_5'Flank|IL5RA_uc011asl.1_5'Flank|IL5RA_uc011asm.1_5'Flank|IL5RA_uc010hbt.2_5'Flank|IL5RA_uc011asn.1_5'Flank|IL5RA_uc010hbu.2_5'Flank	NM_000564	NP_000555			interleukin 5 receptor, alpha isoform 1						cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4259795	4259795	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4259795delA	uc003bps.1	-							NM_182760				sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4533459	4533460	+	5'Flank	DEL	AA	-	-	rs141464593		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4533459_4533460delAA	uc003bqa.2	+						ITPR1_uc010hbz.2_5'Flank|ITPR1_uc010hca.1_5'Flank|ITPR1_uc011asu.1_5'Flank	NM_001099952	NP_001093422			inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5439543	5439543	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5439543delT								EDEM1 (177894 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6513514	6513517	+	IGR	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6513514_6513517delAAAA								None (None upstream) : GRM7 (389285 downstream)																																			---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7340488	7340488	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7340488delT	uc003bqm.2	+	3	1128	c.854delT	c.(853-855)ATTfs	p.I285fs	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Frame_Shift_Del_p.I285fs|GRM7_uc003bql.2_Frame_Shift_Del_p.I285fs|GRM7_uc003bqn.1_5'UTR	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	285	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	8257855	8257856	+	Intron	DEL	GT	-	-	rs143365860	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8257855_8257856delGT	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	8447588	8447588	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8447588delA	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	8642074	8642076	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8642074_8642076delTTT								LOH3CR2A (26494 upstream) : C3orf32 (19193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8867445	8867446	+	IGR	INS	-	A	A	rs111297516		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8867445_8867446insA								OXTR (56145 upstream) : RAD18 (54115 downstream)																																			---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9077296	9077297	+	Intron	INS	-	GAAA	GAAA	rs138889566	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9077296_9077297insGAAA	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brj.1_3'UTR	NM_014850	NP_055665			SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9714262	9714262	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9714262delT	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993			jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
OGG1	4968	broad.mit.edu	37	3	9808174	9808174	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9808174delA	uc003bsm.2	+	7					OGG1_uc003bsk.2_3'UTR|OGG1_uc003bsl.2_3'UTR|OGG1_uc003bsn.2_3'UTR|OGG1_uc003bso.2_3'UTR|CAMK1_uc003bst.2_Intron|CAMK1_uc003bsu.2_Intron	NM_016821	NP_058214			8-oxoguanine DNA-glycosylase 1 isoform 2a						depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)												BER_DNA_glycosylases					---	---	---	---
CIDEC	63924	broad.mit.edu	37	3	9915308	9915308	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9915308delA	uc003btq.2	-						CIDEC_uc003bto.2_Intron|CIDEC_uc010hcp.2_Intron|CIDEC_uc003btp.2_Intron|CIDEC_uc003btr.2_Intron|CIDEC_uc003bts.2_Intron	NM_022094	NP_071377			cell death-inducing DFFA-like effector c						apoptosis|induction of apoptosis	cytosol|focal adhesion|nucleus				central_nervous_system(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10128180	10128180	+	Intron	DEL	T	-	-	rs80125759		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10128180delT	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron|C3orf24_uc003buz.2_Intron	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	3	10172627	10172628	+	IGR	INS	-	A	A	rs113053441		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10172627_10172628insA								C3orf10 (3754 upstream) : VHL (10691 downstream)																																			---	---	---	---
LOC285370	285370	broad.mit.edu	37	3	10804206	10804206	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10804206delT	uc003bvx.1	-							NR_027102				Homo sapiens cDNA FLJ36079 fis, clone TESTI2019860.												0																		---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10919312	10919313	+	Intron	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10919312_10919313delAT	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10960518	10960518	+	Intron	DEL	T	-	-	rs34883736		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10960518delT	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10971111	10971111	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10971111delG	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11383767	11383767	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11383767delG	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11512962	11512963	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11512962_11512963insA	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	11920306	11920306	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11920306delT								C3orf31 (31954 upstream) : SYN2 (125556 downstream)																																			---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12365260	12365260	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12365260delA	uc003bwr.2	+						PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron|PPARG_uc003bwq.1_Intron|PPARG_uc010hdz.1_Intron|PPARG_uc003bwt.1_Intron	NM_138712	NP_619726			peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12450918	12450918	+	Intron	DEL	A	-	-	rs73027225		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12450918delA	uc003bwx.2	+						PPARG_uc003bwr.2_Intron|PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron|PPARG_uc010hea.1_Intron	NM_015869	NP_056953			peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						---	---	---	---
Unknown	0	broad.mit.edu	37	3	12487123	12487124	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12487123_12487124delCT								PPARG (11269 upstream) : TSEN2 (38807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	12753203	12753203	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12753203delT								RAF1 (47503 upstream) : TMEM40 (22189 downstream)																																			---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	13112667	13112667	+	Intron	DEL	G	-	-	rs67621733		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13112667delG	uc011auw.1	-							NM_001134382	NP_001127854			IQ motif and Sec7 domain 1 isoform a						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	13124281	13124281	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13124281delC								IQSEC1 (9664 upstream) : NUP210 (233456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13297118	13297118	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13297118delT								IQSEC1 (182501 upstream) : NUP210 (60619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13308082	13308083	+	IGR	DEL	TT	-	-	rs113470359		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13308082_13308083delTT								IQSEC1 (193465 upstream) : NUP210 (49654 downstream)																																			---	---	---	---
LOC285375	285375	broad.mit.edu	37	3	13724763	13724764	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13724763_13724764delCA	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0																		---	---	---	---
LOC285375	285375	broad.mit.edu	37	3	13741681	13741682	+	Intron	INS	-	A	A	rs78605044		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13741681_13741682insA	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	13846266	13846267	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13846266_13846267delTG								LOC285375 (58134 upstream) : WNT7A (13815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	14592535	14592535	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14592535delG								GRIP2 (8947 upstream) : C3orf19 (100718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	14828421	14828421	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14828421delT								C3orf20 (13881 upstream) : FGD5 (32048 downstream)																																			---	---	---	---
SH3BP5	9467	broad.mit.edu	37	3	15385720	15385720	+	5'Flank	DEL	A	-	-	rs36069993		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15385720delA	uc003bzr.1	-							NM_001018009	NP_001018009			SH3-domain binding protein 5 (BTK-associated)						intracellular signal transduction	mitochondrion	protein kinase inhibitor activity|SH3 domain binding				0																		---	---	---	---
HACL1	26061	broad.mit.edu	37	3	15601609	15601609	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15601609delT	uc011avr.1	-											Homo sapiens acetylcholinesterase collagen-like tail subunit (COLQ) mRNA, complete cds.						fatty acid alpha-oxidation	peroxisomal matrix	carbon-carbon lyase activity|identical protein binding|magnesium ion binding|thiamine pyrophosphate binding				0																		---	---	---	---
HACL1	26061	broad.mit.edu	37	3	15611498	15611498	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15611498delA	uc003caf.2	-						HACL1_uc011avr.1_Intron|HACL1_uc011avs.1_Intron|HACL1_uc011avt.1_Intron|HACL1_uc003cag.2_Intron|HACL1_uc011avu.1_Intron|HACL1_uc010hep.2_Intron	NM_012260	NP_036392			2-hydroxyphytanoyl-CoA lyase						fatty acid alpha-oxidation	peroxisomal matrix	carbon-carbon lyase activity|identical protein binding|magnesium ion binding|thiamine pyrophosphate binding				0																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15752582	15752582	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15752582delT	uc003caj.1	-						ANKRD28_uc003cai.1_Intron|ANKRD28_uc011avz.1_Intron|ANKRD28_uc003cak.1_Intron|ANKRD28_uc011awa.1_Intron|ANKRD28_uc003cal.1_Intron|ANKRD28_uc003cam.2_Intron	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16179996	16179996	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16179996delT	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17171836	17171836	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17171836delG								PLCL2 (39739 upstream) : TBC1D5 (26819 downstream)																																			---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17416087	17416087	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17416087delA	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17549546	17549546	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17549546delA	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17923755	17923755	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17923755delT								TBC1D5 (139515 upstream) : SATB1 (465511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18269386	18269386	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18269386delT	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	19007369	19007369	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19007369delA								SATB1 (527117 upstream) : KCNH8 (182648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20539246	20539246	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20539246delA								SGOL1 (311563 upstream) : VENTXP7 (907972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20970808	20970809	+	IGR	INS	-	T	T	rs143092806	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20970808_20970809insT								SGOL1 (743125 upstream) : VENTXP7 (476409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21031291	21031291	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21031291delT								SGOL1 (803608 upstream) : VENTXP7 (415927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21394295	21394295	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21394295delA								None (None upstream) : VENTXP7 (52923 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21569756	21569756	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21569756delA	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973			zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	22968049	22968049	+	IGR	DEL	A	-	-	rs36063410		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22968049delA								ZNF385D (553926 upstream) : UBE2E2 (276604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23025483	23025483	+	IGR	DEL	A	-	-	rs72017075		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23025483delA								ZNF385D (611360 upstream) : UBE2E2 (219170 downstream)																																			---	---	---	---
UBE2E2	7325	broad.mit.edu	37	3	23424965	23424967	+	Intron	DEL	TTT	-	-	rs34970044		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23424965_23424967delTTT	uc003ccg.2	+						UBE2E2_uc010hfc.2_Intron	NM_152653	NP_689866			ubiquitin-conjugating enzyme E2E 2						ISG15-protein conjugation|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination	nucleolus	ATP binding|ISG15 ligase activity|ubiquitin-protein ligase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	24047013	24047013	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24047013delT								NR1D2 (24904 upstream) : LOC152024 (90767 downstream)																																			---	---	---	---
THRB	7068	broad.mit.edu	37	3	24219980	24219981	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24219980_24219981insA	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
RARB	5915	broad.mit.edu	37	3	25484913	25484913	+	Intron	DEL	T	-	-	rs35044701		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25484913delT	uc011awl.1	+						RARB_uc003cdi.1_Intron|RARB_uc003cdh.2_Intron	NM_016152	NP_057236			retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)													---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25761138	25761138	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25761138delA	uc003cdl.2	-						NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_Intron	NM_018297	NP_060767			N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25792763	25792763	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25792763delA	uc003cdl.2	-						NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_Intron	NM_018297	NP_060767			N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25820210	25820210	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25820210delA	uc003cdl.2	-						NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_5'Flank	NM_018297	NP_060767			N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	26072779	26072779	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26072779delA								OXSM (236755 upstream) : LRRC3B (591521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26303459	26303459	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26303459delA								OXSM (467435 upstream) : LRRC3B (360841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27097523	27097524	+	IGR	INS	-	T	T	rs143431541	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27097523_27097524insT								LRRC3B (345260 upstream) : NEK10 (54871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27558516	27558516	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27558516delA								SLC4A7 (32678 upstream) : EOMES (199372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27658675	27658675	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27658675delT								SLC4A7 (132837 upstream) : EOMES (99213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28859893	28859893	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28859893delT								ZCWPW2 (293263 upstream) : RBMS3 (463050 downstream)																																			---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29519178	29519179	+	Intron	DEL	AA	-	-	rs72277424		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29519178_29519179delAA	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29628772	29628773	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29628772_29628773delAG	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
Unknown	0	broad.mit.edu	37	3	30557945	30557946	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30557945_30557946delAA								RBMS3 (511326 upstream) : TGFBR2 (90048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30642893	30642893	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30642893delT								RBMS3 (596274 upstream) : TGFBR2 (5101 downstream)																																			---	---	---	---
TGFBR2	7048	broad.mit.edu	37	3	30665635	30665635	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30665635delA	uc003ceo.2	+						TGFBR2_uc003cen.2_Intron	NM_003242	NP_003233			transforming growth factor, beta receptor II						activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis	caveola|external side of plasma membrane	ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding			pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1)	26																		---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30817064	30817065	+	Intron	INS	-	T	T	rs142507733	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30817064_30817065insT	uc003cep.2	-							NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30886008	30886008	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30886008delA	uc003cep.2	-						GADL1_uc003ceq.1_Intron	NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31913356	31913357	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31913356_31913357delAC	uc003cev.2	-						OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254			oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	32077054	32077055	+	IGR	INS	-	A	A	rs35533294		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32077054_32077055insA								ZNF860 (43934 upstream) : GPD1L (71089 downstream)																																			---	---	---	---
GPD1L	23171	broad.mit.edu	37	3	32165071	32165072	+	Intron	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32165071_32165072insC	uc003cew.2	+							NM_015141	NP_055956			glycerol-3-phosphate dehydrogenase 1-like						glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0																		---	---	---	---
GPD1L	23171	broad.mit.edu	37	3	32196248	32196249	+	Intron	DEL	TT	-	-	rs35621451		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32196248_32196249delTT	uc003cew.2	+							NM_015141	NP_055956			glycerol-3-phosphate dehydrogenase 1-like						glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32416347	32416347	+	IGR	DEL	C	-	-	rs4038470		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32416347delC								CMTM8 (4536 upstream) : CMTM7 (16816 downstream)																																			---	---	---	---
TRIM71	131405	broad.mit.edu	37	3	32915571	32915571	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32915571delG	uc003cff.2	+							NM_001039111	NP_001034200			tripartite motif-containing 71						multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
GLB1	2720	broad.mit.edu	37	3	33093631	33093631	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33093631delC	uc003cfi.1	-						GLB1_uc003cfh.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron	NM_000404	NP_000395			galactosidase, beta 1 isoform a preproprotein						carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)																---	---	---	---
SUSD5	26032	broad.mit.edu	37	3	33193912	33193913	+	3'UTR	DEL	AA	-	-	rs67768894		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33193912_33193913delAA	uc003cfo.1	-	5						NM_015551	NP_056366			sushi domain containing 5 precursor						cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33317558	33317559	+	5'Flank	DEL	TT	-	-	rs34582904		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33317558_33317559delTT	uc003cfp.2	+						FBXL2_uc011axm.1_5'Flank|FBXL2_uc011axn.1_5'Flank|FBXL2_uc011axo.1_5'Flank|FBXL2_uc011axp.1_5'Flank|FBXL2_uc011axq.1_5'Flank|FBXL2_uc011axr.1_5'Flank	NM_012157	NP_036289			F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1																		---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33426822	33426822	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33426822delG	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289			F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	33509270	33509270	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33509270delA								UBP1 (27373 upstream) : CLASP2 (28471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34087256	34087257	+	IGR	INS	-	T	T	rs6550246	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34087256_34087257insT								PDCD6IP (176062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34289938	34289939	+	IGR	DEL	GG	-	-	rs113178067		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34289938_34289939delGG								PDCD6IP (378744 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34313402	34313402	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34313402delT								PDCD6IP (402208 upstream) : None (None downstream)																																			---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35785764	35785765	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35785764_35785765insT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_Intron|ARPP21_uc003cgg.2_Intron|uc011axz.1_5'Flank|MIR128-2_hsa-mir-128-2|MI0000727_5'Flank	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	36065221	36065221	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36065221delT								ARPP21 (229234 upstream) : STAC (356876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36147057	36147058	+	IGR	INS	-	A	A	rs143520329	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36147057_36147058insA								ARPP21 (311070 upstream) : STAC (275039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36810381	36810381	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36810381delT								DCLK3 (29029 upstream) : TRANK1 (57930 downstream)																																			---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37193546	37193547	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37193546_37193547insA	uc003cgp.2	-						LRRFIP2_uc011ayf.1_Intron|LRRFIP2_uc003cgr.2_Intron|LRRFIP2_uc003cgs.3_Intron|LRRFIP2_uc003cgt.3_Intron	NM_006309	NP_006300			leucine rich repeat (in FLII) interacting						Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37337538	37337538	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37337538delT	uc003cgv.2	+						GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Intron	NM_002078	NP_002069			golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
C3orf35	339883	broad.mit.edu	37	3	37432914	37432914	+	Intron	DEL	A	-	-	rs4678960		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37432914delA	uc003cgy.1	+						C3orf35_uc003cgz.1_Intron					Homo sapiens mRNA for AP20 region protein (APRG1 gene), isoform A.							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37547431	37547431	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37547431delT	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
CTDSPL	10217	broad.mit.edu	37	3	38017151	38017151	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38017151delG	uc003chg.2	+						CTDSPL_uc003chh.2_Intron|CTDSPL_uc003chi.2_Intron	NM_001008392	NP_001008393			small CTD phosphatase 3 isoform 1							nucleus	metal ion binding|phosphoprotein phosphatase activity				0		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)														---	---	---	---
CTDSPL	10217	broad.mit.edu	37	3	38021249	38021250	+	Intron	INS	-	CA	CA	rs139766577	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38021249_38021250insCA	uc003chg.2	+						CTDSPL_uc003chh.2_Intron|CTDSPL_uc003chi.2_Intron	NM_001008392	NP_001008393			small CTD phosphatase 3 isoform 1							nucleus	metal ion binding|phosphoprotein phosphatase activity				0		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	38075644	38075646	+	IGR	DEL	AAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38075644_38075646delAAC								PLCD1 (4490 upstream) : DLEC1 (5050 downstream)																																			---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38633139	38633140	+	Intron	DEL	AA	-	-	rs67153133		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38633139_38633140delAA	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhj.1_Intron	NM_198056	NP_932173			voltage-gated sodium channel type V alpha						blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	39203351	39203351	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39203351delA								CSRNP1 (7298 upstream) : XIRP1 (21356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39392291	39392291	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39392291delA								CCR8 (17120 upstream) : SLC25A38 (32524 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39486067	39486068	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39486067_39486068insT								RPSA (32037 upstream) : MOBP (23002 downstream)																																			---	---	---	---
MOBP	4336	broad.mit.edu	37	3	39527434	39527434	+	Intron	DEL	A	-	-	rs112020703		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39527434delA	uc010hht.2	+						MOBP_uc003cju.2_Intron|MOBP_uc003cjv.2_Intron|MOBP_uc003cjw.2_Intron	NM_182935	NP_891980			myelin-associated oligodendrocyte basic protein						nervous system development	nucleolus|perinuclear region of cytoplasm|soluble fraction				ovary(1)|central_nervous_system(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.082)|Kidney(284;0.0998)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	39738771	39738771	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39738771delA								MOBP (170916 upstream) : MYRIP (112532 downstream)																																			---	---	---	---
RPL14	9045	broad.mit.edu	37	3	40502686	40502687	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40502686_40502687delAA	uc003ckg.2	+						RPL14_uc003ckh.2_Intron|RPL14_uc003cki.2_Intron	NM_003973	NP_003964			ribosomal protein L14						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40740450	40740450	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40740450delA								ZNF621 (159407 upstream) : CTNNB1 (495951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40803346	40803346	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40803346delA								ZNF621 (222303 upstream) : CTNNB1 (433055 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41451440	41451440	+	Intron	DEL	A	-	-	rs36107176		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41451440delA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41795748	41795749	+	Intron	INS	-	A	A	rs58341418	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41795748_41795749insA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41973526	41973526	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41973526delA	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42202061	42202061	+	Intron	DEL	G	-	-	rs59260540		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									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																		---	---	---	---
SEC22C	9117	broad.mit.edu	37	3	42602873	42602874	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42602873_42602874insT	uc003clj.2	-						SEC22C_uc003clh.2_Intron|SEC22C_uc011azo.1_Intron|SEC22C_uc010hic.2_Intron|SEC22C_uc003cli.2_Intron	NM_032970	NP_116752			SEC22 vesicle trafficking protein homolog C						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.222)														---	---	---	---
NKTR	4820	broad.mit.edu	37	3	42678146	42678146	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42678146delA	uc003clo.2	+						NKTR_uc003clm.1_Intron|NKTR_uc003clp.2_Intron|NKTR_uc011azp.1_Intron|NKTR_uc003clq.1_Intron|NKTR_uc003clr.1_Intron|NKTR_uc003cls.2_Intron	NM_005385	NP_005376			natural killer-tumor recognition sequence						protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)														---	---	---	---
HHATL	57467	broad.mit.edu	37	3	42740981	42740981	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42740981delT	uc003clw.2	-						HHATL_uc003clx.2_Intron	NM_020707	NP_065758			hedgehog acyltransferase-like						negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)														---	---	---	---
HHATL	57467	broad.mit.edu	37	3	42741572	42741573	+	Intron	INS	-	TG	TG	rs138596367	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42741572_42741573insTG	uc003clw.2	-						HHATL_uc003clx.2_Intron	NM_020707	NP_065758			hedgehog acyltransferase-like						negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)														---	---	---	---
CCBP2	1238	broad.mit.edu	37	3	42892773	42892773	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42892773delT	uc003cme.2	+						CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmf.2_Intron|CCBP2_uc003cmg.2_Intron	NM_001296	NP_001287			chemokine binding protein 2						chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity			lung(4)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.241)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	43207349	43207349	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43207349delA								C3orf39 (59784 upstream) : SNRK (120655 downstream)																																			---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43605544	43605545	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43605544_43605545delTT	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545			transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2																		---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43647213	43647213	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43647213delT	uc003cmv.2	-	2	303	c.132delA	c.(130-132)AAAfs	p.K44fs	ANO10_uc011azs.1_Frame_Shift_Del_p.K44fs|ANO10_uc003cmw.2_Frame_Shift_Del_p.K44fs|ANO10_uc010hil.2_Frame_Shift_Del_p.K44fs|ANO10_uc011azt.1_Frame_Shift_Del_p.K44fs	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K	44	Cytoplasmic (Potential).				cell death	chloride channel complex	chloride channel activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	43835277	43835277	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43835277delT								ABHD5 (71061 upstream) : MIR138-1 (320427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	43999905	43999905	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43999905delT								ABHD5 (235689 upstream) : MIR138-1 (155799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	44001386	44001387	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44001386_44001387insA								ABHD5 (237170 upstream) : MIR138-1 (154317 downstream)																																			---	---	---	---
C3orf23	285343	broad.mit.edu	37	3	44399693	44399694	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44399693_44399694insT	uc010him.2	+						C3orf23_uc003cnd.3_Intron|C3orf23_uc003cne.3_Intron|C3orf23_uc003cnb.3_Intron|C3orf23_uc003cnc.3_Intron	NM_173826	NP_776187			hypothetical protein LOC285343 isoform 1							mitochondrion				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44816592	44816593	+	Intron	INS	-	A	A	rs35117351		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44816592_44816593insA	uc003cnx.3	+						KIF15_uc010hiq.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
CDCP1	64866	broad.mit.edu	37	3	45148706	45148706	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45148706delT	uc003com.2	-							NM_022842	NP_073753			CUB domain-containing protein 1 isoform 1							extracellular region|integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45442314	45442314	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45442314delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
SACM1L	22908	broad.mit.edu	37	3	45765062	45765062	+	Intron	DEL	A	-	-	rs34076210		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45765062delA	uc003cos.2	+						SACM1L_uc011bag.1_Intron|SACM1L_uc011bah.1_Intron	NM_014016	NP_054735			suppressor of actin 1							Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)														---	---	---	---
SACM1L	22908	broad.mit.edu	37	3	45771336	45771336	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45771336delT	uc003cos.2	+						SACM1L_uc011bag.1_Intron|SACM1L_uc011bah.1_Intron	NM_014016	NP_054735			suppressor of actin 1							Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)														---	---	---	---
CCR9	10803	broad.mit.edu	37	3	45934650	45934650	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45934650delT	uc003coz.1	+						LZTFL1_uc003coy.1_Intron|LZTFL1_uc011bak.1_Intron|CCR9_uc010hiv.1_Intron|CCR9_uc003cpa.1_Intron	NM_031200	NP_112477			chemokine (C-C motif) receptor 9 isoform A						cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)														---	---	---	---
CCRL2	9034	broad.mit.edu	37	3	46447370	46447370	+	5'Flank	DEL	T	-	-	rs72366463		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46447370delT	uc003cpp.3	+						CCRL2_uc010hjg.2_5'Flank|CCRL2_uc010hjf.2_5'Flank	NM_003965	NP_003956			chemokine (C-C motif) receptor-like 2 isoform 1						chemotaxis|inflammatory response	integral to plasma membrane	CCR chemokine receptor binding|chemokine receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)														---	---	---	---
LRRC2	79442	broad.mit.edu	37	3	46618758	46618759	+	Intron	INS	-	CA	CA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46618758_46618759insCA	uc003cpu.3	-						TDGF1_uc003cpv.2_5'Flank	NM_024750	NP_079026			leucine rich repeat containing 2											ovary(1)	1		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46837724	46837724	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46837724delT	uc011ban.1	-						uc011bao.1_Intron					Homo sapiens cDNA FLJ35279 fis, clone PROST2006766, highly similar to Testis-specific protease-like protein 50 precursor.																														---	---	---	---
CCDC12	151903	broad.mit.edu	37	3	46980341	46980342	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46980341_46980342insA	uc011baq.1	-						CCDC12_uc003cqo.2_Intron|CCDC12_uc011bar.1_Intron	NM_144716	NP_653317			coiled-coil domain containing 12												0		Prostate(884;0.0143)|Ovarian(412;0.0448)|Acute lymphoblastic leukemia(5;0.143)		OV - Ovarian serous cystadenocarcinoma(275;2.2e-56)|BRCA - Breast invasive adenocarcinoma(193;0.00136)|KIRC - Kidney renal clear cell carcinoma(197;0.00703)|Kidney(197;0.00809)														---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47292002	47292002	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47292002delT	uc010hjp.2	-						KIF9_uc003cqx.2_Intron|KIF9_uc003cqy.2_Intron|KIF9_uc011bat.1_Intron|KIF9_uc011bau.1_Intron	NM_001134878	NP_001128350			kinesin family member 9 isoform 2						blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)														---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47307211	47307211	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47307211delC	uc010hjp.2	-						KIF9_uc003cqx.2_Intron|KIF9_uc003cqy.2_Intron|KIF9_uc011bat.1_Intron|KIF9_uc011bau.1_Intron	NM_001134878	NP_001128350			kinesin family member 9 isoform 2						blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)														---	---	---	---
PTPN23	25930	broad.mit.edu	37	3	47444853	47444853	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47444853delT	uc003crf.1	+						PTPN23_uc011baw.1_Intron|PTPN23_uc011bax.1_Intron|PTPN23_uc011bay.1_Intron	NM_015466	NP_056281			protein tyrosine phosphatase, non-receptor type						cilium morphogenesis	cilium|cytoplasmic membrane-bounded vesicle|microtubule basal body	protein tyrosine phosphatase activity			breast(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
MAP4	4134	broad.mit.edu	37	3	47899204	47899205	+	Intron	DEL	TT	-	-	rs112833712		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47899204_47899205delTT	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc003crw.2_Intron|MAP4_uc003crx.2_Intron|MAP4_uc011bbe.1_Intron|MAP4_uc003cry.2_Intron|MAP4_uc003csa.3_Intron|MAP4_uc003crz.3_Intron	NM_002375	NP_002366			microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)														---	---	---	---
MAP4	4134	broad.mit.edu	37	3	47960427	47960427	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47960427delT	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_Intron	NM_002375	NP_002366			microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48177735	48177735	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48177735delT								MAP4 (46966 upstream) : CDC25A (20933 downstream)																																			---	---	---	---
CDC25A	993	broad.mit.edu	37	3	48231017	48231017	+	5'Flank	DEL	A	-	-	rs72454550		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48231017delA	uc003csh.1	-						CDC25A_uc003csi.1_5'Flank	NM_001789	NP_001780			cell division cycle 25A isoform a						cell cycle checkpoint|cell division|cell proliferation|cellular response to UV|DNA replication|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|kidney(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)														---	---	---	---
ATRIP	84126	broad.mit.edu	37	3	48491177	48491182	+	Intron	DEL	AAAAAA	-	-	rs35574872		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48491177_48491182delAAAAAA	uc003ctf.1	+						ATRIP_uc011bbj.1_Intron|ATRIP_uc003ctg.1_Intron	NM_130384	NP_569055			ATR interacting protein isoform 1						DNA damage checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding|protein serine/threonine kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)									Other_conserved_DNA_damage_response_genes					---	---	---	---
NCKIPSD	51517	broad.mit.edu	37	3	48721452	48721453	+	Intron	INS	-	AG	AG	rs9818173		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48721452_48721453insAG	uc003cun.2	-						NCKIPSD_uc003cum.2_Intron|NCKIPSD_uc010hkh.1_Intron	NM_016453	NP_057537			NCK interacting protein with SH3 domain isoform						cytoskeleton organization|NLS-bearing substrate import into nucleus|signal transduction	intermediate filament|nucleus	cytoskeletal protein binding|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
PRKAR2A	5576	broad.mit.edu	37	3	48802068	48802068	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48802068delT	uc010hki.1	-						PRKAR2A_uc003cux.1_Intron|PRKAR2A_uc003cuy.1_Intron	NM_004157	NP_004148			cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|membrane fraction	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)														---	---	---	---
PRKAR2A	5576	broad.mit.edu	37	3	48827291	48827291	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48827291delG	uc010hki.1	-						PRKAR2A_uc003cux.1_Intron|PRKAR2A_uc003cuy.1_Intron	NM_004157	NP_004148			cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|membrane fraction	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49350962	49350962	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49350962delA	uc003cwq.2	-						USP4_uc003cwo.2_5'Flank|USP4_uc003cwp.2_5'Flank|USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
BSN	8927	broad.mit.edu	37	3	49646702	49646703	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49646702_49646703delTT	uc003cxe.3	+							NM_003458	NP_003449			bassoon protein						synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)														---	---	---	---
RBM5	10181	broad.mit.edu	37	3	50133758	50133760	+	Intron	DEL	AAA	-	-	rs10711228		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50133758_50133760delAAA	uc003cyg.2	+						RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron|RBM5_uc003cyf.2_Intron|RBM5_uc011bdj.1_Intron|RBM5_uc011bdk.1_Intron	NM_005778	NP_005769			RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
RBM5	10181	broad.mit.edu	37	3	50138137	50138137	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50138137delT	uc003cyg.2	+						RBM5_uc003cyf.2_3'UTR|RBM5_uc011bdj.1_Intron|RBM5_uc011bdk.1_Intron	NM_005778	NP_005769			RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
RBM5	10181	broad.mit.edu	37	3	50154390	50154390	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50154390delA	uc003cyg.2	+						RBM5_uc011bdj.1_Intron|RBM5_uc011bdk.1_Intron|RBM5_uc003cyh.2_Intron|uc003cyi.1_RNA	NM_005778	NP_005769			RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
C3orf45	132228	broad.mit.edu	37	3	50320617	50320620	+	Intron	DEL	AAAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50320617_50320620delAAAC	uc003cyz.2	+							NM_153215	NP_694947			hypothetical protein LOC132228							integral to membrane				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)														---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50411305	50411306	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50411305_50411306delAG	uc003daq.2	-						CACNA2D2_uc003dap.2_Intron	NM_006030	NP_006021			calcium channel, voltage-dependent, alpha						energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	50574351	50574352	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50574351_50574352delAC								CACNA2D2 (33459 upstream) : C3orf18 (21111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	50626854	50626856	+	IGR	DEL	TTT	-	-	rs35884757		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50626854_50626856delTTT								HEMK1 (4435 upstream) : CISH (17030 downstream)																																			---	---	---	---
MAPKAPK3	7867	broad.mit.edu	37	3	50685257	50685257	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50685257delG	uc003day.1	+						MAPKAPK3_uc003daz.1_Intron|MAPKAPK3_uc003dba.1_Intron|MAPKAPK3_uc010hlr.1_Intron	NM_004635	NP_004626			mitogen-activated protein kinase-activated						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	50863607	50863607	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50863607delT	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	51787503	51787503	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51787503delT								GRM2 (34880 upstream) : IQCF6 (25075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	51794750	51794751	+	IGR	DEL	TT	-	-	rs113981979		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51794750_51794751delTT								GRM2 (42127 upstream) : IQCF6 (17827 downstream)																																			---	---	---	---
RPL29	6159	broad.mit.edu	37	3	52029542	52029542	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52029542delC	uc003dcs.2	-							NM_000992	NP_000983			ribosomal protein L29						embryo implantation|endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|protein binding|RNA binding|structural constituent of ribosome				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
WDR82	80335	broad.mit.edu	37	3	52290063	52290064	+	3'UTR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52290063_52290064delCA	uc003ddl.2	-	9					WDR82_uc003ddk.2_3'UTR	NM_025222	NP_079498			WD repeat domain 82						histone H3-K4 methylation	chromatin|PTW/PP1 phosphatase complex|Set1C/COMPASS complex	protein binding				0				BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)														---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52550118	52550119	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52550118_52550119insG	uc003dej.2	+	38	4082_4083	c.4008_4009insG	c.(4006-4011)CTAGGGfs	p.L1336fs	STAB1_uc003dek.1_5'Flank	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	1336_1337	Laminin EGF-like 1.|Extracellular (Potential).				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52600182	52600182	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52600182delA	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52604911	52604911	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52604911delT	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
ITIH1	3697	broad.mit.edu	37	3	52818893	52818893	+	Intron	DEL	A	-	-	rs138291855		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52818893delA	uc003dfs.2	+						ITIH1_uc010hmn.1_Intron|ITIH1_uc003dft.2_Intron|ITIH1_uc010hmo.1_Intron	NM_002215	NP_002206			inter-alpha (globulin) inhibitor H1						hyaluronan metabolic process|leukocyte activation	extracellular region	calcium ion binding|serine-type endopeptidase inhibitor activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)														---	---	---	---
RFT1	91869	broad.mit.edu	37	3	53130400	53130400	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53130400delA	uc003dgj.2	-						RFT1_uc003dgk.2_Intron	NM_052859	NP_443091			RFT1 homolog						carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53766369	53766369	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53766369delC	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Intron|CACNA1D_uc003dgx.1_Intron	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
SELK	58515	broad.mit.edu	37	3	53920274	53920274	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53920274delT	uc011bet.1	-							NM_021237	NP_067060			selenoprotein K						response to oxidative stress	endoplasmic reticulum					0				BRCA - Breast invasive adenocarcinoma(193;0.000146)|KIRC - Kidney renal clear cell carcinoma(284;0.00549)|Kidney(284;0.00619)|OV - Ovarian serous cystadenocarcinoma(275;0.113)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54183325	54183326	+	Intron	INS	-	ACAT	ACAT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54183325_54183326insACAT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54540198	54540198	+	Intron	DEL	T	-	-	rs71844438		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54540198delT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54867618	54867620	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54867618_54867620delAAA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	55052208	55052208	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55052208delT	uc003dhf.2	+						CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	55078628	55078628	+	Intron	DEL	T	-	-	rs113048712		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55078628delT	uc003dhf.2	+						CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56170841	56170841	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56170841delA	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56240709	56240709	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56240709delA	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56242342	56242342	+	Intron	DEL	C	-	-	rs34126230		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56242342delC	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56373684	56373685	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56373684_56373685delTC	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
CCDC66	285331	broad.mit.edu	37	3	56628711	56628711	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56628711delA	uc003dhz.2	+						CCDC66_uc003dhy.2_Intron|CCDC66_uc003dhu.2_Intron|CCDC66_uc003dhx.2_Intron	NM_001141947	NP_001135419			coiled-coil domain containing 66 isoform 1											breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)														---	---	---	---
C3orf63	23272	broad.mit.edu	37	3	56655747	56655747	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56655747delT	uc003did.3	-	23					CCDC66_uc003dhy.2_3'UTR|CCDC66_uc003dhz.2_3'UTR|CCDC66_uc003dhu.2_3'UTR|CCDC66_uc003dhx.2_RNA|CCDC66_uc003dia.2_3'UTR|C3orf63_uc003dib.3_3'UTR|C3orf63_uc003dic.3_3'UTR|C3orf63_uc003die.3_3'UTR	NM_015224	NP_056039			retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)														---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57874632	57874633	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57874632_57874633insT	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_5'Flank|SLMAP_uc011bfa.1_5'Flank|SLMAP_uc003djh.2_5'Flank|SLMAP_uc003dji.1_5'Flank	NM_007159	NP_009090			sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57882416	57882416	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57882416delA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090			sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58122409	58122409	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58122409delT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58148218	58148219	+	Intron	INS	-	T	T	rs141807680	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58148218_58148219insT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
FAM107A	11170	broad.mit.edu	37	3	58581427	58581428	+	Intron	INS	-	CA	CA	rs151159375	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58581427_58581428insCA	uc003dko.2	-							NM_007177	NP_009108			downregulated in renal cell carcinoma						regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	58666451	58666451	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58666451delT								FAM3D (13890 upstream) : C3orf67 (44836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59524004	59524011	+	IGR	DEL	CCCTCCCT	-	-	rs144518572		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59524004_59524011delCCCTCCCT								C3orf67 (488246 upstream) : FHIT (211027 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60158167	60158168	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60158167_60158168insT	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60312417	60312417	+	Intron	DEL	A	-	-	rs1569351	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60312417delA	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
FHIT	2272	broad.mit.edu	37	3	61093196	61093196	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61093196delT	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62258846	62258846	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62258846delT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc011bfi.1_Intron|uc010hno.2_Intron|uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	62295565	62295565	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62295565delA	uc010hno.2	-						uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron					Homo sapiens cDNA FLJ12839 fis, clone NT2RP2003237.																														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63461967	63461967	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63461967delA	uc003dlq.2	+						SYNPR_uc003dlp.2_Intron|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Intron|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243			synaptoporin isoform 2							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64184686	64184687	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64184686_64184687delTT	uc003dmf.2	-							NM_198859	NP_942559			prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64248301	64248301	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64248301delA								PRICKLE2 (37170 upstream) : ADAMTS9 (253032 downstream)																																			---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64623676	64623677	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64623676_64623677insT	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc003dmk.1_Intron	NM_182920	NP_891550			ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64775526	64775527	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64775526_64775527delAC	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																														---	---	---	---
SLC25A26	115286	broad.mit.edu	37	3	66280289	66280289	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66280289delA	uc011bfq.1	+						SLC25A26_uc011bfs.1_Intron|SLC25A26_uc011bft.1_Intron|SLC25A26_uc011bfr.1_Intron	NM_173471	NP_775742			solute carrier family 25, member 26 isoform a							integral to membrane|mitochondrial inner membrane|nucleus	S-adenosylmethionine transmembrane transporter activity			pancreas(1)	1		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69336796	69336796	+	Intron	DEL	T	-	-	rs78688753		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69336796delT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69580548	69580548	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69580548delA	uc003dnw.2	-											Homo sapiens mRNA for KIAA1013 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	72782585	72782586	+	IGR	INS	-	A	A	rs141597894	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72782585_72782586insA								RYBP (286811 upstream) : SHQ1 (15844 downstream)																																			---	---	---	---
GXYLT2	727936	broad.mit.edu	37	3	72935076	72935078	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72935076_72935078delTTT	uc003dpg.2	+							NM_001080393	NP_001073862			glycosyltransferase 8 domain containing 4						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	73034781	73034781	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73034781delT								GXYLT2 (10261 upstream) : PPP4R2 (11338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75202122	75202122	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75202122delT								CNTN3 (631779 upstream) : FAM86D (268583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75614023	75614030	+	IGR	DEL	TGGATGGA	-	-	rs111597949		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75614023_75614030delTGGATGGA								FAM86D (129757 upstream) : MIR1324 (65884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75741762	75741764	+	IGR	DEL	TTA	-	-	rs140744949		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75741762_75741764delTTA								MIR1324 (61753 upstream) : ZNF717 (17030 downstream)																																			---	---	---	---
ZNF717	100131827	broad.mit.edu	37	3	75809905	75809906	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75809905_75809906insA	uc011bgi.1	-						ZNF717_uc003dpw.3_Intron	NM_001128223	NP_001121695			zinc finger protein 717						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	76630010	76630010	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76630010delA								ZNF717 (795340 upstream) : ROBO2 (459284 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77222175	77222175	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77222175delA	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79231717	79231722	+	Intron	DEL	GTGTGC	-	-	rs144525370	by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79231717_79231722delGTGTGC	uc003dqe.2	-							NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79618277	79618278	+	Intron	DEL	CA	-	-	rs72113115		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79618277_79618278delCA	uc003dqe.2	-							NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	80283199	80283199	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80283199delA								ROBO1 (466140 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80475806	80475807	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80475806_80475807insT								ROBO1 (658747 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80619586	80619587	+	IGR	DEL	AA	-	-	rs76836736		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80619586_80619587delAA								ROBO1 (802527 upstream) : GBE1 (919263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80913011	80913012	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80913011_80913012delAA								None (None upstream) : GBE1 (625838 downstream)																																			---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81801901	81801901	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81801901delA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	3	84650317	84650317	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84650317delT								None (None upstream) : CADM2 (357816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84709433	84709433	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84709433delT	uc003dqi.2	-											Homo sapiens cDNA clone IMAGE:4824471.																														---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89268317	89268317	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89268317delT	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224			ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)											TSP Lung(6;0.00050)			---	---	---	---
ARL13B	200894	broad.mit.edu	37	3	93768421	93768421	+	Intron	DEL	A	-	-	rs79420917		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93768421delA	uc003drc.2	+						ARL13B_uc010hop.2_Intron|ARL13B_uc003drd.2_Intron|ARL13B_uc003dre.2_Intron|ARL13B_uc003drf.2_Intron|ARL13B_uc003drg.2_Intron	NM_182896	NP_878899			ADP-ribosylation factor-like 2-like 1 isoform 1								GTP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	94548676	94548676	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94548676delA								NSUN3 (703046 upstream) : LOC255025 (108431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95254865	95254865	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95254865delT								LOC255025 (359786 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96349739	96349741	+	IGR	DEL	AGT	-	-	rs144351932		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96349739_96349741delAGT								None (None upstream) : EPHA6 (183684 downstream)																																			---	---	---	---
MINA	84864	broad.mit.edu	37	3	97669754	97669754	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97669754delA	uc003drz.1	-						MINA_uc003dry.1_5'Flank|MINA_uc003dsa.1_Intron|MINA_uc003dsb.1_Intron|MINA_uc003dsc.1_Intron|MINA_uc010hpa.1_Intron	NM_001042533	NP_001035998			MYC induced nuclear antigen isoform a						ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
TBC1D23	55773	broad.mit.edu	37	3	99998485	99998485	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99998485delT	uc003dtt.2	+						TBC1D23_uc003dts.2_Intron	NM_018309	NP_060779			TBC1 domain family, member 23							intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
NIT2	56954	broad.mit.edu	37	3	100058630	100058630	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100058630delT	uc003dtv.2	+						NIT2_uc011bha.1_Intron	NM_020202	NP_064587			nitrilase family, member 2						nitrogen compound metabolic process		omega-amidase activity			ovary(1)	1																		---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100087870	100087870	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100087870delA	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100091656	100091657	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100091656_100091657insA	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100471886	100471886	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100471886delT	uc003dun.2	-						ABI3BP_uc003duj.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
CEP97	79598	broad.mit.edu	37	3	101484459	101484459	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101484459delT	uc003dvk.1	+	11					CEP97_uc011bhf.1_3'UTR|CEP97_uc003dvl.1_3'UTR|CEP97_uc003dvm.1_3'UTR	NM_024548	NP_078824			centrosomal protein 97kDa							centrosome|nucleus	protein binding			ovary(2)	2																		---	---	---	---
FAM55C	91775	broad.mit.edu	37	3	101520972	101520972	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101520972delA	uc003dvn.2	+						FAM55C_uc010hpn.2_Intron	NM_145037	NP_659474			hypothetical protein LOC91775 precursor							extracellular region				ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	103395803	103395803	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103395803delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104534480	104534481	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104534480_104534481insA								None (None upstream) : ALCAM (551232 downstream)																																			---	---	---	---
CBLB	868	broad.mit.edu	37	3	105399175	105399176	+	Intron	INS	-	A	A	rs138620615	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105399175_105399176insA	uc003dwc.2	-						CBLB_uc003dwa.2_Intron|CBLB_uc011bhi.1_Intron	NM_170662	NP_733762			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9								Mis S		AML								---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108719524	108719524	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108719524delA	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	109313018	109313018	+	IGR	DEL	T	-	-	rs71671800		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109313018delT								FLJ25363 (99004 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109753314	109753315	+	IGR	INS	-	TTTC	TTTC	rs139589445	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109753314_109753315insTTTC								FLJ25363 (539300 upstream) : None (None downstream)																																			---	---	---	---
PVRL3	25945	broad.mit.edu	37	3	110830731	110830732	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110830731_110830732delTG	uc003dxt.1	+						PVRL3_uc003dxu.1_Intron	NM_015480	NP_056295			poliovirus receptor-related 3 precursor						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	111127455	111127455	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111127455delA								PVRL3 (215082 upstream) : CD96 (133471 downstream)																																			---	---	---	---
PLCXD2	257068	broad.mit.edu	37	3	111409221	111409221	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111409221delT	uc003dya.2	+						PLCXD2_uc003dyb.2_Intron|PLCXD2_uc003dxz.2_Intron	NM_001134478	NP_001127950			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113079774	113079775	+	Intron	DEL	AA	-	-	rs111698499		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113079774_113079775delAA	uc003ead.1	-											RecName: Full=WD repeat protein 52.; Flags: Fragment;											central_nervous_system(1)	1																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113147493	113147493	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113147493delT	uc003eae.1	-							NM_018338	NP_060808			WD repeat domain 52 isoform 2											central_nervous_system(1)	1																		---	---	---	---
ZDHHC23	254887	broad.mit.edu	37	3	113675094	113675094	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113675094delA	uc003eau.2	+						ZDHHC23_uc003eav.2_Intron|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841			zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114099335	114099336	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114099335_114099336insT	uc003ebi.2	-						ZBTB20_uc003ebj.2_Intron|ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron|uc003ebo.1_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114245787	114245787	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114245787delT	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115342642	115342642	+	Intron	DEL	T	-	-	rs76382208		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115342642delT	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036			growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)														---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115401995	115401998	+	Intron	DEL	CACA	-	-	rs6804591		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115401995_115401998delCACA	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036			growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115576983	115576984	+	Intron	DEL	TC	-	-	rs112998359		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115576983_115576984delTC	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115973308	115973309	+	Intron	INS	-	AGG	AGG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115973308_115973309insAGG	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	116667224	116667224	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116667224delT								LOC285194 (231339 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117393339	117393339	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117393339delA								LOC285194 (957454 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118143113	118143113	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118143113delA								None (None upstream) : IGSF11 (476368 downstream)																																			---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119019689	119019690	+	Intron	INS	-	G	G	rs111532699		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119019689_119019690insG	uc003ecj.3	+							NM_020754	NP_065805			Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	119139234	119139234	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119139234delG								ARHGAP31 (912 upstream) : TMEM39A (10467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	120253204	120253205	+	IGR	DEL	CA	-	-	rs143265000		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120253204_120253205delCA								FSTL1 (83286 upstream) : NDUFB4 (61923 downstream)																																			---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	121037300	121037300	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121037300delT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795			syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121412439	121412439	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121412439delA	uc003eei.3	-						GOLGB1_uc010hrc.2_Intron|GOLGB1_uc003eej.3_Intron	NM_004487	NP_004478			golgi autoantigen, golgin subfamily b,						Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121447905	121447905	+	Intron	DEL	A	-	-	rs78490595		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121447905delA	uc003eei.3	-						GOLGB1_uc010hrc.2_Intron|GOLGB1_uc003eej.3_Intron|GOLGB1_uc011bjm.1_Intron|GOLGB1_uc010hrd.1_Intron	NM_004487	NP_004478			golgi autoantigen, golgin subfamily b,						Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121449835	121449835	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121449835delG	uc003eei.3	-						GOLGB1_uc010hrc.2_Intron|GOLGB1_uc003eej.3_Intron|GOLGB1_uc011bjm.1_5'Flank|GOLGB1_uc010hrd.1_Intron	NM_004487	NP_004478			golgi autoantigen, golgin subfamily b,						Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
EAF2	55840	broad.mit.edu	37	3	121573659	121573659	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121573659delA	uc003een.2	+	3	426	c.327delA	c.(325-327)GTAfs	p.V109fs	EAF2_uc003eeo.2_Intron	NM_018456	NP_060926	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	109					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)														---	---	---	---
CD86	942	broad.mit.edu	37	3	121822304	121822304	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121822304delT	uc003eet.2	+						CD86_uc011bjo.1_Intron|CD86_uc011bjp.1_Intron|CD86_uc003eeu.2_Intron	NM_175862	NP_787058			CD86 antigen isoform 1						interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)													---	---	---	---
PDIA5	10954	broad.mit.edu	37	3	122811188	122811188	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122811188delT	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801			protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123600692	123600692	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123600692delA	uc003ego.2	-						MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron	NM_053025	NP_444253			myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124024713	124024714	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124024713_124024714insA	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124353549	124353549	+	Intron	DEL	T	-	-	rs72005387		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124353549delT	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc011bjz.1_5'Flank|KALRN_uc003ehj.2_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
MUC13	56667	broad.mit.edu	37	3	124651411	124651411	+	Intron	DEL	A	-	-	rs77819358		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124651411delA	uc003ehq.1	-							NM_033049	NP_149038			mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124810218	124810218	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124810218delT	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc003eht.3_Intron|SLC12A8_uc003ehu.3_Intron|SLC12A8_uc010hry.2_Intron	NM_024628	NP_078904			solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124823919	124823919	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124823919delA	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc003eht.3_Intron|SLC12A8_uc003ehu.3_Intron|SLC12A8_uc010hry.2_Intron	NM_024628	NP_078904			solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	125063764	125063764	+	Intron	DEL	T	-	-	rs74441142		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125063764delT	uc003ehx.3	-						ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799			zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
SLC41A3	54946	broad.mit.edu	37	3	125787175	125787176	+	Intron	INS	-	G	G	rs141146518	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125787175_125787176insG	uc003eij.2	-						SLC41A3_uc003eil.2_Intron|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_Intron|SLC41A3_uc010hsd.1_Intron	NM_001008485	NP_001008485			solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)														---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125836958	125836958	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125836958delG	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc003ein.1_5'Flank	NM_012190	NP_036322			aldehyde dehydrogenase 1 family, member L1						10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)													---	---	---	---
ZXDC	79364	broad.mit.edu	37	3	126181067	126181067	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126181067delA	uc003eiv.2	-						ZXDC_uc010hsh.2_Intron|ZXDC_uc003eix.2_Intron	NM_025112	NP_079388			ZXD family zinc finger C isoform 1						positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126216641	126216645	+	Intron	DEL	GGCTT	-	-	rs71797104		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126216641_126216645delGGCTT	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240			urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126220914	126220915	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126220914_126220915delTG	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240			urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
RUVBL1	8607	broad.mit.edu	37	3	127810145	127810146	+	Intron	INS	-	G	G	rs143644091	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127810145_127810146insG	uc003ekh.2	-						RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Intron|RUVBL1_uc010hss.2_Intron	NM_003707	NP_003698			RuvB-like 1						cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)														---	---	---	---
RAB7A	7879	broad.mit.edu	37	3	128532445	128532446	+	3'UTR	DEL	CG	-	-	rs139417205	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128532445_128532446delCG	uc003eks.1	+	6					RAB7A_uc010hsv.1_3'UTR|RAB7A_uc003ekt.2_Frame_Shift_Del_p.T193fs	NM_004637	NP_004628			RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	128542529	128542529	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128542529delT								RAB7A (8888 upstream) : ACAD9 (55804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	128766967	128766967	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128766967delA								CCDC48 (7384 upstream) : GP9 (12678 downstream)																																			---	---	---	---
MBD4	8930	broad.mit.edu	37	3	129152182	129152182	+	Intron	DEL	T	-	-	rs72112332		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129152182delT	uc003emh.1	-						MBD4_uc003emi.1_Intron|MBD4_uc003emj.1_Intron|MBD4_uc003emk.1_Intron|MBD4_uc011bkw.1_Intron	NM_003925	NP_003916			methyl-CpG binding domain protein 4						depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2													BER_DNA_glycosylases					---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129170911	129170911	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129170911delT	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_uc011bkx.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																		---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130600232	130600235	+	Intron	DEL	TCTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130600232_130600235delTCTC	uc011bli.1	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron	NM_001001487	NP_001001487			calcium-transporting ATPase 2C1 isoform 1b						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
NEK11	79858	broad.mit.edu	37	3	130871047	130871047	+	Intron	DEL	T	-	-	rs150507740	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130871047delT	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_Intron	NM_024800	NP_079076			NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	131144744	131144744	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131144744delT								NUDT16 (39815 upstream) : MRPL3 (36302 downstream)																																			---	---	---	---
TOPBP1	11073	broad.mit.edu	37	3	133347615	133347616	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133347615_133347616delAG	uc003eps.2	-						TOPBP1_uc003ept.1_5'Flank	NM_007027	NP_008958			topoisomerase (DNA) II binding protein 1						DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7													Other_conserved_DNA_damage_response_genes					---	---	---	---
Unknown	0	broad.mit.edu	37	3	133960986	133960987	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133960986_133960987insA								RYK (-8600 upstream) : RYK (-85009 downstream)																																			---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134902090	134902093	+	Intron	DEL	CTTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134902090_134902093delCTTC	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	135614035	135614035	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135614035delT								EPHB1 (634730 upstream) : PPP2R3A (70532 downstream)																																	OREG0015822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136356715	136356715	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136356715delT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003ere.2_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136456112	136456112	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136456112delT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003ere.2_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137988856	137988856	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137988856delT	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
MRAS	22808	broad.mit.edu	37	3	138123869	138123869	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138123869delT	uc003esh.3	+	6					MRAS_uc011bmi.1_3'UTR|MRAS_uc003esi.3_3'UTR|MRAS_uc011bmj.1_3'UTR	NM_012219	NP_036351			muscle RAS oncogene homolog precursor						actin cytoskeleton organization|muscle organ development|Ras protein signal transduction	intracellular|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138628338	138628338	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138628338delC								PIK3CB (150153 upstream) : FOXL2 (34729 downstream)																																			---	---	---	---
ZBTB38	253461	broad.mit.edu	37	3	141145858	141145859	+	Intron	INS	-	T	T	rs140144379	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141145858_141145859insT	uc003etw.2	+						ZBTB38_uc010hun.2_Intron|ZBTB38_uc010huo.2_Intron|ZBTB38_uc003ety.2_Intron|ZBTB38_uc010hup.2_Intron	NM_001080412	NP_001073881			zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	141386412	141386412	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141386412delT								RASA2 (55215 upstream) : RNF7 (70639 downstream)																																			---	---	---	---
ATP1B3	483	broad.mit.edu	37	3	141606032	141606032	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141606032delG	uc003eug.1	+						ATP1B3_uc011bne.1_Intron|ATP1B3_uc003euh.1_Intron	NM_001679	NP_001670			Na+/K+ -ATPase beta 3 subunit						ATP biosynthetic process|blood coagulation|leukocyte migration	melanosome|sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity				0																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142051517	142051517	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142051517delA	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																		---	---	---	---
ATR	545	broad.mit.edu	37	3	142226961	142226961	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142226961delA	uc003eux.3	-							NM_001184	NP_001175			ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20													Other_conserved_DNA_damage_response_genes					---	---	---	---
ATR	545	broad.mit.edu	37	3	142279407	142279407	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142279407delT	uc003eux.3	-							NM_001184	NP_001175			ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20													Other_conserved_DNA_damage_response_genes					---	---	---	---
Unknown	0	broad.mit.edu	37	3	143917566	143917566	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143917566delC								C3orf58 (206357 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144304115	144304115	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144304115delA								C3orf58 (592906 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146342443	146342444	+	IGR	INS	-	CACA	CACA	rs71633973		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146342443_146342444insCACA								PLSCR5 (18440 upstream) : ZIC4 (761393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146995077	146995078	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146995077_146995078delAA								PLSCR5 (671074 upstream) : ZIC4 (108759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148258962	148258963	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148258962_148258963delTT								None (None upstream) : AGTR1 (156695 downstream)																																			---	---	---	---
CPA3	1359	broad.mit.edu	37	3	148582960	148582960	+	5'Flank	DEL	A	-	-	rs143382113		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148582960delA	uc003ewm.2	+							NM_001870	NP_001861			carboxypeptidase A3 precursor						proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)															---	---	---	---
PFN2	5217	broad.mit.edu	37	3	149683502	149683503	+	3'UTR	INS	-	T	T	rs72586335		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149683502_149683503insT	uc003ext.1	-	3					PFN2_uc003exs.1_3'UTR|PFN2_uc003exu.1_3'UTR|PFN2_uc011bnu.1_Intron	NM_053024	NP_444252			profilin 2 isoform a						actin cytoskeleton organization|regulation of actin polymerization or depolymerization	actin cytoskeleton|cytoplasm	actin binding|phosphatidylinositol-4,5-bisphosphate binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150840548	150840548	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150840548delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eym.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150987985	150987992	+	Intron	DEL	GTGTGTGT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150987985_150987992delGTGTGTGT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY14_uc003eys.1_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150994998	150995000	+	Intron	DEL	TTT	-	-	rs71726969		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150994998_150995000delTTT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY14_uc003eys.1_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	151228301	151228301	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151228301delA								IGSF10 (51804 upstream) : AADACL2 (223403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154732901	154732901	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154732901delA								GPR149 (585397 upstream) : MME (9012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155135655	155135655	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155135655delA								MME (234137 upstream) : PLCH1 (62016 downstream)																																			---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155197738	155197739	+	3'UTR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155197738_155197739delAA	uc011bok.1	-	23					PLCH1_uc011boj.1_3'UTR|PLCH1_uc011bol.1_3'UTR	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155208506	155208506	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155208506delT	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156860460	156860460	+	IGR	DEL	G	-	-	rs6805601	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156860460delG								LEKR1 (96542 upstream) : CCNL1 (3837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157236147	157236148	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157236147_157236148insT								VEPH1 (14732 upstream) : C3orf55 (25011 downstream)																																			---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	158014219	158014220	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158014219_158014220delTG	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
RARRES1	5918	broad.mit.edu	37	3	158416851	158416852	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158416851_158416852delCT	uc003fci.2	-							NM_206963	NP_996846			retinoic acid receptor responder (tazarotene						negative regulation of cell proliferation	integral to membrane					0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)													---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159504060	159504060	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159504060delT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron|SCHIP1_uc010hvz.1_Intron	NM_014575	NP_055390			schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	159690273	159690273	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159690273delT	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																														---	---	---	---
KPNA4	3840	broad.mit.edu	37	3	160253357	160253358	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160253357_160253358insA	uc003fdn.2	-							NM_002268	NP_002259			karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
B3GALNT1	8706	broad.mit.edu	37	3	160820005	160820006	+	Intron	INS	-	A	A	rs140892792	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160820005_160820006insA	uc003fdv.2	-						B3GALNT1_uc003fdw.2_Intron|B3GALNT1_uc003fdx.2_Intron|B3GALNT1_uc003fdy.2_Intron|B3GALNT1_uc003fdz.2_Intron|B3GALNT1_uc003fea.2_Intron|B3GALNT1_uc011bpa.1_5'Flank	NM_033169	NP_149359			UDP-Gal:betaGlcNAc beta						protein glycosylation	Golgi membrane|integral to membrane	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161813911	161813914	+	IGR	DEL	TTCC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161813911_161813914delTTCC								OTOL1 (592183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162063593	162063593	+	IGR	DEL	A	-	-	rs72014396		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162063593delA								OTOL1 (841865 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164344167	164344168	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164344167_164344168delAC								MIR720 (284929 upstream) : SI (352519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164567543	164567543	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164567543delA								MIR720 (508305 upstream) : SI (129144 downstream)																																			---	---	---	---
GOLIM4	27333	broad.mit.edu	37	3	167803614	167803614	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167803614delT	uc003ffe.2	-						GOLIM4_uc011bpe.1_Intron|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313			golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5																		---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169953309	169953309	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169953309delT	uc003fgs.2	+							NM_002740	NP_002731			protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169956150	169956151	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169956150_169956151insA	uc003fgs.2	+							NM_002740	NP_002731			protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170457212	170457213	+	Intron	INS	-	CA	CA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170457212_170457213insCA	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593			claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170727950	170727950	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170727950delT	uc003fhe.1	-						SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Intron	NM_000340	NP_000331			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170819514	170819514	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170819514delA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhg.2_5'UTR	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170843675	170843675	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170843675delA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	171312993	171312993	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171312993delG								TNIK (134796 upstream) : PLD1 (5627 downstream)																																			---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	171853046	171853047	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171853046_171853047delTG	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron|FNDC3B_uc003fhx.2_Intron	NM_022763	NP_073600			fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)														---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172820433	172820433	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172820433delC	uc003fin.3	-							NM_031955	NP_114161			spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173863316	173863317	+	Intron	INS	-	A	A	rs146959793	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173863316_173863317insA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	174116219	174116219	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174116219delA								NLGN1 (115103 upstream) : NAALADL2 (460892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	174446439	174446439	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174446439delT	uc003fir.2	+						uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175020638	175020639	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175020638_175020639delTG	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	NM_207015	NP_996898			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
TBL1XR1	79718	broad.mit.edu	37	3	176879408	176879408	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176879408delA	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron|TBL1XR1_uc003fiy.2_Intron	NM_024665	NP_078941			transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	177305847	177305848	+	IGR	INS	-	G	G	rs148905327	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177305847_177305848insG								TBL1XR1 (390799 upstream) : KCNMB2 (948376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177428378	177428378	+	IGR	DEL	A	-	-	rs34873119		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177428378delA								TBL1XR1 (513330 upstream) : KCNMB2 (825846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177926038	177926038	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177926038delC								None (None upstream) : KCNMB2 (328186 downstream)																																			---	---	---	---
KCNMB2	10242	broad.mit.edu	37	3	178553241	178553241	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178553241delT	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron|KCNMB2_uc011bqa.1_Intron|KCNMB2_uc011bqb.1_Intron	NM_181361	NP_852006			calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)															---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178913049	178913050	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178913049_178913050delAA	uc003fjk.2	+							NM_006218	NP_006209			phosphoinositide-3-kinase, catalytic, alpha						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)				57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			---	---	---	---
USP13	8975	broad.mit.edu	37	3	179479203	179479203	+	Intron	DEL	T	-	-	rs74695249		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179479203delT	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
ATP11B	23200	broad.mit.edu	37	3	182630237	182630237	+	Intron	DEL	T	-	-	rs140832448		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182630237delT	uc003flb.2	+						ATP11B_uc003flc.2_Intron|ATP11B_uc010hxg.2_Intron|ATP11B_uc010hxh.1_Intron	NM_014616	NP_055431			ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)															---	---	---	---
DCUN1D1	54165	broad.mit.edu	37	3	182663038	182663038	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182663038delT	uc003fld.1	-						DCUN1D1_uc011bqn.1_Intron	NM_020640	NP_065691			RP42 homolog							ubiquitin ligase complex	protein binding			ovary(1)	1	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182833646	182833646	+	5'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182833646delA	uc003flg.2	-	1										RecName: Full=Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial;          Short=MCCase subunit alpha;          EC=6.4.1.4; AltName: Full=3-methylcrotonyl-CoA carboxylase 1; AltName: Full=3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; AltName: Full=3-methylcrotonyl-CoA carboxylase biotin-containing subunit; Flags: Precursor;						biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)													---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183497334	183497334	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183497334delA	uc003fly.2	+						YEATS2_uc003flz.2_Intron	NM_018023	NP_060493			YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183656094	183656094	+	Intron	DEL	T	-	-	rs111835263		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183656094delT	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron	NM_005688	NP_005679			ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183665257	183665257	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183665257delA	uc003fmg.2	-	23	3434	c.3269delT	c.(3268-3270)TTGfs	p.L1090fs	ABCC5_uc011bqt.1_Frame_Shift_Del_p.L618fs|ABCC5_uc010hxl.2_Frame_Shift_Del_p.L1047fs	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	1090	ABC transmembrane type-1 2.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
EIF2B5	8893	broad.mit.edu	37	3	183858566	183858567	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183858566_183858567insG	uc003fmp.2	+						EIF2B5_uc003fmq.2_Intron|EIF2B5_uc003fmr.2_5'Flank	NM_003907	NP_003898			eukaryotic translation initiation factor 2B,						astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184232390	184232391	+	IGR	INS	-	A	A	rs67114682		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184232390_184232391insA								CHRD (124771 upstream) : EPHB3 (47196 downstream)																																			---	---	---	---
EPHB3	2049	broad.mit.edu	37	3	184297073	184297073	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184297073delA	uc003foz.2	+							NM_004443	NP_004434			ephrin receptor EphB3 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	185756166	185756167	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185756166_185756167insT								TRA2B (100242 upstream) : ETV5 (7941 downstream)																																			---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186045180	186045180	+	Intron	DEL	T	-	-	rs36076414		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186045180delT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
RFC4	5984	broad.mit.edu	37	3	186509259	186509259	+	Intron	DEL	A	-	-	rs75285776		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186509259delA	uc003fqz.2	-						RFC4_uc011bsc.1_Intron|RFC4_uc011bsd.1_3'UTR	NM_002916	NP_002907			replication factor C 4						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)														---	---	---	---
RTP2	344892	broad.mit.edu	37	3	187416873	187416873	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187416873delA	uc003fro.1	-							NM_001004312	NP_001004312			receptor transporting protein 2						protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding				0	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0515)														---	---	---	---
LPP	4026	broad.mit.edu	37	3	188247950	188247953	+	Intron	DEL	ACTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188247950_188247953delACTT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
Unknown	0	broad.mit.edu	37	3	189245987	189245987	+	IGR	DEL	C	-	-	rs6797969		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189245987delC								TPRG1 (204717 upstream) : TP63 (103229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189857361	189857362	+	IGR	INS	-	AT	AT	rs142857861	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189857361_189857362insAT								LEPREL1 (17135 upstream) : CLDN1 (166141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189873231	189873231	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189873231delC								LEPREL1 (33005 upstream) : CLDN1 (150272 downstream)																																			---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192078485	192078485	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192078485delT	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360			fibroblast growth factor 12 isoform 1						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
C3orf59	151963	broad.mit.edu	37	3	192635405	192635405	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192635405delT	uc011bsp.1	-							NM_178496	NP_848591			hypothetical protein LOC151963												0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)														---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193017093	193017093	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193017093delT	uc011bsq.1	-							NM_198505	NP_940907			ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193166170	193166170	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193166170delT	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc010hzi.2_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193364840	193364840	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193364840delT	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375			optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193396104	193396104	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193396104delT	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375			optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	193456116	193456116	+	IGR	DEL	T	-	-	rs77483905		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193456116delT								OPA1 (40517 upstream) : LOC100128023 (254768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194776279	194776281	+	IGR	DEL	CGC	-	-	rs74881321		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194776279_194776281delCGC								FAM43A (366515 upstream) : C3orf21 (12734 downstream)																																			---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194804757	194804758	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194804757_194804758delAA	uc003fum.3	-						C3orf21_uc003ful.2_Intron|C3orf21_uc003fuk.2_Intron	NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194822606	194822606	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194822606delA	uc003fum.3	-						C3orf21_uc003ful.2_Intron|C3orf21_uc003fuk.2_Intron	NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195433716	195433716	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195433716delT	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																														---	---	---	---
TFRC	7037	broad.mit.edu	37	3	195789950	195789950	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195789950delA	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225			transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)				T	BCL6	NHL								---	---	---	---
Unknown	0	broad.mit.edu	37	3	195873431	195873431	+	Intron	DEL	A	-	-	rs77597930		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195873431delA	uc011bts.1	+						uc011btt.1_Intron					Homo sapiens cDNA FLJ25996 fis, clone DMC06615.																														---	---	---	---
TCTEX1D2	255758	broad.mit.edu	37	3	196032910	196032910	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196032910delA	uc003fwi.2	-							NM_152773	NP_689986			Tctex1 domain containing 2								protein binding			ovary(1)|breast(1)	2	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
UBXN7	26043	broad.mit.edu	37	3	196088571	196088571	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196088571delT	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron	NM_015562	NP_056377			UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
RNF168	165918	broad.mit.edu	37	3	196207689	196207689	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196207689delT	uc003fwq.2	-						RNF168_uc010iah.2_Intron	NM_152617	NP_689830			ring finger protein 168						double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196976400	196976400	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196976400delA	uc003fxo.3	-						DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196977039	196977039	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196977039delA	uc003fxo.3	-						DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	197172062	197172062	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197172062delG								DLG1 (145919 upstream) : BDH1 (64593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	609854	609858	+	IGR	DEL	TTTTT	-	-	rs142617762	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:609854_609858delTTTTT								PIGG (76535 upstream) : PDE6B (9505 downstream)																																			---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	641866	641866	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:641866delA	uc003gap.2	+						PDE6B_uc003gao.3_Intron	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
PCGF3	10336	broad.mit.edu	37	4	750005	750006	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:750005_750006delTT	uc011bva.1	+						PCGF3_uc003gbd.1_Intron|PCGF3_uc003gbe.2_Intron|PCGF3_uc010ibh.2_Intron|PCGF3_uc003gbg.1_Intron|PCGF3_uc003gbh.2_Intron	NM_006315	NP_006306			ring finger protein 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	832134	832134	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:832134delC								CPLX1 (12189 upstream) : GAK (10932 downstream)																																			---	---	---	---
GAK	2580	broad.mit.edu	37	4	860180	860181	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:860180_860181insG	uc003gbm.3	-	22	3213_3214	c.3014_3015insC	c.(3013-3015)CCAfs	p.P1005fs	GAK_uc003gbn.3_Frame_Shift_Ins_p.P926fs|GAK_uc010ibi.2_Frame_Shift_Ins_p.P186fs|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Frame_Shift_Ins_p.P858fs	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	1005					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
SLC26A1	10861	broad.mit.edu	37	4	984869	984869	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:984869delG	uc003gcb.2	-						SLC26A1_uc003gbx.2_Intron|IDUA_uc003gby.2_Intron|IDUA_uc003gbz.2_Intron|IDUA_uc003gca.2_Intron|SLC26A1_uc003gcc.2_Intron	NM_213613	NP_998778			solute carrier family 26, member 1 isoform a							integral to membrane|plasma membrane	secondary active sulfate transmembrane transporter activity			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
FGFRL1	53834	broad.mit.edu	37	4	1019055	1019056	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1019055_1019056delCA	uc003gce.2	+	7	1596_1597	c.1435_1436delCA	c.(1435-1437)CACfs	p.H479fs	FGFRL1_uc003gcf.2_Frame_Shift_Del_p.H479fs|FGFRL1_uc003gcg.2_Frame_Shift_Del_p.H479fs|FGFRL1_uc010ibo.2_Frame_Shift_Del_p.H479fs	NM_021923	NP_068742	Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	479	His-rich.|Cytoplasmic (Potential).				regulation of cell growth	integral to membrane|plasma membrane	fibroblast growth factor receptor activity|heparin binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1532109	1532109	+	IGR	DEL	A	-	-	rs113172680		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1532109delA								CRIPAK (142327 upstream) : FAM53A (109500 downstream)																																			---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1919853	1919853	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1919853delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geh.1_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
Unknown	0	broad.mit.edu	37	4	3552140	3552141	+	IGR	INS	-	A	A	rs147507427		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3552140_3552141insA								LRPAP1 (17916 upstream) : ADRA2C (215934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3609800	3609800	+	IGR	DEL	G	-	-	rs67423032		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3609800delG								LRPAP1 (75576 upstream) : ADRA2C (158275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3624509	3624509	+	IGR	DEL	C	-	-	rs111475753		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3624509delC								LRPAP1 (90285 upstream) : ADRA2C (143566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3634997	3634998	+	IGR	INS	-	CCCTC	CCCTC	rs112046897		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3634997_3634998insCCCTC								LRPAP1 (100773 upstream) : ADRA2C (133077 downstream)																																			---	---	---	---
EVC	2121	broad.mit.edu	37	4	5722868	5722868	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5722868delC	uc003gil.1	+						EVC_uc003gim.1_Intron	NM_153717	NP_714928			Ellis van Creveld syndrome protein						muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
EVC	2121	broad.mit.edu	37	4	5750156	5750156	+	Intron	DEL	A	-	-	rs13143108	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5750156delA	uc003gil.1	+						EVC_uc003gim.1_Intron|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928			Ellis van Creveld syndrome protein						muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
PPP2R2C	5522	broad.mit.edu	37	4	6564200	6564201	+	Intron	INS	-	T	T	rs140179979		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6564200_6564201insT	uc011bwe.1	-							NM_181876	NP_870991			gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	7111053	7111060	+	IGR	DEL	GAATGAAT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7111053_7111060delGAATGAAT								FLJ36777 (5950 upstream) : SORCS2 (83314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	7134938	7134938	+	IGR	DEL	C	-	-	rs35339290		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7134938delC								FLJ36777 (29835 upstream) : SORCS2 (59436 downstream)																																			---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7811544	7811544	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7811544delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7847611	7847611	+	Intron	DEL	G	-	-	rs112820006		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7847611delG	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	8330884	8330899	+	IGR	DEL	CCTGGACCCCACAGTC	-	-	rs11274710		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8330884_8330899delCCTGGACCCCACAGTC								HTRA3 (22054 upstream) : ACOX3 (37111 downstream)																																			---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	9846645	9846645	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9846645delT	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425			solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13582681	13582681	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13582681delA	uc003gmz.1	-							NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	13753515	13753530	+	Intron	DEL	CCATCCATCCATCCAC	-	-	rs150190394	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13753515_13753530delCCATCCATCCATCCAC	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13753519	13753530	+	Intron	DEL	CCATCCATCCAC	-	-	rs57762413		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13753519_13753530delCCATCCATCCAC	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13754240	13754240	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13754240delT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13792496	13792496	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13792496delT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	14756650	14756650	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14756650delT	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	15075403	15075404	+	IGR	INS	-	AACT	AACT	rs142359135	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15075403_15075404insAACT								CPEB2 (3629 upstream) : C1QTNF7 (266156 downstream)																																			---	---	---	---
TAPT1	202018	broad.mit.edu	37	4	16169907	16169908	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16169907_16169908insT	uc010ied.1	-						TAPT1_uc011bxd.1_Intron|TAPT1_uc011bxe.1_Intron	NM_153365	NP_699196			transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0																		---	---	---	---
TAPT1	202018	broad.mit.edu	37	4	16189981	16189981	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16189981delA	uc010ied.1	-						TAPT1_uc011bxd.1_Intron|TAPT1_uc011bxe.1_Intron	NM_153365	NP_699196			transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0																		---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16889542	16889542	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16889542delA	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	17036772	17036775	+	IGR	DEL	GTGT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17036772_17036775delGTGT								LDB2 (136348 upstream) : QDPR (451245 downstream)																																			---	---	---	---
NCAPG	64151	broad.mit.edu	37	4	17819135	17819135	+	Intron	DEL	T	-	-	rs2302211	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17819135delT	uc003gpp.2	+						NCAPG_uc011bxj.1_Intron	NM_022346	NP_071741			chromosome condensation protein G						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)														---	---	---	---
LCORL	254251	broad.mit.edu	37	4	17952420	17952420	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17952420delA	uc003gpq.2	-						LCORL_uc011bxk.1_Intron	NM_153686	NP_710153			ligand dependent nuclear receptor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	18280989	18280990	+	IGR	DEL	GT	-	-	rs141416646	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18280989_18280990delGT								LCORL (257604 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19323776	19323776	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19323776delA								None (None upstream) : SLIT2 (931459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19405900	19405900	+	IGR	DEL	T	-	-	rs34033302		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19405900delT								None (None upstream) : SLIT2 (849335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19527091	19527092	+	IGR	DEL	AG	-	-	rs148047735		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19527091_19527092delAG								None (None upstream) : SLIT2 (728143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20009493	20009493	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20009493delA								None (None upstream) : SLIT2 (245742 downstream)																																			---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20377417	20377417	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20377417delA	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778			slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	22218150	22218150	+	IGR	DEL	T	-	-	rs78121351		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22218150delT								KCNIP4 (267776 upstream) : GPR125 (170849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	22289681	22289681	+	IGR	DEL	T	-	-	rs113594581		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22289681delT								KCNIP4 (339307 upstream) : GPR125 (99318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	22678704	22678704	+	IGR	DEL	A	-	-	rs148265375	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22678704delA								GPR125 (161032 upstream) : GBA3 (15844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24076055	24076056	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24076055_24076056insT								PPARGC1A (184355 upstream) : MIR573 (445759 downstream)																																			---	---	---	---
SEPSECS	51091	broad.mit.edu	37	4	25158358	25158358	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25158358delG	uc003grg.2	-						SEPSECS_uc003gri.2_Intron|SEPSECS_uc003grh.2_Intron	NM_153825	NP_722547			Sep (O-phosphoserine) tRNA:Sec (selenocysteine)						selenocysteine incorporation	cytoplasm|nucleus	pyridoxal phosphate binding|transferase activity, transferring selenium-containing groups|tRNA binding				0		Breast(46;0.173)			Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	26783421	26783422	+	IGR	DEL	TT	-	-	rs77613062		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26783421_26783422delTT								TBC1D19 (26506 upstream) : STIM2 (78942 downstream)																																			---	---	---	---
STIM2	57620	broad.mit.edu	37	4	26978425	26978426	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26978425_26978426insA	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	27548039	27548039	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27548039delA								STIM2 (522231 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28107869	28107880	+	IGR	DEL	AAGAAGGAAGGG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28107869_28107880delAAGAAGGAAGGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28377422	28377423	+	IGR	INS	-	T	T	rs143273563	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28377422_28377423insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29577112	29577112	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29577112delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29729481	29729483	+	IGR	DEL	AAA	-	-	rs34277856		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29729481_29729483delAAA								None (None upstream) : PCDH7 (992554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30074550	30074553	+	IGR	DEL	ACAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30074550_30074553delACAC								None (None upstream) : PCDH7 (647484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31429801	31429802	+	IGR	INS	-	C	C	rs138589318	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31429801_31429802insC								PCDH7 (281380 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32225692	32225692	+	IGR	DEL	A	-	-	rs113889933		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32225692delA								None (None upstream) : None (None downstream)																																			---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	35970148	35970155	+	Intron	DEL	ACACACAC	-	-	rs150078331		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35970148_35970155delACACACAC	uc003gso.2	-											Homo sapiens cDNA clone IMAGE:5296543.						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37358113	37358113	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37358113delA	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	37822924	37822924	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37822924delA								RELL1 (134925 upstream) : PGM2 (5358 downstream)																																			---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	37902693	37902693	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37902693delA	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_5'Flank	NM_015173	NP_055988			TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	38140082	38140082	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38140082delA	uc003gtb.2	+	20					TBC1D1_uc011byd.1_3'UTR|TBC1D1_uc010ifd.2_3'UTR|TBC1D1_uc003gtd.2_3'UTR	NM_015173	NP_055988			TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	38735110	38735111	+	IGR	INS	-	TGG	TGG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38735110_38735111insTGG								KLF3 (31982 upstream) : TLR10 (39152 downstream)																																			---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39184298	39184299	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39184298_39184299delAG	uc003gtv.2	+						WDR19_uc010ifl.1_Intron|WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron	NM_025132	NP_079408			WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478849	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849delA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	39534075	39534076	+	Intron	INS	-	CTCA	CTCA	rs148675598	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39534075_39534076insCTCA	uc003gum.1	+											Homo sapiens cDNA FLJ31996 fis, clone NT2RP7009253.																														---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39876054	39876054	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39876054delT	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869			PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	41828073	41828074	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41828073_41828074insT								PHOX2B (77086 upstream) : TMEM33 (109063 downstream)																																			---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42037517	42037519	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42037517_42037519delTTT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42088254	42088254	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42088254delT	uc003gwl.2	+	18					SLC30A9_uc011byx.1_3'UTR	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42424927	42424927	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42424927delA	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Intron	NM_006095	NP_006086			ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	43901421	43901421	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43901421delA								GRXCR1 (868748 upstream) : KCTD8 (274501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	44057640	44057640	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44057640delT								None (None upstream) : KCTD8 (118282 downstream)																																			---	---	---	---
GUF1	60558	broad.mit.edu	37	4	44682662	44682662	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44682662delT	uc003gww.3	+						GUF1_uc010ifz.1_Intron	NM_021927	NP_068746			GUF1 GTPase homolog						translation	mitochondrial inner membrane	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	46029908	46029908	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46029908delA								None (None upstream) : GABRG1 (7881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46409017	46409018	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46409017_46409018delAA								GABRA2 (16596 upstream) : COX7B2 (327831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46517269	46517272	+	IGR	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46517269_46517272delAAAA								GABRA2 (124848 upstream) : COX7B2 (219577 downstream)																																			---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47712605	47712606	+	Intron	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47712605_47712606insC	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_Intron	NM_006587	NP_006578			corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47860011	47860011	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47860011delT	uc010igh.2	-						NFXL1_uc003gxo.2_Intron|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
TXK	7294	broad.mit.edu	37	4	48136088	48136088	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48136088delA	uc003gxx.3	-						TXK_uc003gxy.1_Intron	NM_003328	NP_003319			TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48568134	48568134	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48568134delT	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyi.1_5'Flank	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625211	48625213	+	Intron	DEL	AAC	-	-	rs776579	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625211_48625213delAAC	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	49138460	49138460	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49138460delT								CWH43 (74367 upstream) : None (None downstream)																																			---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52926826	52926826	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52926826delT	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron	NM_145263	NP_660306			spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53242671	53242671	+	IGR	DEL	T	-	-	rs34449125		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53242671delT								SPATA18 (279214 upstream) : USP46 (214458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53533703	53533704	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53533703_53533704insT								USP46 (8201 upstream) : KIAA0114 (44917 downstream)																																			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54439722	54439722	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54439722delG	uc003haa.2	+						LNX1_uc003hag.3_Intron|LNX1_uc003hah.3_Intron	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)			---	---	---	---
GSX2	170825	broad.mit.edu	37	4	54966752	54966752	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54966752delG	uc010igp.1	+	1	505	c.241delG	c.(241-243)GGGfs	p.G81fs	PDGFRA_uc003haa.2_Intron	NM_133267	NP_573574	Q9BZM3	GSX2_HUMAN	GS homeobox 2	81						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(7;0.00671)|Lung NSC(11;0.0154)|all_neural(26;0.0209)|Glioma(25;0.08)|all_epithelial(27;0.147)		LUSC - Lung squamous cell carcinoma(32;0.00216)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	55346004	55346004	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55346004delA								PDGFRA (181593 upstream) : KIT (178091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55427698	55427699	+	IGR	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55427698_55427699insAC								PDGFRA (263287 upstream) : KIT (96396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56071026	56071026	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56071026delT								KDR (79264 upstream) : SRD5A3 (141383 downstream)																																			---	---	---	---
CEP135	9662	broad.mit.edu	37	4	56886646	56886646	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56886646delA	uc003hbi.2	+						CEP135_uc003hbj.2_Intron	NM_025009	NP_079285			centrosome protein 4						centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
SRP72	6731	broad.mit.edu	37	4	57354057	57354057	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57354057delT	uc003hbv.2	+						SRP72_uc010ihe.2_Intron|SRP72_uc003hbw.1_Intron	NM_006947	NP_008878			signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
HOPX	84525	broad.mit.edu	37	4	57514738	57514738	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57514738delA	uc011cad.1	-	3					HOPX_uc003hcc.2_3'UTR|HOPX_uc003hca.2_3'UTR|HOPX_uc003hcb.2_3'UTR|HOPX_uc003hcd.2_RNA|HOPX_uc003hce.2_RNA|HOPX_uc003hbz.2_3'UTR	NM_001145459	NP_001138931			HOP homeobox isoform b						negative regulation of cell differentiation|trophectodermal cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
IGFBP7	3490	broad.mit.edu	37	4	57901629	57901629	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57901629delT	uc003hcn.2	-						IGFBP7_uc011cag.1_Intron	NM_001553	NP_001544			insulin-like growth factor binding protein 7						cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding			lung(2)|central_nervous_system(1)	3	Glioma(25;0.08)|all_neural(26;0.181)				Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	58482107	58482107	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58482107delT								IGFBP7 (505568 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58840836	58840837	+	IGR	INS	-	T	T	rs111563380		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58840836_58840837insT								IGFBP7 (864297 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59834468	59834468	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59834468delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64381161	64381161	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64381161delA								None (None upstream) : TECRL (763024 downstream)																																			---	---	---	---
STAP1	26228	broad.mit.edu	37	4	68442902	68442902	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68442902delT	uc003hde.3	+						STAP1_uc003hdf.2_Intron	NM_012108	NP_036240			signal transducing adaptor family member 1						cellular membrane fusion|intracellular protein transport	cytoplasm					0																		---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68530891	68530891	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68530891delA	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697			ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	70066030	70066032	+	5'Flank	DEL	ATT	-	-	rs60147183		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70066030_70066032delATT	uc003hei.1	+											Homo sapiens cDNA FLJ42278 fis, clone TLIVE2002562.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	70084871	70084871	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70084871delA								UGT2B11 (4422 upstream) : UGT2B28 (61346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70294612	70294613	+	IGR	DEL	TC	-	-	rs67295654		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70294612_70294613delTC								UGT2B28 (133845 upstream) : UGT2B4 (51271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70336142	70336143	+	IGR	INS	-	T	T	rs60338734		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70336142_70336143insT								UGT2B28 (175375 upstream) : UGT2B4 (9741 downstream)																																			---	---	---	---
SLC4A4	8671	broad.mit.edu	37	4	72098300	72098301	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72098300_72098301insA	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron	NM_001098484	NP_001091954			solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	72517964	72517964	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72517964delA								SLC4A4 (80161 upstream) : GC (89449 downstream)																																			---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73177069	73177070	+	Intron	DEL	TT	-	-	rs34684425		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73177069_73177070delTT	uc003hgk.1	-						ADAMTS3_uc003hgl.2_Intron	NM_014243	NP_055058			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
COX18	285521	broad.mit.edu	37	4	73928092	73928092	+	Intron	DEL	A	-	-	rs76321913		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73928092delA	uc003hgm.1	-						COX18_uc003hgn.1_Intron|COX18_uc011cbc.1_Intron|COX18_uc010iih.1_Intron	NM_173827	NP_776188			mitochondrial COX18 precursor						protein insertion into mitochondrial membrane|respiratory chain complex IV assembly	integral to mitochondrial inner membrane	protein transporter activity				0	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
COX18	285521	broad.mit.edu	37	4	73930892	73930893	+	Intron	INS	-	G	G	rs79402424		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73930892_73930893insG	uc003hgm.1	-						COX18_uc003hgn.1_Intron|COX18_uc011cbc.1_Intron|COX18_uc010iih.1_Intron	NM_173827	NP_776188			mitochondrial COX18 precursor						protein insertion into mitochondrial membrane|respiratory chain complex IV assembly	integral to mitochondrial inner membrane	protein transporter activity				0	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	75212555	75212555	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75212555delA								EPGN (32168 upstream) : EREG (18305 downstream)																																			---	---	---	---
CDKL2	8999	broad.mit.edu	37	4	76554460	76554460	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76554460delA	uc003hiq.2	-						CDKL2_uc011cbp.1_Intron|CDKL2_uc010iix.1_Intron	NM_003948	NP_003939			cyclin-dependent kinase-like 2						sex differentiation|signal transduction	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(2)|stomach(2)|breast(2)|skin(1)	7			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
NUP54	53371	broad.mit.edu	37	4	77045737	77045740	+	Intron	DEL	TATT	-	-	rs10567710		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77045737_77045740delTATT	uc003hjs.2	-						NUP54_uc010ije.2_Intron|NUP54_uc011cbs.1_Intron|NUP54_uc011cbt.1_Intron|NUP54_uc003hjt.2_Intron	NM_017426	NP_059122			nucleoporin 54kDa						carbohydrate metabolic process|glucose transport|mRNA transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleoplasm				ovary(1)|lung(1)	2																		---	---	---	---
CCNG2	901	broad.mit.edu	37	4	78080431	78080431	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78080431delA	uc003hkq.3	+						CCNG2_uc003hkn.3_Intron|CCNG2_uc011ccc.1_Intron|CCNG2_uc003hkp.3_Intron	NM_004354	NP_004345			cyclin G2						cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3																		---	---	---	---
CCNG2	901	broad.mit.edu	37	4	78082930	78082931	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78082930_78082931insT	uc003hkq.3	+						CCNG2_uc003hkn.3_Intron|CCNG2_uc011ccc.1_Intron|CCNG2_uc003hkp.3_Intron	NM_004354	NP_004345			cyclin G2						cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78326478	78326479	+	IGR	INS	-	TTTG	TTTG	rs147492930	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78326478_78326479insTTTG								CCNG2 (235268 upstream) : CXCL13 (106428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79678012	79678012	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79678012delT								ANXA3 (146410 upstream) : BMP2K (19520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	80482577	80482577	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80482577delA	uc003hlv.2	+											Homo sapiens cDNA FLJ41919 fis, clone PERIC2002272.																														---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81855695	81855696	+	Intron	DEL	TT	-	-	rs7666537	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81855695_81855696delTT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
BMP3	651	broad.mit.edu	37	4	81972331	81972331	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81972331delA	uc003hmg.3	+							NM_001201	NP_001192			bone morphogenetic protein 3 preproprotein						cartilage development|cell differentiation|cell-cell signaling|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(4)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	82284270	82284270	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82284270delA								PRKG2 (148052 upstream) : RASGEF1B (63949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82989139	82989139	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82989139delA								RASGEF1B (596078 upstream) : HNRNPD (285328 downstream)																																			---	---	---	---
HNRNPD	3184	broad.mit.edu	37	4	83280825	83280825	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83280825delA	uc003hmm.1	-						HNRNPD_uc003hml.1_Intron|HNRNPD_uc003hmn.1_Intron|HNRNPD_uc003hmo.1_Intron|HNRNPD_uc003hmp.1_Intron|HNRNPD_uc010ijr.1_Intron|HNRNPD_uc011cci.1_Intron	NM_031370	NP_112738			heterogeneous nuclear ribonucleoprotein D						nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent|RNA catabolic process|transcription, DNA-dependent	cytosol|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|telomeric DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	84867453	84867454	+	Intron	INS	-	AC	AC	rs140149650	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84867453_84867454insAC	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86853871	86853871	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86853871delT	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron|ARHGAP24_uc010ikf.2_Intron|ARHGAP24_uc003hpm.2_Intron	NM_001025616	NP_001020787			Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87694134	87694134	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87694134delA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron|PTPN13_uc003hqc.1_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87705769	87705769	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87705769delA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron|PTPN13_uc003hqc.1_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88605311	88605312	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88605311_88605312delTT								DMP1 (19801 upstream) : IBSP (115390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	88642141	88642141	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88642141delT								DMP1 (56631 upstream) : IBSP (78561 downstream)																																			---	---	---	---
MEPE	56955	broad.mit.edu	37	4	88767362	88767362	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88767362delA	uc003hqy.2	+	4	1381	c.1342delA	c.(1342-1344)AAAfs	p.K448fs	MEPE_uc010ikn.2_Frame_Shift_Del_p.K335fs	NM_020203	NP_064588	Q9NQ76	MEPE_HUMAN	matrix, extracellular phosphoglycoprotein with	448					skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			ovary(1)|lung(1)|skin(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	89243601	89243601	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89243601delA	uc003hro.2	+											Homo sapiens, clone IMAGE:5199401, mRNA.																														---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89397280	89397280	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89397280delT	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407			hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89415297	89415297	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89415297delT	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407			hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	92976855	92976855	+	IGR	DEL	A	-	-	rs34972232		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92976855delA								FAM190A (453486 upstream) : GRID2 (248695 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94358620	94358620	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94358620delT	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94441491	94441491	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94441491delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94495706	94495707	+	Intron	INS	-	AG	AG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94495706_94495707insAG	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	95034103	95034104	+	IGR	INS	-	GAAGTTAT	GAAGTTAT	rs140117274	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95034103_95034104insGAAGTTAT								ATOH1 (282961 upstream) : SMARCAD1 (94655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	95271424	95271425	+	IGR	INS	-	A	A	rs11389169		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95271424_95271425insA								HPGDS (7397 upstream) : PDLIM5 (101613 downstream)																																			---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95508282	95508282	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95508282delT	uc003hti.2	+						PDLIM5_uc003htf.2_3'UTR|PDLIM5_uc003htg.2_3'UTR|PDLIM5_uc011cdx.1_Intron|PDLIM5_uc003hth.2_Intron|PDLIM5_uc003htj.2_Intron|PDLIM5_uc003htk.2_Intron|PDLIM5_uc011cdy.1_Intron|PDLIM5_uc003htl.2_Intron	NM_006457	NP_006448			PDZ and LIM domain 5 isoform a						regulation of dendritic spine morphogenesis|regulation of synaptogenesis	actin cytoskeleton|cell junction|cytosol|postsynaptic density|postsynaptic membrane|synaptosome	actin binding|actinin binding|protein kinase C binding|zinc ion binding			ovary(1)|skin(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)														---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	96032036	96032037	+	Intron	INS	-	A	A	rs144757873	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96032036_96032037insA	uc003htm.3	+						BMPR1B_uc010ilb.2_Intron|BMPR1B_uc003htn.3_Intron	NM_001203	NP_001194			bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	97438784	97438787	+	IGR	DEL	CAAC	-	-	rs35598650		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97438784_97438787delCAAC								PDHA2 (676160 upstream) : None (None downstream)																																			---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98878000	98878000	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98878000delC	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98947473	98947473	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98947473delA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99509544	99509544	+	Intron	DEL	A	-	-	rs77445258		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99509544delA	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	99639387	99639387	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99639387delT								TSPAN5 (59660 upstream) : EIF4E (160220 downstream)																																			---	---	---	---
METAP1	23173	broad.mit.edu	37	4	99960367	99960367	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99960367delT	uc003huf.3	+						METAP1_uc003hug.2_Intron	NM_015143	NP_055958			methionyl aminopeptidase 1						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis|regulation of translation	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)														---	---	---	---
ADH6	130	broad.mit.edu	37	4	100137538	100137538	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100137538delA	uc003hup.3	-						uc003hum.1_Intron|ADH6_uc003huo.2_Intron|ADH6_uc011cef.1_Intron|ADH6_uc010ile.2_Intron	NM_000672	NP_000663			class V alcohol dehydrogenase isoform 2						ethanol oxidation|response to ethanol|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|electron carrier activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)|NADH(DB00157)													---	---	---	---
ADH1C	126	broad.mit.edu	37	4	100258102	100258103	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100258102_100258103insT	uc003huu.2	-							NM_000669	NP_000660			class I alcohol dehydrogenase, gamma subunit						ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
MAPKSP1	8649	broad.mit.edu	37	4	100806896	100806896	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100806896delT	uc003hvg.2	-						MAPKSP1_uc003hvi.2_Intron|MAPKSP1_uc003hvh.2_Intron	NM_021970	NP_068805			MAPK scaffold protein 1						cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	Ragulator complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	100988766	100988767	+	IGR	INS	-	GTGT	GTGT	rs147919362	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100988766_100988767insGTGT								LOC256880 (115146 upstream) : DDIT4L (118262 downstream)																																			---	---	---	---
EMCN	51705	broad.mit.edu	37	4	101337123	101337124	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101337123_101337124insA	uc003hvr.2	-						EMCN_uc011cel.1_Intron|EMCN_uc011cem.1_Intron	NM_016242	NP_057326			endomucin isoform 1							extracellular region|integral to membrane|plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102951572	102951572	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102951572delT	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
NHEDC1	150159	broad.mit.edu	37	4	103897246	103897247	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103897246_103897247insA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912			Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	104335419	104335419	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104335419delA								CENPE (215853 upstream) : TACR3 (175206 downstream)																																			---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106644547	106644547	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106644547delA	uc003hxz.3	+						GSTCD_uc003hxx.2_Intron|GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron|GSTCD_uc010ils.1_Intron	NM_001031720	NP_001026890			glutathione S-transferase, C-terminal domain							cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)														---	---	---	---
DKK2	27123	broad.mit.edu	37	4	108007671	108007672	+	Intron	INS	-	T	T	rs143178197	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108007671_108007672insT	uc010ilw.1	-											Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110412673	110412673	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110412673delA	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314			SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
CASP6	839	broad.mit.edu	37	4	110622281	110622281	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110622281delT	uc003hzn.1	-						CASP6_uc003hzo.1_Intron	NM_001226	NP_001217			caspase 6 isoform alpha preproprotein						cellular component disassembly involved in apoptosis|induction of apoptosis|proteolysis	cytosol|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)|breast(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)														---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113570754	113570754	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113570754delA	uc003iay.2	+	9	1484	c.1206delA	c.(1204-1206)TTAfs	p.L402fs	LARP7_uc003iaz.2_Frame_Shift_Del_p.L409fs|LARP7_uc003iba.2_Frame_Shift_Del_p.L323fs|LARP7_uc003ibb.2_Frame_Shift_Del_p.L402fs|uc011cfy.1_5'Flank|MIR367_hsa-mir-367|MI0000775_5'Flank|MIR302D_hsa-mir-302d|MI0000774_5'Flank|uc011cfz.1_5'Flank|MIR302A_hsa-mir-302a|MI0000738_5'Flank|MIR302C_hsa-mir-302c|MI0000773_5'Flank|MIR302B_hsa-mir-302b|MI0000772_5'Flank|uc011cga.1_5'Flank	NM_016648	NP_057732	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	402					RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114300948	114300948	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114300948delA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Intron|ANK2_uc010imr.2_Intron|ANK2_uc010ims.2_Intron	NM_001148	NP_001139			ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	115277983	115277984	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115277983_115277984delTT								ARSJ (377105 upstream) : UGT8 (241627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115433558	115433558	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115433558delT								ARSJ (532680 upstream) : UGT8 (86053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115714455	115714456	+	IGR	INS	-	A	A	rs139225722	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115714455_115714456insA								UGT8 (116253 upstream) : NDST4 (34475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	116599123	116599123	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116599123delA								NDST4 (564091 upstream) : MIR1973 (621758 downstream)																																			---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119163440	119163441	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119163440_119163441insA	uc003ibx.2	+							NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
MYOZ2	51778	broad.mit.edu	37	4	120064358	120064358	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120064358delT	uc003icp.3	+							NM_016599	NP_057683			myozenin 2								protein phosphatase 2B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	120125285	120125285	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120125285delA	uc011cgi.1	-											SubName: Full=cDNA FLJ40807 fis, clone TRACH2009268;																														---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123166161	123166161	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123166161delT	uc003ieh.2	+						KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	124561525	124561525	+	IGR	DEL	T	-	-	rs79747824		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124561525delT								SPRY1 (236618 upstream) : LOC285419 (9897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125364380	125364380	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125364380delT								LOC285419 (512862 upstream) : ANKRD50 (221088 downstream)																																			---	---	---	---
ANKRD50	57182	broad.mit.edu	37	4	125594671	125594672	+	Intron	INS	-	GCAGCAGTT	GCAGCAGTT	rs147212548	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125594671_125594672insGCAGCAGTT	uc003ifg.3	-						ANKRD50_uc011cgo.1_Intron|ANKRD50_uc010inw.2_Intron	NM_020337	NP_065070			ankyrin repeat domain 50											central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	126079677	126079678	+	IGR	DEL	AA	-	-	rs111658453		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126079677_126079678delAA								ANKRD50 (445790 upstream) : FAT4 (157889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126101888	126101889	+	IGR	INS	-	GGAA	GGAA	rs146889215	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126101888_126101889insGGAA								ANKRD50 (468001 upstream) : FAT4 (135678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126898673	126898673	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126898673delT								MIR2054 (470211 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127123027	127123027	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127123027delC								MIR2054 (694565 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128073072	128073072	+	IGR	DEL	A	-	-	rs5861819		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128073072delA								None (None upstream) : INTU (481048 downstream)																																			---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128724724	128724724	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128724724delT	uc003ifm.2	+						HSPA4L_uc010iny.1_Intron|HSPA4L_uc011cgr.1_Intron	NM_014278	NP_055093			heat shock 70kDa protein 4-like						protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MFSD8	256471	broad.mit.edu	37	4	128863072	128863072	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128863072delA	uc003ifp.2	-						MFSD8_uc011cgu.1_Intron|MFSD8_uc011cgv.1_Intron|MFSD8_uc011cgw.1_Intron|MFSD8_uc011cgx.1_Intron	NM_152778	NP_689991			major facilitator superfamily domain containing						cell death|transmembrane transport	integral to membrane|lysosomal membrane				ovary(1)|liver(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	131118519	131118519	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131118519delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134465924	134465924	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134465924delA								PCDH10 (353193 upstream) : PABPC4L (651567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136025880	136025880	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136025880delT								PABPC4L (902977 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136377885	136377886	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136377885_136377886delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139212475	139212476	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139212475_139212476delAC								SLC7A11 (48972 upstream) : CCRN4L (724467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139377196	139377196	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139377196delA								SLC7A11 (213693 upstream) : CCRN4L (559747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	140149665	140149667	+	IGR	DEL	TTT	-	-	rs10611583		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140149665_140149667delTTT								ELF2 (51293 upstream) : C4orf49 (37650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	140359751	140359751	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140359751delT								NAA15 (47816 upstream) : RAB33B (15210 downstream)																																			---	---	---	---
MAML3	55534	broad.mit.edu	37	4	141043028	141043028	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141043028delG	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187			mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	141375167	141375168	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141375167_141375168delTG	uc003iij.1	-											Homo sapiens similar to RIKEN cDNA 4933434I20, mRNA (cDNA clone IMAGE:5267198).																														---	---	---	---
SMAD1	4086	broad.mit.edu	37	4	146479231	146479232	+	3'UTR	INS	-	A	A	rs34142651		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146479231_146479232insA	uc003ikc.2	+	7					SMAD1_uc003ikd.2_3'UTR|SMAD1_uc010iov.2_3'UTR|SMAD1_uc011cic.1_3'UTR	NM_005900	NP_005891			Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)															OREG0016348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TTC29	83894	broad.mit.edu	37	4	147804088	147804089	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147804088_147804089delCT	uc003ikw.3	-						TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron	NM_031956	NP_114162			tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)																	---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149115867	149115867	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149115867delT	uc003ilj.3	-						NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892			nuclear receptor subfamily 3, group C, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	150089143	150089144	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150089143_150089144delTT								NR3C2 (725500 upstream) : DCLK2 (910936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150802295	150802298	+	IGR	DEL	AAAG	-	-	rs71945875		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150802295_150802298delAAAG								None (None upstream) : DCLK2 (197782 downstream)																																			---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151042223	151042223	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151042223delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350			doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151769931	151769931	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151769931delT	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
TMEM154	201799	broad.mit.edu	37	4	153549791	153549792	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153549791_153549792delTT	uc003imw.1	-							NM_152680	NP_689893			transmembrane protein 154 precursor							integral to membrane					0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	154001424	154001425	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154001424_154001425insC								FHDC1 (100576 upstream) : TRIM2 (72845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154813579	154813579	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154813579delT								SFRP2 (103351 upstream) : DCHS2 (341948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154937824	154937824	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154937824delT								SFRP2 (227596 upstream) : DCHS2 (217703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155427925	155427925	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155427925delT								DCHS2 (14995 upstream) : PLRG1 (29738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155436196	155436196	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155436196delT								DCHS2 (23266 upstream) : PLRG1 (21467 downstream)																																			---	---	---	---
PLRG1	5356	broad.mit.edu	37	4	155470615	155470615	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155470615delA	uc003iny.2	-						PLRG1_uc003inz.2_Intron|PLRG1_uc011cil.1_Intron	NM_002669	NP_002660			pleiotropic regulator 1 (PRL1 homolog,							catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	157895904	157895905	+	IGR	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157895904_157895905insAC								PDGFC (3358 upstream) : GLRB (101372 downstream)																																			---	---	---	---
GRIA2	2891	broad.mit.edu	37	4	158142152	158142152	+	5'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158142152delA	uc003ipm.3	+	1					GRIA2_uc011cit.1_Intron|GRIA2_uc003ipl.3_5'UTR|GRIA2_uc003ipk.3_Intron|GRIA2_uc010iqh.1_5'Flank	NM_001083619	NP_001077088			glutamate receptor, ionotropic, AMPA 2 isoform 2						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	159102823	159102824	+	Intron	INS	-	A	A	rs139248671	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159102823_159102824insA	uc003ipu.1	+						uc003ipv.1_Intron					Homo sapiens cDNA FLJ39473 fis, clone PROST2012890.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	159231364	159231364	+	IGR	DEL	T	-	-	rs112093051		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159231364delT								TMEM144 (54926 upstream) : RXFP1 (211683 downstream)																																			---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160259360	160259361	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160259360_160259361insA	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	161793765	161793765	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161793765delA								None (None upstream) : FSTL5 (511286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	164021251	164021252	+	IGR	DEL	AC	-	-	rs35183384		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164021251_164021252delAC								FSTL5 (936065 upstream) : NAF1 (26608 downstream)																																			---	---	---	---
NPY5R	4889	broad.mit.edu	37	4	164271376	164271377	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164271376_164271377insT	uc003iqn.2	+							NM_006174	NP_006165			neuropeptide Y receptor Y5						cardiac left ventricle morphogenesis|outflow tract morphogenesis	integral to plasma membrane				lung(6)|skin(1)	7	all_hematologic(180;0.166)	Prostate(90;0.109)																---	---	---	---
C4orf43	55319	broad.mit.edu	37	4	164428219	164428219	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164428219delA	uc003iqq.3	+	2	319	c.38delA	c.(37-39)GAAfs	p.E13fs		NM_018352	NP_060822	Q96EY4	CD043_HUMAN	hypothetical protein LOC55319	13											0																		---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164876500	164876500	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164876500delA	uc003iqs.1	-							NM_017923	NP_060393			membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	165778507	165778507	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165778507delC								MARCH1 (473305 upstream) : TRIM61 (97093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	165991220	165991220	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165991220delA								TRIM60 (28324 upstream) : TMEM192 (6011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	166117972	166117973	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166117972_166117973delCA								TMEM192 (83948 upstream) : KLHL2 (10797 downstream)																																			---	---	---	---
CPE	1363	broad.mit.edu	37	4	166353147	166353147	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166353147delA	uc003irg.3	+							NM_001873	NP_001864			carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	166586890	166586891	+	IGR	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166586890_166586891delAT								CPE (167409 upstream) : TLL1 (207519 downstream)																																			---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	167658472	167658472	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167658472delT	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron	NM_016950	NP_058646			testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)														---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	167993486	167993486	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167993486delT	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron|SPOCK3_uc011cjw.1_Intron	NM_016950	NP_058646			testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	168615664	168615665	+	IGR	INS	-	AA	AA	rs149869713	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168615664_168615665insAA								SPOCK3 (459923 upstream) : ANXA10 (398042 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169145281	169145281	+	Intron	DEL	T	-	-	rs76603259		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169145281delT	uc003irp.2	-						DDX60_uc003iro.2_Intron	NM_017631	NP_060101			DEAD (Asp-Glu-Ala-Asp) box polypeptide 60								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169595698	169595701	+	Intron	DEL	AGAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169595698_169595701delAGAA	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	172884407	172884407	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172884407delA	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
GALNT7	51809	broad.mit.edu	37	4	174177663	174177663	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174177663delT	uc003isz.3	+							NM_017423	NP_059119			polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	176020196	176020196	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176020196delA								ADAM29 (120866 upstream) : GPM6A (533893 downstream)																																			---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176895018	176895018	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176895018delT	uc003iug.2	-						GPM6A_uc003iuh.2_Intron	NM_005277	NP_005268			glycoprotein M6A isoform 1							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	177811243	177811244	+	IGR	DEL	TA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177811243_177811244delTA								VEGFC (97348 upstream) : NEIL3 (419747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180421766	180421766	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180421766delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180957054	180957055	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180957054_180957055insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181520509	181520509	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181520509delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182953085	182953085	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182953085delT	uc003iva.1	-											Homo sapiens cDNA FLJ31634 fis, clone NT2RI2003419.																														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183522467	183522467	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183522467delT	uc003ivd.1	+							NM_001080477	NP_001073946			odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183659323	183659323	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183659323delA	uc003ivd.1	+						ODZ3_uc003ive.1_Intron	NM_001080477	NP_001073946			odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183659381	183659381	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183659381delA	uc003ivd.1	+						ODZ3_uc003ive.1_Intron	NM_001080477	NP_001073946			odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	184250557	184250557	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184250557delA								WWC2 (8630 upstream) : CDKN2AIP (115232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184265377	184265377	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184265377delT								WWC2 (23450 upstream) : CDKN2AIP (100412 downstream)																																			---	---	---	---
C4orf41	60684	broad.mit.edu	37	4	184618471	184618471	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184618471delA	uc003ivx.2	+						C4orf41_uc003ivw.2_Intron|C4orf41_uc010isc.2_Intron|C4orf41_uc003ivy.2_Intron	NM_021942	NP_068761			hypothetical protein LOC60684 isoform a												0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)														---	---	---	---
CCDC111	201973	broad.mit.edu	37	4	185578560	185578560	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185578560delA	uc003iwk.2	+						CCDC111_uc010isd.1_Intron|CCDC111_uc003iwj.2_Intron|CCDC111_uc003iwl.2_Intron|CCDC111_uc003iwm.2_Intron|CCDC111_uc003iwn.2_Intron	NM_152683	NP_689896			coiled-coil domain containing 111						DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	185783294	185783295	+	IGR	INS	-	GT	GT	rs141694948	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185783294_185783295insGT								ACSL1 (36079 upstream) : HELT (156700 downstream)																																			---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186244502	186244503	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186244502_186244503delTT	uc003ixh.2	+						SNX25_uc010ish.2_Intron|SNX25_uc003ixi.2_Intron	NM_031953	NP_114159			sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186819030	186819030	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186819030delA	uc003iyl.2	-						SORBS2_uc003iym.2_Intron|SORBS2_uc011cky.1_Intron	NM_021069	NP_066547			sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	187017354	187017354	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187017354delT								TLR3 (11104 upstream) : FAM149A (47861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189426437	189426438	+	Intron	INS	-	T	T	rs67554324		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189426437_189426438insT	uc003izp.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189813734	189813734	+	IGR	DEL	A	-	-	rs74819376		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189813734delA								TRIML1 (745085 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189920092	189920092	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189920092delT								TRIML1 (851443 upstream) : FRG1 (941882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190488619	190488619	+	IGR	DEL	T	-	-	rs71756780		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190488619delT								None (None upstream) : FRG1 (373355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190559616	190559617	+	IGR	DEL	CT	-	-	rs144428514		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190559616_190559617delCT								None (None upstream) : FRG1 (302357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190581868	190581869	+	IGR	INS	-	G	G	rs140449999		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190581868_190581869insG								None (None upstream) : FRG1 (280105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190585243	190585244	+	IGR	INS	-	AGAC	AGAC	rs145767148		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190585243_190585244insAGAC								None (None upstream) : FRG1 (276730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190588073	190588073	+	IGR	DEL	A	-	-	rs71600706		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190588073delA								None (None upstream) : FRG1 (273901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190600955	190600956	+	IGR	DEL	TT	-	-	rs138908875		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190600955_190600956delTT								None (None upstream) : FRG1 (261018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190617712	190617713	+	IGR	INS	-	GAG	GAG	rs138153158		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190617712_190617713insGAG								None (None upstream) : FRG1 (244261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190845907	190845907	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190845907delC	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190895961	190895961	+	IGR	DEL	T	-	-	rs67074602		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190895961delT								FRG1 (11603 upstream) : TUBB4Q (7718 downstream)																																			---	---	---	---
AHRR	57491	broad.mit.edu	37	5	318453	318454	+	Intron	INS	-	C	C	rs138856982	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:318453_318454insC	uc003jav.2	+						AHRR_uc003jaw.2_Intron|AHRR_uc010isy.2_Intron	NM_020731	NP_065782			arylhydrocarbon receptor repressor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)															---	---	---	---
ZDHHC11	79844	broad.mit.edu	37	5	816663	816664	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:816663_816664insA	uc011cma.1	-						ZDHHC11_uc010itc.2_Intron|ZDHHC11_uc003jbj.2_Intron	NM_024786	NP_079062			zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)															---	---	---	---
SLC6A19	340024	broad.mit.edu	37	5	1205878	1205879	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1205878_1205879insA	uc003jbw.3	+							NM_001003841	NP_001003841			solute carrier family 6, member 19						cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)															---	---	---	---
LPCAT1	79888	broad.mit.edu	37	5	1465586	1465587	+	Intron	INS	-	CA	CA	rs144976974	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1465586_1465587insCA	uc003jcm.2	-						LPCAT1_uc003jcl.2_Intron	NM_024830	NP_079106			lysophosphatidylcholine acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	2037451	2037451	+	IGR	DEL	T	-	-	rs72257259		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2037451delT								IRX4 (154571 upstream) : IRX2 (708830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2389931	2389931	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2389931delC								IRX4 (507051 upstream) : IRX2 (356350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2612775	2612775	+	IGR	DEL	A	-	-	rs73735834	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2612775delA								IRX4 (729895 upstream) : IRX2 (133506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3105750	3105754	+	IGR	DEL	AGAGA	-	-	rs140476308		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3105750_3105754delAGAGA								C5orf38 (350238 upstream) : IRX1 (490414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4352369	4352369	+	IGR	DEL	A	-	-	rs261149	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4352369delA								IRX1 (750853 upstream) : LOC340094 (682103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6702468	6702469	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6702468_6702469insA								SRD5A1 (32795 upstream) : PAPD7 (12249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6877981	6877981	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6877981delA								PAPD7 (120820 upstream) : ADCY2 (518362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7045029	7045029	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7045029delT								PAPD7 (287868 upstream) : ADCY2 (351314 downstream)																																			---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7615182	7615183	+	Intron	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7615182_7615183delGA	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7650331	7650332	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7650331_7650332delAC	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	7990044	7990045	+	IGR	DEL	TT	-	-	rs70940774		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7990044_7990045delTT								MTRR (88811 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8222464	8222464	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8222464delA								MTRR (321231 upstream) : SEMA5A (812674 downstream)																																			---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9183196	9183196	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9183196delG	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10107274	10107274	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10107274delA								LOC285692 (203338 upstream) : FAM173B (119164 downstream)																																			---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11131901	11131901	+	Intron	DEL	A	-	-	rs74992743		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11131901delA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11259456	11259456	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11259456delA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	12404860	12404861	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12404860_12404861insT								CTNND2 (500750 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	12887073	12887073	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12887073delT								CTNND2 (982963 upstream) : DNAH5 (803364 downstream)																																			---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13807853	13807853	+	Intron	DEL	A	-	-	rs75973070		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13807853delA	uc003jfd.2	-							NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14210706	14210707	+	Intron	INS	-	T	T	rs149933919	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14210706_14210707insT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14813593	14813593	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14813593delA	uc003jfm.3	-							NM_054027	NP_473368			progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15606401	15606402	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15606401_15606402delCA	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	16249867	16249867	+	IGR	DEL	C	-	-	rs11326912		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16249867delC								MARCH11 (69970 upstream) : ZNF622 (201762 downstream)																																			---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16727305	16727305	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16727305delT	uc003jft.3	-						MYO10_uc011cnd.1_Intron|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16763788	16763789	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16763788_16763789insA	uc003jft.3	-	13	1870_1871	c.1402_1403insT	c.(1402-1404)TCTfs	p.S468fs	MYO10_uc010itx.2_Frame_Shift_Ins_p.S91fs	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	468	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17527122	17527122	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17527122delC	uc011cnf.1	-											DQ583034																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	18490445	18490446	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18490445_18490446delAC								None (None upstream) : CDH18 (982711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18683631	18683631	+	IGR	DEL	A	-	-	rs111682500		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18683631delA								None (None upstream) : CDH18 (789526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18956692	18956693	+	IGR	DEL	TA	-	-	rs28716577	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18956692_18956693delTA								None (None upstream) : CDH18 (516464 downstream)																																			---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19746956	19746957	+	Intron	INS	-	AT	AT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19746956_19746957insAT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19805820	19805820	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19805820delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	20095674	20095675	+	IGR	INS	-	AAGAAAGG	AAGAAAGG	rs59909046		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20095674_20095675insAAGAAAGG								CDH18 (107367 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23491664	23491664	+	IGR	DEL	T	-	-	rs34016337		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23491664delT								CDH12 (637933 upstream) : PRDM9 (16060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25411433	25411434	+	IGR	INS	-	TC	TC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25411433_25411434insTC								CDH10 (766522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26356262	26356263	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26356262_26356263insC								None (None upstream) : CDH9 (524446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27084716	27084716	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27084716delA								CDH9 (46027 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27433684	27433685	+	IGR	INS	-	AC	AC	rs144303245	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27433684_27433685insAC								CDH9 (394995 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28313505	28313505	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28313505delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29106321	29106321	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29106321delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31568832	31568833	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31568832_31568833insA								C5orf22 (13668 upstream) : PDZD2 (70684 downstream)																																			---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31725534	31725534	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31725534delT	uc003jhl.2	+							NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31783500	31783500	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31783500delG	uc003jhl.2	+							NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31941067	31941068	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31941067_31941068insA	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
TARS	6897	broad.mit.edu	37	5	33468174	33468174	+	3'UTR	DEL	A	-	-	rs71801512		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33468174delA	uc003jhy.2	+	19					TARS_uc011cob.1_3'UTR|TARS_uc011coc.1_3'UTR|TARS_uc003jhz.2_3'UTR|TARS_uc011cod.1_3'UTR	NM_152295	NP_689508			threonyl-tRNA synthetase						threonyl-tRNA aminoacylation	cytosol	ATP binding|protein homodimerization activity|threonine-tRNA ligase activity			ovary(2)	2					L-Threonine(DB00156)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	34184889	34184889	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34184889delA								C1QTNF3 (141572 upstream) : RAI14 (471544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34576920	34576921	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34576920_34576921delAA								C1QTNF3 (533603 upstream) : RAI14 (79512 downstream)																																			---	---	---	---
TTC23L	153657	broad.mit.edu	37	5	34861084	34861084	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34861084delT	uc003jiu.2	+							NM_144725	NP_653326			tetratricopeptide repeat domain 23-like								binding			central_nervous_system(1)	1																		---	---	---	---
PRLR	5618	broad.mit.edu	37	5	35066375	35066375	+	Intron	DEL	T	-	-	rs77557478		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35066375delT	uc003jjm.2	-						PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron	NM_000949	NP_000940			prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35664381	35664386	+	Intron	DEL	AAAAAA	-	-	rs34622548		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35664381_35664386delAAAAAA	uc003jjo.2	+						SPEF2_uc003jjn.1_Intron|SPEF2_uc003jjq.3_Intron	NM_024867	NP_079143			KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
IL7R	3575	broad.mit.edu	37	5	35875697	35875697	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35875697delT	uc003jjs.2	+						IL7R_uc011coo.1_3'UTR|IL7R_uc011cop.1_Intron	NM_002185	NP_002176			interleukin 7 receptor precursor						immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	36433367	36433368	+	IGR	DEL	TG	-	-	rs144054085		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36433367_36433368delTG								RANBP3L (131356 upstream) : SLC1A3 (173089 downstream)																																			---	---	---	---
SLC1A3	6507	broad.mit.edu	37	5	36611936	36611937	+	Intron	INS	-	C	C	rs140356644	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36611936_36611937insC	uc003jkj.3	+						SLC1A3_uc011cox.1_Intron|SLC1A3_uc010iuy.2_Intron	NM_004172	NP_004163			solute carrier family 1 (glial high affinity						D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)													---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37045454	37045454	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37045454delA	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677			delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37120153	37120153	+	Intron	DEL	A	-	-	rs75040582	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120153delA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|C5orf42_uc003jkp.1_Intron|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)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37148318	37148319	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37148318_37148319insT	uc011cpa.1	-	42	8494_8495	c.8263_8264insA	c.(8263-8265)ACAfs	p.T2755fs	C5orf42_uc003jkp.1_RNA|C5orf42_uc011coy.1_Frame_Shift_Ins_p.T1273fs|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Frame_Shift_Ins_p.T1848fs	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	2755										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)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37180363	37180363	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37180363delT	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)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37371440	37371440	+	5'Flank	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37371440delG	uc003jku.1	-						NUP155_uc003jkt.1_5'Flank|NUP155_uc010iuz.1_5'Flank	NM_153485	NP_705618			nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37430977	37430977	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37430977delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	37784427	37784427	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37784427delT								WDR70 (31655 upstream) : GDNF (31327 downstream)																																			---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38326759	38326760	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38326759_38326760insT	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616			EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
OSMR	9180	broad.mit.edu	37	5	38903971	38903971	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38903971delT	uc003jln.1	+							NM_003999	NP_003990			oncostatin M receptor precursor						cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)																	---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38978759	38978759	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38978759delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron	NM_152756	NP_689969			rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)																	---	---	---	---
FYB	2533	broad.mit.edu	37	5	39215566	39215566	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39215566delT	uc011cpl.1	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron	NM_001465	NP_001456			FYN binding protein (FYB-120/130) isoform 1						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
C9	735	broad.mit.edu	37	5	39343037	39343037	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39343037delA	uc003jlv.3	-							NM_001737	NP_001728			complement component 9 precursor						complement activation, alternative pathway|complement activation, classical pathway|cytolysis|hemolysis by symbiont of host erythrocytes	extracellular region|membrane attack complex					0	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)															---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41033968	41033969	+	Splice_Site	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41033968_41033969insA	uc003jmj.3	-	22	2705	c.2215_splice	c.e22-1	p.V739_splice	HEATR7B2_uc003jmi.3_Splice_Site_p.V294_splice	NM_173489	NP_775760			HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
C6	729	broad.mit.edu	37	5	41181560	41181560	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41181560delC	uc003jmk.2	-	7	1038	c.828delG	c.(826-828)GGGfs	p.G276fs	C6_uc003jml.1_Frame_Shift_Del_p.G276fs	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	276	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	41562538	41562539	+	IGR	INS	-	A	A	rs144247459	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41562538_41562539insA								PLCXD3 (51808 upstream) : OXCT1 (167629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	41971308	41971311	+	IGR	DEL	GTGT	-	-	rs142063040		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41971308_41971311delGTGT								FBXO4 (29645 upstream) : GHR (452715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	43001529	43001529	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43001529delT								SEPP1 (175531 upstream) : C5orf39 (37654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	43071890	43071890	+	Intron	DEL	T	-	-	rs68155609		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43071890delT	uc010ivk.2	+											Homo sapiens cDNA, FLJ18440.																														---	---	---	---
NNT	23530	broad.mit.edu	37	5	43666736	43666736	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43666736delT	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
NNT	23530	broad.mit.edu	37	5	43683907	43683907	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43683907delT	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45263458	45263459	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45263458_45263459delAA	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	46398042	46398042	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46398042delT								HCN1 (701822 upstream) : None (None downstream)																																			---	---	---	---
ITGA1	3672	broad.mit.edu	37	5	52177359	52177360	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52177359_52177360delTC	uc003jou.2	+						ITGA1_uc003jov.2_Intron	NM_181501	NP_852478			integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)																---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53515412	53515413	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53515412_53515413insT	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	53654171	53654171	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53654171delA								ARL15 (47768 upstream) : HSPB3 (97274 downstream)																																			---	---	---	---
IL31RA	133396	broad.mit.edu	37	5	55147283	55147283	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55147283delA	uc003jql.2	+						IL31RA_uc003jqk.2_5'Flank|IL31RA_uc011cqj.1_5'Flank|IL31RA_uc003jqm.2_5'Flank|IL31RA_uc003jqn.2_5'Flank|IL31RA_uc010iwa.1_5'Flank|IL31RA_uc003jqo.2_5'Flank	NM_139017	NP_620586			gp130-like monocyte receptor						anti-apoptosis|defense response|homeostatic process|JAK-STAT cascade|macrophage differentiation|MAPKKK cascade|monocyte differentiation|negative regulation of macrophage activation|positive regulation of cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|plasma membrane	cytokine receptor activity|protein kinase binding|transcription coactivator activity			ovary(1)	1		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)																---	---	---	---
ANKRD55	79722	broad.mit.edu	37	5	55396383	55396384	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55396383_55396384delTG	uc003jqu.2	-						ANKRD55_uc003jqt.2_Intron	NM_024669	NP_078945			ankyrin repeat domain 55 isoform 1											skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)																---	---	---	---
ANKRD55	79722	broad.mit.edu	37	5	55466398	55466398	+	Intron	DEL	A	-	-	rs34684342		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55466398delA	uc003jqu.2	-							NM_024669	NP_078945			ankyrin repeat domain 55 isoform 1											skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	56436986	56436987	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56436986_56436987delTG								MIER3 (169485 upstream) : GPBP1 (32788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56854071	56854072	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56854071_56854072delGA								ACTBL2 (75435 upstream) : PLK2 (895740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57740742	57740742	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57740742delA								ACTBL2 (962106 upstream) : PLK2 (9070 downstream)																																			---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	58635776	58635776	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58635776delA	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron|PDE4D_uc003jrw.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59028220	59028221	+	Intron	INS	-	CACA	CACA	rs147635311	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59028220_59028221insCACA	uc003jsa.2	-						PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59182750	59182750	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59182750delA	uc003jsa.2	-						PDE4D_uc003jsb.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59764444	59764444	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59764444delT	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	60451369	60451369	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60451369delA								NDUFAF2 (2506 upstream) : C5orf43 (2167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	60874382	60874382	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60874382delT								ZSWIM6 (32384 upstream) : FLJ37543 (59254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	62222641	62222642	+	IGR	DEL	GT	-	-	rs112639156		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62222641_62222642delGT								ISCA1P1 (149471 upstream) : None (None downstream)																																			---	---	---	---
CWC27	10283	broad.mit.edu	37	5	64305480	64305481	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64305480_64305481delCT	uc003jtn.1	+						CWC27_uc010iwt.1_Intron	NM_005869	NP_005860			serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64466698	64466698	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64466698delT	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64695351	64695351	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64695351delT	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron|ADAMTS6_uc003jtr.1_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64707337	64707337	+	Intron	DEL	T	-	-	rs140796974	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64707337delT	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron|ADAMTS6_uc003jtr.1_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
C5orf44	80006	broad.mit.edu	37	5	64942853	64942854	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64942853_64942854delTT	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217			hypothetical protein LOC80006 isoform 2											ovary(1)	1																		---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66276808	66276808	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66276808delT	uc003jut.1	+						MAST4_uc003jur.3_Intron|MAST4_uc010iwz.2_Intron|MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66300755	66300755	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66300755delT	uc003jut.1	+						MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc010ixa.2_RNA|MAST4_uc003juv.2_5'UTR|MAST4_uc003juw.2_5'Flank	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	66531588	66531589	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66531588_66531589delAC								CD180 (38971 upstream) : PIK3R1 (980015 downstream)														p.0?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	5	67634077	67634077	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67634077delC								PIK3R1 (36430 upstream) : SLC30A5 (755741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67761904	67761904	+	IGR	DEL	T	-	-	rs12516964		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67761904delT								PIK3R1 (164257 upstream) : SLC30A5 (627914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67878160	67878160	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67878160delA								PIK3R1 (280513 upstream) : SLC30A5 (511658 downstream)																																			---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69717512	69717512	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69717512delG	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron|GTF2H2B_uc003jza.3_Intron|GTF2H2B_uc003jzd.1_5'Flank	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69730715	69730715	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69730715delT	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
NAIP	4671	broad.mit.edu	37	5	70357180	70357180	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70357180delC	uc003kat.1	-						GTF2H2_uc003kav.3_Intron|GTF2H2_uc003kau.3_Intron|GTF2H2_uc011crt.1_Intron|GTF2H2_uc003kay.1_Intron|GTF2H2_uc003kaz.2_Intron	NM_022892	NP_075043			NLR family, apoptosis inhibitory protein isoform						anti-apoptosis|apoptosis|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70820157	70820157	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70820157delT	uc003kbp.1	+						BDP1_uc003kbo.2_Intron|BDP1_uc003kbq.1_Intron	NM_018429	NP_060899			transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)														---	---	---	---
MCCC2	64087	broad.mit.edu	37	5	70952822	70952822	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70952822delA	uc003kbs.3	+	17					MCCC2_uc003kbt.3_RNA	NM_022132	NP_071415			methylcrotonoyl-Coenzyme A carboxylase 2 (beta)						leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)													---	---	---	---
ZNF366	167465	broad.mit.edu	37	5	71769494	71769495	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71769494_71769495insT	uc003kce.1	-							NM_152625	NP_689838			zinc finger protein 366						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72608740	72608741	+	IGR	INS	-	CTC	CTC	rs141809889	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72608740_72608741insCTC								TMEM174 (137772 upstream) : FOXD1 (133346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72637726	72637727	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72637726_72637727delAA								TMEM174 (166758 upstream) : FOXD1 (104360 downstream)																																			---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73030257	73030258	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73030257_73030258insG	uc011csq.1	+						RGNEF_uc003kcx.2_Intron|RGNEF_uc003kcy.1_Intron|RGNEF_uc010izf.2_Intron	NM_001080479	NP_001073948			Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	73844898	73844898	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73844898delA								RGNEF (607485 upstream) : ENC1 (78337 downstream)																																			---	---	---	---
HEXB	3074	broad.mit.edu	37	5	73993176	73993178	+	Intron	DEL	AGA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73993176_73993178delAGA	uc003kdf.3	+						HEXB_uc003kdd.2_Intron|HEXB_uc003kde.2_Intron|HEXB_uc010izh.2_Intron	NM_000521	NP_000512			hexosaminidase B preproprotein						cell death	lysosome	cation binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)														---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74135799	74135799	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74135799delA	uc003kdm.2	-						FAM169A_uc010izm.2_Intron|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74184200	74184200	+	Intron	DEL	A	-	-	rs71962816		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74184200delA	uc010izm.2	-							NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
COL4A3BP	10087	broad.mit.edu	37	5	74675414	74675414	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74675414delT	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704			alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)														---	---	---	---
COL4A3BP	10087	broad.mit.edu	37	5	74754819	74754819	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74754819delT	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704			alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)														---	---	---	---
POLK	51426	broad.mit.edu	37	5	74879036	74879036	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74879036delT	uc003kdw.2	+						POLK_uc003kdx.2_Intron|POLK_uc003kdy.2_Intron|POLK_uc003keb.2_Intron|POLK_uc010izq.2_Intron|POLK_uc003kec.2_Intron|POLK_uc010izr.2_Intron|POLK_uc010izs.2_Intron|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron|POLK_uc003kef.2_Intron	NM_016218	NP_057302			DNA-directed DNA polymerase kappa						DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	5	75674871	75674871	+	IGR	DEL	C	-	-	rs114478151		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75674871delC								SV2C (53455 upstream) : IQGAP2 (24278 downstream)																																			---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75795980	75795980	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75795980delA	uc003kek.2	+							NM_006633	NP_006624			IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	77177753	77177753	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77177753delA								TBCA (105568 upstream) : AP3B1 (120398 downstream)																																			---	---	---	---
DMGDH	29958	broad.mit.edu	37	5	78347091	78347091	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78347091delA	uc003kfs.2	-						DMGDH_uc011cte.1_Intron|DMGDH_uc011ctf.1_Intron|DMGDH_uc011ctg.1_Intron	NM_013391	NP_037523			dimethylglycine dehydrogenase precursor						choline metabolic process|glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|dimethylglycine dehydrogenase activity|electron carrier activity			ovary(2)|liver(1)|skin(1)	4		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)														---	---	---	---
PAPD4	167153	broad.mit.edu	37	5	78936848	78936849	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78936848_78936849delTT	uc010jae.1	+						PAPD4_uc003kgb.2_Intron|PAPD4_uc010jaf.1_Intron|PAPD4_uc003kga.2_Intron|PAPD4_uc003kfz.2_Intron	NM_001114393	NP_001107865			PAP associated domain containing 4						histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79209122	79209122	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79209122delA								CMYA5 (113074 upstream) : MTX3 (63419 downstream)																																			---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79809324	79809324	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79809324delT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111			hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81139203	81139203	+	IGR	DEL	A	-	-	rs58197261		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81139203delA								SSBP2 (92131 upstream) : ATG10 (128641 downstream)																																			---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81463888	81463889	+	Intron	INS	-	T	T	rs148617168	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81463888_81463889insT	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81484628	81484628	+	Intron	DEL	T	-	-	rs75961266		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81484628delT	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81539134	81539134	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81539134delA	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81614226	81614226	+	IGR	DEL	A	-	-	rs71756795		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81614226delA								ATP6AP1L (80 upstream) : TMEM167A (734441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81816617	81816617	+	IGR	DEL	A	-	-	rs66515521		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81816617delA								ATP6AP1L (202471 upstream) : TMEM167A (532050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	82061527	82061528	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82061527_82061528delGA								ATP6AP1L (447381 upstream) : TMEM167A (287139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	83121281	83121282	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83121281_83121282delTG								HAPLN1 (104385 upstream) : EDIL3 (116844 downstream)																																			---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83546141	83546142	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83546141_83546142delAG	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702			EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	84754136	84754136	+	IGR	DEL	T	-	-	rs74626528		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84754136delT								None (None upstream) : NBPF22P (824126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85727456	85727456	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85727456delA								NBPF22P (134094 upstream) : COX7C (186328 downstream)																																			---	---	---	---
COX7C	1350	broad.mit.edu	37	5	85913794	85913794	+	5'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85913794delA	uc003kir.2	+	1						NM_001867	NP_001858			cytochrome c oxidase subunit VIIc precursor						respiratory electron transport chain	integral to membrane|mitochondrial inner membrane	cytochrome-c oxidase activity				0		all_cancers(142;7e-06)|Lung NSC(167;0.000601)|all_lung(232;0.000693)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;1.56e-40)|Epithelial(54;3.17e-34)|all cancers(79;3.36e-29)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90173280	90173280	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90173280delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	90470176	90470176	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90470176delA								GPR98 (10144 upstream) : ARRDC3 (194365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	90939488	90939489	+	IGR	DEL	TG	-	-	rs33929105		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90939488_90939489delTG								LOC100129716 (222957 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91235663	91235664	+	IGR	DEL	CA	-	-	rs72432484		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91235663_91235664delCA								LOC100129716 (519132 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92097428	92097428	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92097428delA								None (None upstream) : FLJ42709 (647637 downstream)																																			---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94222578	94222579	+	Intron	DEL	GT	-	-	rs141189125	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94222578_94222579delGT	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kkz.2_Intron|MCTP1_uc003kku.2_Intron	NM_024717	NP_078993			multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)														---	---	---	---
CAST	831	broad.mit.edu	37	5	96082019	96082019	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96082019delT	uc003klz.1	+						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc011cuq.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron|CAST_uc003kmh.2_Intron|CAST_uc010jbj.2_Intron|CAST_uc010jbk.2_Intron|CAST_uc010jbl.1_Intron|CAST_uc003kmi.2_Intron|CAST_uc003kmj.2_Intron	NM_001042443	NP_001035908			calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)														---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96124323	96124323	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96124323delA	uc003kmm.2	-	11	1937	c.1590delT	c.(1588-1590)TTTfs	p.F530fs	ERAP1_uc003kml.2_Frame_Shift_Del_p.F530fs|ERAP1_uc010jbm.1_Frame_Shift_Del_p.F342fs|ERAP1_uc003kmn.2_Frame_Shift_Del_p.F530fs	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding	530	Lumenal (Potential).				angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	97628800	97628800	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97628800delA								None (None upstream) : RGMB (476199 downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98219783	98219783	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98219783delT	uc003knf.2	-							NM_001270	NP_001261			chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98228483	98228483	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98228483delT	uc003knf.2	-							NM_001270	NP_001261			chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	100941383	100941384	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100941383_100941384delAC								ST8SIA4 (702396 upstream) : SLCO4C1 (628310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101186071	101186072	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101186071_101186072insT								ST8SIA4 (947084 upstream) : SLCO4C1 (383622 downstream)																																			---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107270770	107270770	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107270770delT	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108133721	108133722	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108133721_108133722delTT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108575249	108575249	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108575249delA								FER (51876 upstream) : PJA2 (95162 downstream)																																			---	---	---	---
PJA2	9867	broad.mit.edu	37	5	108673064	108673064	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108673064delA	uc003kos.3	-							NM_014819	NP_055634			praja 2, RING-H2 motif containing						long-term memory|regulation of protein kinase A signaling cascade	cell junction|endoplasmic reticulum membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	ligase activity|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)														---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109155837	109155837	+	Intron	DEL	A	-	-	rs41295843	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109155837delA	uc003kou.1	+							NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	109229677	109229678	+	IGR	INS	-	CACACA	CACACA	rs138956447	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109229677_109229678insCACACA								MAN2A1 (26248 upstream) : TMEM232 (395256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110159925	110159925	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110159925delC								SLC25A46 (61443 upstream) : TSLP (245853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110470573	110470573	+	IGR	DEL	A	-	-	rs71741258		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110470573delA								WDR36 (4372 upstream) : CAMK4 (89075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	111476561	111476561	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111476561delA								C5orf13 (163933 upstream) : EPB41L4A (1577 downstream)																																			---	---	---	---
APC	324	broad.mit.edu	37	5	112090529	112090529	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112090529delT	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron	NM_001127511	NP_001120983			adenomatous polyposis coli						canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity			large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)			12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	112836088	112836088	+	IGR	DEL	T	-	-	rs113985458		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112836088delT								MCC (11561 upstream) : YTHDC2 (13322 downstream)																																			---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112884516	112884517	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112884516_112884517insT	uc003kqn.2	+						YTHDC2_uc010jce.1_Intron|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739			YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	115106723	115106723	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115106723delA								TMED7-TICAM2 (144853 upstream) : CDO1 (33709 downstream)																																			---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115822792	115822792	+	Intron	DEL	A	-	-	rs111384042		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115822792delA	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847			sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	116275138	116275138	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116275138delG								SEMA6A (364587 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116305313	116305313	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116305313delA								SEMA6A (394762 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117804301	117804301	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117804301delA								None (None upstream) : DTWD2 (368270 downstream)																																			---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118310505	118310505	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118310505delA	uc003ksa.2	-							NM_173666	NP_775937			DTW domain containing 2												0		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)														---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118445836	118445836	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118445836delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc003ksc.1_Intron	NM_005509	NP_005500			Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	118926110	118926110	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118926110delA								HSD17B4 (48083 upstream) : FAM170A (39144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120292948	120292948	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120292948delT								PRR16 (269986 upstream) : FTMT (894702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121160905	121160905	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121160905delT								None (None upstream) : FTMT (26745 downstream)																																			---	---	---	---
SNX24	28966	broad.mit.edu	37	5	122322201	122322201	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122322201delT	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754			SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	122346905	122346905	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122346905delA								SNX24 (2004 upstream) : PPIC (12175 downstream)																																			---	---	---	---
PRDM6	93166	broad.mit.edu	37	5	122523286	122523286	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122523286delT	uc003kti.2	+	8					PRDM6_uc003ktj.2_RNA	NM_001136239	NP_001129711			PR domain containing 6						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	122572158	122572159	+	IGR	DEL	TT	-	-	rs35571960		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122572158_122572159delTT								PRDM6 (48414 upstream) : CEP120 (108421 downstream)																																			---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122930883	122930883	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122930883delT	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Intron	NM_004384	NP_004375			casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	123830498	123830498	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123830498delA								CSNK1G3 (878036 upstream) : ZNF608 (142112 downstream)																																			---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125813245	125813245	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125813245delT	uc003ktu.2	+						GRAMD3_uc011cwt.1_Intron|GRAMD3_uc011cwv.1_Intron|GRAMD3_uc011cww.1_Intron|GRAMD3_uc011cwx.1_Intron|GRAMD3_uc011cwy.1_Intron|GRAMD3_uc011cwz.1_Intron|GRAMD3_uc011cwu.1_Intron	NM_023927	NP_076416			GRAM domain containing 3 isoform 2											central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
LMNB1	4001	broad.mit.edu	37	5	126168356	126168356	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126168356delT	uc003kud.1	+						LMNB1_uc010jdb.1_Intron|LMNB1_uc011cxb.1_Intron	NM_005573	NP_005564			lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	126436136	126436136	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126436136delT								FLJ44606 (26964 upstream) : MEGF10 (190320 downstream)																																			---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126691007	126691007	+	Intron	DEL	A	-	-	rs78858205		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126691007delA	uc003kuh.3	+						MEGF10_uc010jdc.1_Intron|MEGF10_uc010jdd.1_Intron|MEGF10_uc003kui.3_Intron	NM_032446	NP_115822			multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)														---	---	---	---
PRRC1	133619	broad.mit.edu	37	5	126866120	126866120	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126866120delT	uc003kuk.2	+						PRRC1_uc003kuj.3_Intron	NM_130809	NP_570721			proline-rich coiled-coil 1							Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)														---	---	---	---
SLC12A2	6558	broad.mit.edu	37	5	127474214	127474215	+	Intron	INS	-	TA	TA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127474214_127474215insTA	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron	NM_001046	NP_001037			solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127641136	127641137	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127641136_127641137insT	uc003kuu.2	-							NM_001999	NP_001990			fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	129756603	129756603	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129756603delA								CHSY3 (234277 upstream) : HINT1 (738272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130111524	130111525	+	IGR	DEL	GC	-	-	rs113219080	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130111524_130111525delGC								CHSY3 (589198 upstream) : HINT1 (383350 downstream)																																			---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130764956	130764956	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130764956delA	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvm.1_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	131382160	131382162	+	IGR	DEL	AAA	-	-	rs112635535		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131382160_131382162delAAA								ACSL6 (34290 upstream) : IL3 (14185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	131581827	131581828	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131581827_131581828delAG								P4HA2 (18271 upstream) : PDLIM4 (11523 downstream)																																			---	---	---	---
KIF3A	11127	broad.mit.edu	37	5	132035887	132035887	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132035887delT	uc003kxo.2	-						KIF3A_uc003kxm.2_Intron|KIF3A_uc003kxn.2_Intron|KIF3A_uc011cxf.1_Intron|KIF3A_uc003kxp.2_Intron	NM_007054	NP_008985			kinesin family member 3A						blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132259064	132259065	+	Intron	DEL	GA	-	-	rs150967298		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132259064_132259065delGA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron	NM_014423	NP_055238			ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	132443349	132443350	+	IGR	INS	-	TT	TT	rs147683224	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132443349_132443350insTT								HSPA4 (2641 upstream) : FSTL4 (88802 downstream)																																			---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137509232	137509233	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137509232_137509233delAC	uc003lcf.1	-						BRD8_uc003lcc.1_Intron|BRD8_uc003lcg.2_Intron|BRD8_uc003lci.2_Intron|BRD8_uc003lch.2_Intron|BRD8_uc011cym.1_Intron|BRD8_uc010jer.1_Intron|BRD8_uc011cyn.1_Intron|BRD8_uc010jes.1_Intron	NM_139199	NP_631938			bromodomain containing 8 isoform 2						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)															---	---	---	---
GFRA3	2676	broad.mit.edu	37	5	137596456	137596456	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137596456delA	uc003lcn.2	-						GFRA3_uc003lco.2_Intron	NM_001496	NP_001487			GDNF family receptor alpha 3 preproprotein						peripheral nervous system development	anchored to membrane|cytoplasm|extrinsic to membrane|intracellular membrane-bounded organelle	receptor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
SIL1	64374	broad.mit.edu	37	5	138303459	138303459	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138303459delC	uc003ldm.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron|SIL1_uc003ldq.1_Intron	NM_022464	NP_071909			SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											Marinesco-Sj_gren_syndrome				---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139214524	139214525	+	Intron	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139214524_139214525delAT	uc003leu.1	+							NM_032289	NP_115665			pleckstrin and Sec7 domain containing 2						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139862299	139862299	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139862299delA	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfv.1_5'Flank	NM_020690	NP_065741			ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139876029	139876029	+	Intron	DEL	T	-	-	rs11370973		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139876029delT	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfv.1_Intron	NM_020690	NP_065741			ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139905676	139905676	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139905676delA	uc003lfs.1	+	26	4712	c.4588delA	c.(4588-4590)AAAfs	p.K1530fs	ANKHD1_uc003lfr.2_Frame_Shift_Del_p.K1530fs|ANKHD1_uc003lfu.1_Frame_Shift_Del_p.K1010fs|ANKHD1-EIF4EBP3_uc011czh.1_Frame_Shift_Del_p.K269fs|ANKHD1_uc003lfw.2_Frame_Shift_Del_p.K168fs|ANKHD1_uc010jfl.2_5'UTR|ANKHD1-EIF4EBP3_uc003lfx.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1530						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA5	56143	broad.mit.edu	37	5	140203783	140203783	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140203783delT	uc003lhl.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhj.1_Frame_Shift_Del_p.L808fs	NM_018908	NP_061731			protocadherin alpha 5 isoform 1 precursor						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHAC1	56135	broad.mit.edu	37	5	140318462	140318463	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140318462_140318463delAC	uc003lih.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron	NM_018898	NP_061721			protocadherin alpha subfamily C, 1 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA10	56106	broad.mit.edu	37	5	140859981	140859982	+	Intron	INS	-	A	A	rs113700481		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140859981_140859982insA	uc003lkl.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron	NM_018913	NP_061736			protocadherin gamma subfamily A, 10 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140972055	140972057	+	Intron	DEL	AAC	-	-	rs34501176		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140972055_140972057delAAC	uc003llb.3	-						DIAPH1_uc003llc.3_Intron	NM_005219	NP_005210			diaphanous 1 isoform 1						regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	141072435	141072436	+	IGR	INS	-	T	T	rs72541253		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141072435_141072436insT								ARAP3 (10635 upstream) : PCDH1 (160247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	141596278	141596279	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141596278_141596279insG								NDFIP1 (62272 upstream) : SPRY4 (93713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	141686478	141686479	+	IGR	INS	-	AA	AA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141686478_141686479insAA								NDFIP1 (152472 upstream) : SPRY4 (3513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	141721194	141721195	+	IGR	INS	-	A	A	rs150811845	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141721194_141721195insA								SPRY4 (16574 upstream) : FGF1 (250549 downstream)																																			---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142245601	142245601	+	Intron	DEL	T	-	-	rs10535734		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142245601delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron|uc003lmv.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	143265900	143265901	+	IGR	DEL	AA	-	-	rs11311980		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143265900_143265901delAA								HMHB1 (65618 upstream) : YIPF5 (271830 downstream)																																			---	---	---	---
STK32A	202374	broad.mit.edu	37	5	146742488	146742488	+	Intron	DEL	T	-	-	rs34446286		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146742488delT	uc010jgn.1	+						STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195			serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	146914213	146914213	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146914213delT								DPYSL3 (24789 upstream) : JAKMIP2 (56493 downstream)																																			---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147030211	147030211	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147030211delA	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron|uc003lop.1_Intron|JAKMIP2_uc010jgo.1_Intron	NM_014790	NP_055605			janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147486959	147486959	+	Intron	DEL	T	-	-	rs11951425		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147486959delT	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837			serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SPINK14	408187	broad.mit.edu	37	5	147550587	147550587	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147550587delT	uc003loz.1	+							NM_001001325	NP_001001325			Kazal type serine protease inhibitor 5-like 2							extracellular region	serine-type endopeptidase inhibitor activity				0																		---	---	---	---
ADRB2	154	broad.mit.edu	37	5	148207778	148207778	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148207778delT	uc003lpr.1	+	1					SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015			adrenergic, beta-2-, receptor, surface						activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)													---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148260277	148260277	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148260277delA	uc003lpp.1	-							NM_024577				SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ABLIM3	22885	broad.mit.edu	37	5	148541476	148541477	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148541476_148541477delTG	uc003lpy.2	+						ABLIM3_uc003lpz.1_Intron|ABLIM3_uc003lqa.1_Intron|ABLIM3_uc003lqb.2_Intron|ABLIM3_uc003lqc.1_Intron|ABLIM3_uc003lqd.1_Intron|ABLIM3_uc003lqf.2_Intron|ABLIM3_uc003lqe.1_Intron	NM_014945	NP_055760			actin binding LIM protein family, member 3						axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
CSNK1A1	1452	broad.mit.edu	37	5	148924898	148924898	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148924898delG	uc003lqx.1	-						CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883			casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)														---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150800814	150800814	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150800814delT	uc011dcs.1	+							NM_000405				GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GM2A	2760	broad.mit.edu	37	5	151040004	151040004	+	Intron	DEL	A	-	-	rs6894313	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151040004delA	uc011dcs.1	+							NM_000405				GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	151359878	151359878	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151359878delT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	153221960	153221960	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153221960delT								GRIA1 (28532 upstream) : FAM114A2 (149311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	153241675	153241676	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153241675_153241676delAA								GRIA1 (48247 upstream) : FAM114A2 (129595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	153847967	153847967	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153847967delT								SAP30L (7355 upstream) : HAND1 (6566 downstream)																																			---	---	---	---
C5orf4	10826	broad.mit.edu	37	5	154216217	154216217	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154216217delT	uc003lvs.3	-						C5orf4_uc011dde.1_Intron	NM_032385	NP_115761			hypothetical protein LOC10826						fatty acid biosynthetic process	integral to membrane	iron ion binding|oxidoreductase activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	155093311	155093311	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155093311delT								KIF4B (695626 upstream) : SGCD (41752 downstream)																																			---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155935513	155935514	+	Intron	DEL	AA	-	-	rs111768881		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155935513_155935514delAA	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	156182463	156182463	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156182463delA	uc003lwd.3	+						SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
TIMD4	91937	broad.mit.edu	37	5	156381896	156381896	+	Intron	DEL	T	-	-	rs71922795		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381896delT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388			T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	156688190	156688190	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156688190delA								ITK (6081 upstream) : CYFIP2 (4901 downstream)																																			---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156749861	156749862	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156749861_156749862delTC	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SOX30	11063	broad.mit.edu	37	5	157053272	157053272	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157053272delT	uc003lxb.1	-	5					SOX30_uc003lxc.1_3'UTR|SOX30_uc011dds.1_3'UTR	NM_178424	NP_848511			SRY (sex determining region Y)-box 30 isoform a						regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	159052638	159052639	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159052638_159052639insT								LOC285627 (159354 upstream) : ADRA1B (291101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159214662	159214662	+	IGR	DEL	T	-	-	rs75291550		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159214662delT								LOC285627 (321378 upstream) : ADRA1B (129078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159231376	159231376	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159231376delA								LOC285627 (338092 upstream) : ADRA1B (112364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159932950	159932950	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159932950delC								MIR146A (20493 upstream) : ATP10B (57177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159942586	159942586	+	IGR	DEL	A	-	-	rs11287387		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159942586delA								MIR146A (30129 upstream) : ATP10B (47541 downstream)																																			---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160265656	160265656	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160265656delA	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron	NM_025153	NP_079429			ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	160332894	160332894	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160332894delA								ATP10B (53675 upstream) : LOC285629 (25894 downstream)																																			---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160899415	160899416	+	Intron	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160899415_160899416insAC	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron|GABRB2_uc011dei.1_Intron	NM_021911	NP_068711			gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160919570	160919571	+	Intron	INS	-	TGTG	TGTG	rs138951319	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160919570_160919571insTGTG	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron|GABRB2_uc011dei.1_Intron	NM_021911	NP_068711			gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	161661056	161661056	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161661056delT								GABRG2 (78512 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162848893	162848893	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162848893delT								None (None upstream) : CCNG1 (15684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163217526	163217526	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163217526delT								MAT2B (271193 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164050678	164050678	+	IGR	DEL	A	-	-	rs113462804		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164050678delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165606975	165606975	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165606975delA								None (None upstream) : None (None downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167654814	167654814	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167654814delA	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167820121	167820121	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167820121delA	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053			WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	168892116	168892116	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168892116delA								SLIT3 (163983 upstream) : CCDC99 (118522 downstream)																																			---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169382395	169382396	+	Intron	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169382395_169382396delGA	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|FAM196B_uc003mag.2_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
LCP2	3937	broad.mit.edu	37	5	169677853	169677853	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169677853delT	uc003man.1	-	20	1567	c.1360delA	c.(1360-1362)ACAfs	p.T454fs	C5orf58_uc003mal.2_Intron|LCP2_uc011des.1_Frame_Shift_Del_p.T249fs|LCP2_uc011det.1_Frame_Shift_Del_p.T283fs	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	454	SH2.				immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	170801518	170801518	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170801518delA								TLX3 (62381 upstream) : NPM1 (12602 downstream)																																			---	---	---	---
STK10	6793	broad.mit.edu	37	5	171511675	171511675	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171511675delT	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
STK10	6793	broad.mit.edu	37	5	171587479	171587480	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171587479_171587480delAA	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	171621408	171621409	+	IGR	INS	-	T	T	rs147379693		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171621408_171621409insT								STK10 (6062 upstream) : UBTD2 (15241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172035150	172035161	+	IGR	DEL	TGGATGGATGGA	-	-	rs34479894		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172035150_172035161delTGGATGGATGGA								SH3PXD2B (153623 upstream) : NEURL1B (33115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173236689	173236692	+	IGR	DEL	CTTC	-	-	rs68022912		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173236689_173236692delCTTC								BOD1 (193023 upstream) : CPEB4 (78639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173923058	173923058	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173923058delG								HMP19 (386877 upstream) : MSX2 (228517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174298381	174298384	+	IGR	DEL	ATCC	-	-	rs72128028		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174298381_174298384delATCC								MSX2 (140480 upstream) : DRD1 (569292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174694560	174694560	+	IGR	DEL	A	-	-	rs140302338		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174694560delA								MSX2 (536659 upstream) : DRD1 (173116 downstream)																																			---	---	---	---
SFXN1	94081	broad.mit.edu	37	5	174931420	174931421	+	Intron	DEL	AC	-	-	rs111410028		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174931420_174931421delAC	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591			sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	174975877	174975877	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174975877delA								SFXN1 (20256 upstream) : HRH2 (109163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	175348042	175348044	+	IGR	DEL	ATG	-	-	rs139572932		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175348042_175348044delATG								CPLX2 (37019 upstream) : THOC3 (38492 downstream)																																			---	---	---	---
FAF2	23197	broad.mit.edu	37	5	175912526	175912526	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175912526delT	uc003mej.3	+							NM_014613	NP_055428			UBX domain containing 8						response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	176157406	176157406	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176157406delG								TSPAN17 (71348 upstream) : UNC5A (80154 downstream)																																			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176692490	176692491	+	Intron	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176692490_176692491delGA	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
B4GALT7	11285	broad.mit.edu	37	5	177035489	177035490	+	Intron	DEL	CC	-	-	rs67877012		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177035489_177035490delCC	uc003mhy.2	+						B4GALT7_uc003mhz.2_Intron	NM_007255	NP_009186			xylosylprotein beta 1,4-galactosyltransferase 7						fibril organization|glycosaminoglycan biosynthetic process|negative regulation of fibroblast proliferation|protein modification process|proteoglycan metabolic process	Golgi cisterna membrane|integral to membrane	metal ion binding|xylosylprotein 4-beta-galactosyltransferase activity			pancreas(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
N4BP3	23138	broad.mit.edu	37	5	177550598	177550598	+	3'UTR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177550598delG	uc003mik.1	+	5					N4BP3_uc003mil.1_3'UTR	NM_015111	NP_055926			Nedd4 binding protein 3							cytoplasmic vesicle membrane					0	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
AGXT2L2	85007	broad.mit.edu	37	5	177636636	177636637	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177636636_177636637insT	uc003miz.2	-						HNRNPAB_uc003miu.2_Intron|HNRNPAB_uc003miv.2_Intron|HNRNPAB_uc010jks.2_Intron|HNRNPAB_uc003miw.2_Intron|HNRNPAB_uc003mix.2_Intron|AGXT2L2_uc003miy.2_Intron|AGXT2L2_uc003mjc.2_Intron|AGXT2L2_uc003mja.2_Intron|AGXT2L2_uc003mjb.2_Intron	NM_153373	NP_699204			alanine-glyoxylate aminotransferase 2-like 2							mitochondrion	pyridoxal phosphate binding|transaminase activity			pancreas(1)	1	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.181)|all cancers(165;0.235)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)													---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177675174	177675174	+	Intron	DEL	C	-	-	rs2913852		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177675174delC	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
RUFY1	80230	broad.mit.edu	37	5	178993140	178993140	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178993140delA	uc003mka.1	+						RUFY1_uc003mkb.1_Intron|RUFY1_uc003mkc.1_Intron	NM_025158	NP_079434			RUN and FYVE domain-containing 1 isoform a						endocytosis|protein transport	early endosome membrane	lipid binding|zinc ion binding			ovary(4)|breast(1)	5	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)												HNSCC(44;0.11)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	179360841	179360841	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179360841delT								TBC1D9B (25985 upstream) : RNF130 (21633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	179644015	179644015	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179644015delT								RASGEF1C (7885 upstream) : MAPK9 (16582 downstream)																																			---	---	---	---
BTNL8	79908	broad.mit.edu	37	5	180365545	180365545	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180365545delT	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552			butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	343658	343659	+	Intron	INS	-	GTGTGCATGTTTGCGTGTGCATGTTTGCGTGTGCATGTTTGC	GTGTGCATGTTTGCGTGTGCATGTTTGCGTGTGCATGTTTGC	rs144726926		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:343658_343659insGTGTGCATGTTTGCGTGTGCATGTTTGCGTGTGCATGTTTGC	uc003msx.2	+						DUSP22_uc011dhn.1_Intron|DUSP22_uc003msy.1_Intron	NM_020185	NP_064570			dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	1478502	1478503	+	IGR	INS	-	TGG	TGG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1478502_1478503insTGG								FOXF2 (82671 upstream) : FOXC1 (132178 downstream)																																			---	---	---	---
FOXC1	2296	broad.mit.edu	37	6	1612420	1612420	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1612420delA	uc003mtp.2	+	1						NM_001453	NP_001444			forkhead box C1						anti-apoptosis|artery morphogenesis|blood vessel remodeling|brain development|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|germ cell migration|glycosaminoglycan metabolic process|lacrimal gland development|lymphangiogenesis|metanephros development|negative regulation of mitotic cell cycle|neural crest cell fate commitment|Notch signaling pathway|odontogenesis of dentine-containing tooth|ossification|ovarian follicle development|paraxial mesodermal cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	nuclear heterochromatin|transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2557742	2557744	+	IGR	DEL	TCT	-	-	rs113332174		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2557742_2557744delTCT								GMDS (311896 upstream) : C6orf195 (65228 downstream)																																			---	---	---	---
WRNIP1	56897	broad.mit.edu	37	6	2765183	2765183	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2765183delT	uc003mtz.2	+						WRNIP1_uc003mua.2_5'Flank	NM_020135	NP_064520			Werner helicase interacting protein isoform 1						DNA replication|DNA synthesis involved in DNA repair|regulation of DNA-dependent DNA replication initiation	mitochondrion|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|DNA binding|metal ion binding|protein binding			ovary(1)|pancreas(1)	2	Ovarian(93;0.0412)	all_hematologic(90;0.0895)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	2806040	2806043	+	IGR	DEL	TGTG	-	-	rs112967756		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2806040_2806043delTGTG								WRNIP1 (20062 upstream) : SERPINB1 (27693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3608527	3608527	+	IGR	DEL	C	-	-	rs56188206		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3608527delC								SLC22A23 (151734 upstream) : C6orf145 (114309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4189708	4189708	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4189708delT								PECI (53877 upstream) : CDYL (516685 downstream)																																			---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5500969	5500970	+	Intron	DEL	TT	-	-	rs112735671		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5500969_5500970delTT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	5801787	5801792	+	IGR	DEL	TGTGTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5801787_5801792delTGTGTG								FARS2 (29971 upstream) : NRN1 (196443 downstream)																																			---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6164419	6164419	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6164419delA	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120			coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6220800	6220801	+	Intron	INS	-	TG	TG	rs142158446	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6220800_6220801insTG	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120			coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
DSP	1832	broad.mit.edu	37	6	7577555	7577558	+	Intron	DEL	TGTT	-	-	rs147156728		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7577555_7577558delTGTT	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	9933333	9933333	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9933333delA	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myj.1_Intron|uc003myk.1_Intron|uc003myn.2_Intron|uc010joi.1_Intron|uc010joh.1_Intron|uc011dif.1_Intron|uc011dig.1_Intron					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																														---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10557409	10557410	+	Intron	INS	-	C	C	rs56354713		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10557409_10557410insC	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Frame_Shift_Ins_p.P251fs	NM_145649	NP_663624			glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10576886	10576886	+	Intron	DEL	T	-	-	rs114386156	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10576886delT	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron	NM_145649	NP_663624			glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
MAK	4117	broad.mit.edu	37	6	10822688	10822689	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10822688_10822689delAA	uc003mzl.2	-						SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_Intron|MAK_uc010jou.2_Intron|MAK_uc003mzm.2_Intron|MAK_uc010jov.1_Intron	NM_005906	NP_005897			male germ cell-associated kinase						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)																---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10942593	10942593	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10942593delT	uc003mzo.2	+						SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364			synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)															---	---	---	---
ELOVL2	54898	broad.mit.edu	37	6	10990437	10990437	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10990437delA	uc003mzp.3	-							NM_017770	NP_060240			elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)															---	---	---	---
TBC1D7	51256	broad.mit.edu	37	6	13305209	13305209	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13305209delA	uc003naj.2	-						TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_3'UTR|TBC1D7_uc003nal.2_3'UTR|TBC1D7_uc003nam.2_3'UTR|TBC1D7_uc003nao.2_3'UTR	NM_016495	NP_057579			TBC1 domain family, member 7 isoform a						positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)															---	---	---	---
GFOD1	54438	broad.mit.edu	37	6	13428739	13428743	+	Intron	DEL	TGCGA	-	-	rs140612759		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13428739_13428743delTGCGA	uc003nat.1	-						GFOD1_uc003nas.1_Intron	NM_018988	NP_061861			glucose-fructose oxidoreductase domain							extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)															---	---	---	---
GFOD1	54438	broad.mit.edu	37	6	13477445	13477446	+	Intron	DEL	GG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13477445_13477446delGG	uc003nat.1	-						GFOD1_uc003nas.1_Intron|C6orf114_uc003nav.2_Intron	NM_018988	NP_061861			glucose-fructose oxidoreductase domain							extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	13742076	13742076	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13742076delT								RANBP9 (30280 upstream) : CCDC90A (48945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13768013	13768013	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13768013delA								RANBP9 (56217 upstream) : CCDC90A (23008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14464407	14464408	+	IGR	INS	-	TAC	TAC	rs140373040	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14464407_14464408insTAC								CD83 (327261 upstream) : JARID2 (781326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14945817	14945820	+	IGR	DEL	GAAA	-	-	rs72066990		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14945817_14945820delGAAA								CD83 (808671 upstream) : JARID2 (299914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	16035867	16035867	+	IGR	DEL	G	-	-	rs11334469		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16035867delG								DTNBP1 (372596 upstream) : MYLIP (93450 downstream)																																			---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16440677	16440678	+	Intron	DEL	AA	-	-	rs11460357		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16440677_16440678delAA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16588002	16588002	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16588002delA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	17089058	17089058	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17089058delA								ATXN1 (327337 upstream) : RBM24 (192751 downstream)																																			---	---	---	---
NUP153	9972	broad.mit.edu	37	6	17649330	17649330	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17649330delT	uc003ncd.1	-						NUP153_uc011dje.1_Intron|NUP153_uc010jpl.1_Intron	NM_005124	NP_005115			nucleoporin 153kDa						carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)															---	---	---	---
NUP153	9972	broad.mit.edu	37	6	17669074	17669075	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17669074_17669075delAA	uc003ncd.1	-						NUP153_uc011dje.1_Intron|NUP153_uc010jpl.1_Intron	NM_005124	NP_005115			nucleoporin 153kDa						carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)															---	---	---	---
KDM1B	221656	broad.mit.edu	37	6	18171050	18171050	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18171050delT	uc003ncn.1	+							NM_153042	NP_694587			amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	18566437	18566438	+	Intron	INS	-	TCCC	TCCC	rs147177362	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18566437_18566438insTCCC	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	19007038	19007038	+	IGR	DEL	A	-	-	rs74790736		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19007038delA								MIR548A1 (434927 upstream) : ID4 (830579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19386103	19386103	+	IGR	DEL	A	-	-	rs34630961		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19386103delA								MIR548A1 (813992 upstream) : ID4 (451514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20280744	20280744	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20280744delT								MBOAT1 (68074 upstream) : E2F3 (121393 downstream)																																			---	---	---	---
E2F3	1871	broad.mit.edu	37	6	20404586	20404586	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20404586delT	uc003nda.2	+						E2F3_uc003ncz.2_Intron	NM_001949	NP_001940			E2F transcription factor 3						G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	20528961	20528961	+	IGR	DEL	C	-	-	rs149883701	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20528961delC								E2F3 (35016 upstream) : CDKAL1 (5727 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20647314	20647314	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20647314delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20770318	20770318	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20770318delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21877941	21877941	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21877941delA	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron|FLJ22536_uc003ndk.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
PRL	5617	broad.mit.edu	37	6	22294758	22294758	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22294758delG	uc003ndp.2	-	2	603	c.84delC	c.(82-84)CCCfs	p.P28fs	PRL_uc003ndo.2_Frame_Shift_Del_p.P29fs|PRL_uc003ndq.2_Frame_Shift_Del_p.P28fs|PRL_uc003ndr.1_RNA	NM_000948	NP_000939	P01236	PRL_HUMAN	prolactin precursor	28					cell proliferation|cell surface receptor linked signaling pathway|female pregnancy|lactation|positive regulation of JAK-STAT cascade|regulation of multicellular organism growth	cytosol|extracellular region	hormone activity|prolactin receptor binding				0	Ovarian(93;0.163)																	---	---	---	---
ALDH5A1	7915	broad.mit.edu	37	6	24522707	24522708	+	Intron	DEL	GT	-	-	rs72282015		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24522707_24522708delGT	uc003neg.2	+						ALDH5A1_uc003nef.2_Intron	NM_001080	NP_001071			aldehyde dehydrogenase 5A1 isoform 2 precursor						acetate metabolic process|central nervous system development|galactosylceramide metabolic process|gamma-aminobutyric acid catabolic process|glucose metabolic process|glutamate metabolic process|glutamine metabolic process|glutathione metabolic process|glycerophospholipid metabolic process|neurotransmitter catabolic process|neurotransmitter secretion|protein homotetramerization|respiratory electron transport chain|short-chain fatty acid metabolic process|succinate metabolic process	mitochondrial matrix|soluble fraction	succinate-semialdehyde dehydrogenase activity				0					Chlormerodrin(DB00534)|NADH(DB00157)|Succinic acid(DB00139)													---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24576991	24576991	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24576991delA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron|KIAA0319_uc010jpt.1_Intron	NM_014809	NP_055624			KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24589047	24589047	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24589047delA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron	NM_014809	NP_055624			KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	24803898	24803899	+	IGR	INS	-	T	T	rs148322600	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24803898_24803899insT								GMNN (17622 upstream) : FAM65B (614 downstream)																																			---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25597079	25597082	+	Intron	DEL	ACAC	-	-	rs34651019		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25597079_25597082delACAC	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110			leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26482400	26482400	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26482400delA	uc003nie.1	-											Homo sapiens cDNA FLJ40220 fis, clone TESTI2021667.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	26664098	26664098	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26664098delT								ZNF322A (4135 upstream) : GUSBL1 (175168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27124918	27124918	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27124918delA								HIST1H2AH (9573 upstream) : PRSS16 (90590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27179720	27179720	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27179720delA								HIST1H2AH (64375 upstream) : PRSS16 (35788 downstream)																																			---	---	---	---
PPP1R10	5514	broad.mit.edu	37	6	30585435	30585435	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30585435delA	uc003nqn.1	-						PPP1R10_uc010jsc.1_5'Flank|MRPS18B_uc003nqo.2_5'Flank|MRPS18B_uc011dml.1_5'Flank|MRPS18B_uc010jsd.1_5'Flank	NM_002714	NP_002705			protein phosphatase 1, regulatory subunit 10						protein import into nucleus|transcription, DNA-dependent	PTW/PP1 phosphatase complex	DNA binding|protein phosphatase inhibitor activity|RNA binding|zinc ion binding			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	31440968	31440969	+	IGR	INS	-	T	T	rs138913534	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31440968_31440969insT								HCG26 (784 upstream) : MICB (21689 downstream)																																			---	---	---	---
MCCD1	401250	broad.mit.edu	37	6	31495806	31495812	+	5'Flank	DEL	AAAAAAA	-	-	rs147277013		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31495806_31495812delAAAAAAA	uc003ntp.1	+							NM_001011700	NP_001011700			mitochondrial coiled-coil domain 1 precursor							mitochondrion					0																		---	---	---	---
BAT1	7919	broad.mit.edu	37	6	31507061	31507061	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31507061delG	uc003ntt.2	-						BAT1_uc003nts.2_Intron|BAT1_uc011dnn.1_Intron|BAT1_uc003ntu.2_Intron|BAT1_uc003ntv.2_Intron|BAT1_uc003ntw.2_Intron|BAT1_uc003ntx.2_Intron|BAT1_uc011dno.1_Intron|BAT1_uc011dnp.1_Intron|SNORD117_uc003nty.1_5'Flank|BAT1_uc011dnq.1_Intron	NM_004640	NP_004631			HLA-B associated transcript 1						intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0																		---	---	---	---
LSM2	57819	broad.mit.edu	37	6	31765402	31765402	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31765402delA	uc003nxg.2	-	5					VARS_uc003nxe.2_5'Flank|VARS_uc011doi.1_5'Flank	NM_021177	NP_067000			LSM2 homolog, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytosol|nucleoplasm	U6 snRNA binding				0																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32307341	32307341	+	Intron	DEL	A	-	-	rs34999261		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32307341delA	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32523362	32523363	+	Intron	INS	-	GATA	GATA	rs142676080	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32523362_32523363insGATA	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_Intron|HLA-DRB6_uc003obn.1_Intron|HLA-DRB6_uc003obo.1_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																		---	---	---	---
PSMB9	5698	broad.mit.edu	37	6	32827022	32827023	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32827022_32827023insA	uc003sga.2	+							NM_148954	NP_683756			proteasome beta 9 subunit isoform 2 proprotein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32853222	32853222	+	IGR	DEL	T	-	-	rs11459466		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32853222delT								PPP1R2P1 (5373 upstream) : HLA-DMB (49188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	33208505	33208506	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33208505_33208506delTG								RING1 (28007 upstream) : VPS52 (9543 downstream)																																			---	---	---	---
B3GALT4	8705	broad.mit.edu	37	6	33246525	33246525	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33246525delA	uc003odr.2	+	1						NM_003782	NP_003773			UDP-Gal:betaGlcNAc beta						protein glycosylation	Golgi membrane|integral to membrane	ganglioside galactosyltransferase activity|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
TAPBP	6892	broad.mit.edu	37	6	33273073	33273073	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33273073delG	uc003odx.1	-	4	732	c.561delC	c.(559-561)CCCfs	p.P187fs	TAPBP_uc010jus.1_Frame_Shift_Del_p.P205fs|TAPBP_uc003ody.2_Frame_Shift_Del_p.P187fs|TAPBP_uc003odz.2_Frame_Shift_Del_p.P187fs|TAPBP_uc010jut.1_Frame_Shift_Del_p.P100fs|TAPBP_uc011drc.1_Frame_Shift_Del_p.P187fs	NM_003190	NP_003181	O15533	TPSN_HUMAN	tapasin isoform 1 precursor	187	Lumenal (Potential).				antigen processing and presentation of endogenous peptide antigen via MHC class I|immune response|peptide antigen stabilization|protein complex assembly|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|MHC class I peptide loading complex|microsome	MHC class I protein binding|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
TAPBP	6892	broad.mit.edu	37	6	33280796	33280796	+	Intron	DEL	T	-	-	rs67868917		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33280796delT	uc003odx.1	-						TAPBP_uc010jus.1_Intron|TAPBP_uc003ody.2_Intron|TAPBP_uc003odz.2_Intron|TAPBP_uc010jut.1_Intron|TAPBP_uc011drc.1_Intron	NM_003190	NP_003181			tapasin isoform 1 precursor						antigen processing and presentation of endogenous peptide antigen via MHC class I|immune response|peptide antigen stabilization|protein complex assembly|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|MHC class I peptide loading complex|microsome	MHC class I protein binding|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34782394	34782394	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34782394delT	uc003oju.3	+						UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_Intron	NM_017754	NP_060224			ICBP90 binding protein 1											ovary(3)	3																		---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	34910462	34910462	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34910462delT	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron	NM_015245	NP_056060			ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
PPARD	5467	broad.mit.edu	37	6	35383556	35383557	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35383556_35383557delTG	uc003okm.2	+						PPARD_uc003okl.2_Intron|PPARD_uc003okn.2_Intron|PPARD_uc011dtb.1_Intron|PPARD_uc011dtc.1_Intron|PPARD_uc010jvv.1_Intron	NM_006238	NP_006229			peroxisome proliferative activated receptor,						apoptosis|axon ensheathment|cholesterol metabolic process|decidualization|embryo implantation|fatty acid beta-oxidation|fatty acid transport|generation of precursor metabolites and energy|glucose metabolic process|glucose transport|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fat cell differentiation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|linoleic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1					Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)													---	---	---	---
FKBP5	2289	broad.mit.edu	37	6	35554625	35554625	+	Intron	DEL	T	-	-	rs112376611		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35554625delT	uc011dte.1	-						FKBP5_uc003okx.2_Intron|FKBP5_uc011dtf.1_Intron|FKBP5_uc003oky.2_Intron|FKBP5_uc003okz.2_3'UTR	NM_001145776	NP_001139248			FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1																		---	---	---	---
LOC285847	285847	broad.mit.edu	37	6	35700973	35700973	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35700973delA	uc010jvy.1	-							NR_027117				Homo sapiens cDNA FLJ35985 fis, clone TESTI2014248.												0																		---	---	---	---
C6orf126	389383	broad.mit.edu	37	6	35745414	35745414	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35745414delA	uc010jvz.1	+						C6orf126_uc003olc.1_Intron	NM_207409	NP_997292			hypothetical protein LOC389383 precursor						digestion|lipid catabolic process	extracellular region	enzyme activator activity				0																		---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36193259	36193259	+	Intron	DEL	A	-	-	rs41270094	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36193259delA	uc003olv.3	+						BRPF3_uc010jwb.2_Intron|BRPF3_uc011dtj.1_Intron|BRPF3_uc010jwc.2_Intron|BRPF3_uc011dtk.1_Intron|BRPF3_uc010jwd.2_Intron	NM_015695	NP_056510			bromodomain and PHD finger containing, 3						histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
RNF8	9025	broad.mit.edu	37	6	37322189	37322190	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37322189_37322190insG	uc003onq.3	+						RNF8_uc003onr.3_Intron|RNF8_uc011dtx.1_Intron	NM_003958	NP_003949			ring finger protein 8 isoform 1						cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38831965	38831966	+	Intron	INS	-	T	T	rs142819576	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38831965_38831966insT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	39005203	39005204	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39005203_39005204delCT								DNAH8 (6636 upstream) : GLP1R (11353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	39110556	39110557	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39110556_39110557delTG								C6orf64 (27691 upstream) : KCNK5 (46191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40357709	40357709	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40357709delA								TDRG1 (10078 upstream) : LRFN2 (1664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40903327	40903327	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40903327delA								LRFN2 (348201 upstream) : UNC5CL (91445 downstream)																																			---	---	---	---
LOC221442	221442	broad.mit.edu	37	6	41107172	41107172	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41107172delT	uc003ops.2	+						LOC221442_uc003opu.2_Intron|LOC221442_uc010jxj.1_Intron	NR_026938				Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1709050.												0																		---	---	---	---
TREML3	340206	broad.mit.edu	37	6	41185829	41185829	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41185829delT	uc003oqb.2	-							NR_027256				Homo sapiens TREM-like transcript 3 (TLT3) mRNA, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	41320857	41320857	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41320857delG								NCR2 (2232 upstream) : FOXP4 (193307 downstream)																																			---	---	---	---
PGC	5225	broad.mit.edu	37	6	41710338	41710340	+	Intron	DEL	CTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41710338_41710340delCTT	uc003ora.1	-							NM_002630	NP_002621			progastricsin (pepsinogen C) precursor						digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)															---	---	---	---
RPL7L1	285855	broad.mit.edu	37	6	42850981	42850981	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42850981delT	uc003osq.1	+						RPL7L1_uc011dux.1_Intron|RPL7L1_uc010jxw.1_Intron|RPL7L1_uc003osr.1_Intron|RPL7L1_uc011duy.1_Intron|RPL7L1_uc003oss.1_Intron|RPL7L1_uc003ost.2_Intron|RPL7L1_uc003osu.2_Intron	NM_198486	NP_940888			ribosomal protein L7-like 1						translation	large ribosomal subunit	protein binding|structural constituent of ribosome				0	Colorectal(47;0.196)		Colorectal(64;0.00237)|all cancers(41;0.00288)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.088)															---	---	---	---
PPP2R5D	5528	broad.mit.edu	37	6	42974321	42974321	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42974321delG	uc003oth.2	+	3	312	c.226delG	c.(226-228)GGGfs	p.G76fs	MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Frame_Shift_Del_p.G76fs|PPP2R5D_uc010jyd.2_Intron|PPP2R5D_uc011dva.1_5'UTR|PPP2R5D_uc003oti.2_5'UTR|PPP2R5D_uc003otj.2_5'UTR	NM_006245	NP_006236	Q14738	2A5D_HUMAN	delta isoform of regulatory subunit B56, protein	76					nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
C6orf153	88745	broad.mit.edu	37	6	42993678	42993678	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42993678delA	uc003otp.1	+							NM_033112	NP_149103			hypothetical protein LOC88745						ribosomal small subunit biogenesis|rRNA processing	nucleolus					0			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	43000175	43000175	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43000175delT								C6orf153 (2838 upstream) : CUL7 (5181 downstream)																																			---	---	---	---
KLC4	89953	broad.mit.edu	37	6	43039796	43039796	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43039796delT	uc003otv.1	+						KLC4_uc003otr.1_Intron|KLC4_uc011dvd.1_Intron|KLC4_uc003otw.1_Intron|KLC4_uc003otx.1_Intron|KLC4_uc003oty.1_Intron|KLC4_uc003otz.1_Intron	NM_201521	NP_958929			kinesin-like 8 isoform a							cytoplasm|kinesin complex|microtubule	microtubule motor activity|protein binding			skin(3)|ovary(1)	4			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)															---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43166152	43166152	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43166152delT	uc003ouk.2	+						CUL9_uc003oul.2_Intron|CUL9_uc010jyk.2_Intron	NM_015089	NP_055904			p53-associated parkin-like cytoplasmic protein						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12																		---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43319538	43319539	+	Intron	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43319538_43319539insAC	uc003oux.2	-						ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160			zinc finger protein 318						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
ABCC10	89845	broad.mit.edu	37	6	43414593	43414593	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43414593delT	uc003ouy.1	+						ABCC10_uc003ouz.1_Intron|ABCC10_uc010jyo.1_Intron	NM_033450	NP_258261			ATP-binding cassette, sub-family C, member 10							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	44004730	44004730	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44004730delT	uc003owm.1	-											Homo sapiens cDNA: FLJ21083 fis, clone CAS03150.																														---	---	---	---
SPATS1	221409	broad.mit.edu	37	6	44287324	44287328	+	Intron	DEL	GGCTG	-	-	rs113234765		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44287324_44287328delGGCTG	uc003oxg.2	+											Homo sapiens cDNA FLJ25442 fis, clone TST08489.											skin(1)	1	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	46071381	46071381	+	IGR	DEL	T	-	-	rs34566271		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46071381delT								CLIC5 (23296 upstream) : ENPP4 (26320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	47110947	47110947	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47110947delT								GPR110 (100865 upstream) : TNFRSF21 (88322 downstream)																																			---	---	---	---
GPR111	222611	broad.mit.edu	37	6	47637240	47637243	+	Intron	DEL	AAAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47637240_47637243delAAAC	uc010jzj.1	+						GPR111_uc010jzk.1_Intron|GPR111_uc003oyy.2_Intron	NM_153839	NP_722581			G-protein coupled receptor 111						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	48277096	48277096	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48277096delT								C6orf138 (198153 upstream) : None (None downstream)																																			---	---	---	---
MUT	4594	broad.mit.edu	37	6	49408202	49408202	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49408202delT	uc003ozg.3	-							NM_000255	NP_000246			methylmalonyl Coenzyme A mutase precursor						fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
CENPQ	55166	broad.mit.edu	37	6	49438163	49438163	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49438163delA	uc003ozh.1	+							NM_018132	NP_060602			centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	50173584	50173585	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50173584_50173585delAA								DEFB112 (157220 upstream) : TFAP2D (507672 downstream)																																			---	---	---	---
TFAP2B	7021	broad.mit.edu	37	6	50786809	50786809	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50786809delT	uc003pag.2	+							NM_003221	NP_003212			transcription factor AP-2 beta						nervous system development|positive regulation of transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0	Lung NSC(77;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	50947301	50947301	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50947301delC								TFAP2B (131976 upstream) : PKHD1 (532844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51111537	51111538	+	IGR	DEL	CT	-	-	rs35769285		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51111537_51111538delCT								TFAP2B (296212 upstream) : PKHD1 (368607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51264890	51264890	+	IGR	DEL	T	-	-	rs68055958		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51264890delT								TFAP2B (449565 upstream) : PKHD1 (215255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51312315	51312316	+	IGR	INS	-	ACAC	ACAC	rs11755144		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51312315_51312316insACAC								TFAP2B (496990 upstream) : PKHD1 (167829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	52189951	52189951	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52189951delT								MCM3 (40369 upstream) : PAQR8 (36975 downstream)																																			---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	53936128	53936128	+	Intron	DEL	A	-	-	rs111236677		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53936128delA	uc003pcg.3	+						C6orf142_uc003pcf.2_Intron	NM_138569	NP_612636			hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)																	---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	55971591	55971592	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55971591_55971592insT	uc003pcs.2	-						COL21A1_uc010jzz.2_Intron|COL21A1_uc011dxg.1_Intron|COL21A1_uc011dxh.1_Intron	NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
DST	667	broad.mit.edu	37	6	56438457	56438457	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56438457delT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc010kaa.1_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
RAB23	51715	broad.mit.edu	37	6	57059462	57059462	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57059462delA	uc003pds.2	-						RAB23_uc003pdt.2_Intron|RAB23_uc010kac.2_Intron|RAB23_uc010kad.2_Intron	NM_183227	NP_899050			Ras-related protein Rab-23						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			skin(1)	1	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
RAB23	51715	broad.mit.edu	37	6	57059704	57059704	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57059704delT	uc003pds.2	-						RAB23_uc003pdt.2_Intron|RAB23_uc010kac.2_Intron|RAB23_uc010kad.2_Intron	NM_183227	NP_899050			Ras-related protein Rab-23						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			skin(1)	1	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57215659	57215659	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57215659delT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57272878	57272878	+	Intron	DEL	T	-	-	rs144142029	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57272878delT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57316285	57316286	+	Intron	INS	-	G	G	rs147180550	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57316285_57316286insG	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57348007	57348008	+	Intron	INS	-	T	T	rs141915704	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57348007_57348008insT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57360568	57360569	+	Intron	DEL	AT	-	-	rs140251188		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57360568_57360569delAT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57375548	57375549	+	Intron	INS	-	TTA	TTA	rs150899802		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57375548_57375549insTTA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57434024	57434024	+	Intron	DEL	T	-	-	rs11337337		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57434024delT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57438024	57438026	+	Intron	DEL	AAT	-	-	rs67074144		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57438024_57438026delAAT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57468123	57468123	+	Intron	DEL	G	-	-	rs11307467		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57468123delG	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57472089	57472095	+	Intron	DEL	TTTTCCC	-	-	rs71699756		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57472089_57472095delTTTTCCC	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57510347	57510347	+	Intron	DEL	A	-	-	rs66826354		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57510347delA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	57530835	57530836	+	IGR	INS	-	GAAGA	GAAGA	rs149465930	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57530835_57530836insGAAGA								PRIM2 (17460 upstream) : GUSBL2 (715323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57538773	57538773	+	IGR	DEL	G	-	-	rs10707154		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538773delG								PRIM2 (25398 upstream) : GUSBL2 (707386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57541207	57541208	+	IGR	INS	-	A	A	rs141618997		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57541207_57541208insA								PRIM2 (27832 upstream) : GUSBL2 (704951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57562258	57562258	+	IGR	DEL	T	-	-	rs77194346		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57562258delT								PRIM2 (48883 upstream) : GUSBL2 (683901 downstream)																																			---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62923255	62923255	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62923255delA	uc003peg.2	-							NM_152688	NP_689901			KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	63150898	63150898	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63150898delT								KHDRBS2 (154798 upstream) : LGSN (834959 downstream)																																			---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64413280	64413280	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64413280delA	uc003pep.1	+						PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Intron|PHF3_uc011dxs.1_Intron	NM_015153	NP_055968			PHD finger protein 3						multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
EYS	346007	broad.mit.edu	37	6	64816520	64816521	+	Intron	DEL	TG	-	-	rs35062611		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64816520_64816521delTG	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	66115264	66115264	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66115264delA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	66748804	66748804	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66748804delT								MCART3P (249429 upstream) : None (None downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	70092935	70092935	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70092935delA	uc003pev.3	+						BAI3_uc010kak.2_Intron|BAI3_uc011dxx.1_Intron	NM_001704	NP_001695			brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	70313190	70313190	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70313190delT								BAI3 (213788 upstream) : LMBRD1 (72561 downstream)																																			---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71443828	71443828	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71443828delC	uc003pfr.2	+						SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770			stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	72106305	72106306	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72106305_72106306insA								MIR30C2 (19571 upstream) : MIR30A (6948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72134498	72134500	+	IGR	DEL	TTG	-	-	rs66806901		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72134498_72134500delTTG								C6orf155 (4050 upstream) : RIMS1 (462150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	73308513	73308513	+	IGR	DEL	T	-	-	rs1147570	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73308513delT								RIMS1 (196006 upstream) : KCNQ5 (23058 downstream)																																			---	---	---	---
MTO1	25821	broad.mit.edu	37	6	74171523	74171523	+	5'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74171523delT	uc003pgy.3	+	1					MTO1_uc010kav.2_5'UTR|MTO1_uc003pgz.3_5'UTR|MTO1_uc003pha.3_5'UTR|MTO1_uc003phb.3_Intron|MTO1_uc003phc.1_5'Flank	NM_133645	NP_598400			mitochondrial translation optimization 1 homolog						tRNA processing	mitochondrion	flavin adenine dinucleotide binding			ovary(3)|skin(2)|pancreas(1)	6																OREG0003888	type=REGULATORY REGION|Gene=MTO1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
CD109	135228	broad.mit.edu	37	6	74449760	74449761	+	Intron	INS	-	A	A	rs146359730	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74449760_74449761insA	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74582446	74582446	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74582446delC								CD109 (44406 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75001566	75001566	+	Intron	DEL	T	-	-	rs75997181		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75001566delT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	75143439	75143439	+	Intron	DEL	A	-	-	rs72350522		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75143439delA	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
LCA5	167691	broad.mit.edu	37	6	80201519	80201520	+	Intron	INS	-	TA	TA	rs142509128	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80201519_80201520insTA	uc003pix.2	-						LCA5_uc003piy.2_Intron|LCA5_uc011dyq.1_Intron	NM_001122769	NP_001116241			Leber congenital amaurosis 5						protein transport	cilium axoneme|microtubule basal body	protein binding				0		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	82106061	82106063	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82106061_82106063delAAA								None (None upstream) : FAM46A (349385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82205073	82205073	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82205073delA								None (None upstream) : FAM46A (250375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82253825	82253828	+	IGR	DEL	AAAA	-	-	rs148575411		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82253825_82253828delAAAA								None (None upstream) : FAM46A (201620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82700752	82700752	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82700752delT								FAM46A (238324 upstream) : IBTK (179204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	84202758	84202758	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84202758delT								ME1 (61979 upstream) : PRSS35 (19516 downstream)																																			---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84407044	84407045	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84407044_84407045delCA	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_Intron	NM_014841	NP_055656			synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	86137165	86137165	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86137165delT								TBX18 (663266 upstream) : NT5E (22137 downstream)																																			---	---	---	---
SYNCRIP	10492	broad.mit.edu	37	6	86350406	86350408	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86350406_86350408delAAA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363			synaptotagmin binding, cytoplasmic RNA						CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	86638909	86638909	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86638909delT								SNHG5 (250458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87318827	87318827	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87318827delA								SNHG5 (930376 upstream) : HTR1E (328197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87600619	87600620	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87600619_87600620delGT								None (None upstream) : HTR1E (46404 downstream)																																			---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87955207	87955207	+	Intron	DEL	T	-	-	rs72438234		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87955207delT	uc003plm.3	+							NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
RARS2	57038	broad.mit.edu	37	6	88284072	88284073	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88284072_88284073delAG	uc003pme.2	-						RARS2_uc003pmb.2_Intron|RARS2_uc003pmc.2_Intron|RARS2_uc003pmd.2_Intron|RARS2_uc003pmf.2_Intron	NM_020320	NP_064716			arginyl-tRNA synthetase 2, mitochondrial						arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)												OREG0007385	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
Unknown	0	broad.mit.edu	37	6	88954767	88954767	+	IGR	DEL	C	-	-	rs35750466		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88954767delC								CNR1 (79000 upstream) : RNGTT (365222 downstream)																																			---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89563641	89563644	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89563641_89563644delTTTT	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791			RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)														---	---	---	---
GABRR1	2569	broad.mit.edu	37	6	89893222	89893223	+	Intron	INS	-	GC	GC	rs141495076	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89893222_89893223insGC	uc003pna.2	-						GABRR1_uc011dzv.1_Intron	NM_002042	NP_002033			gamma-aminobutyric acid (GABA) receptor, rho 1						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)													---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	89992913	89992914	+	Intron	INS	-	T	T	rs67760764		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89992913_89992914insT	uc003pnb.2	-							NM_002043	NP_002034			gamma-aminobutyric acid (GABA) receptor, rho 2						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90338817	90338817	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90338817delT	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron|ANKRD6_uc011dzy.1_Intron|ANKRD6_uc010kcd.2_Intron|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.3_Intron|LYRM2_uc010kcf.1_Intron|ANKRD6_uc003pnj.3_Intron	NM_014942	NP_055757			ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90387697	90387697	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90387697delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90409616	90409616	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90409616delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90571823	90571823	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90571823delT	uc003pnr.2	+						CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139			caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91732338	91732339	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91732338_91732339insA								MAP3K7 (435431 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94335529	94335529	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94335529delA								EPHA7 (206229 upstream) : TSG1 (81272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94695353	94695354	+	IGR	INS	-	A	A	rs112883100		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94695353_94695354insA								TSG1 (209154 upstream) : None (None downstream)																																			---	---	---	---
FUT9	10690	broad.mit.edu	37	6	96590203	96590203	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96590203delA	uc003pop.3	+							NM_006581	NP_006572			fucosyltransferase 9 (alpha (1,3)						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)														---	---	---	---
KIAA0776	23376	broad.mit.edu	37	6	96999235	96999235	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96999235delT	uc003por.2	+						KIAA0776_uc010kck.2_Intron	NM_015323	NP_056138			hypothetical protein LOC23376						negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)														---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97051249	97051249	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97051249delT	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	97298420	97298421	+	IGR	INS	-	TCCT	TCCT	rs144115464	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97298420_97298421insTCCT								GPR63 (13067 upstream) : NDUFAF4 (39719 downstream)																																			---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97427787	97427787	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97427787delT	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron	NM_052904	NP_443136			kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	97820068	97820068	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97820068delC	uc003ppd.1	+											Homo sapiens cDNA FLJ34046 fis, clone FCBBF2007610.																														---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102270083	102270084	+	Intron	DEL	AC	-	-	rs143568447		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102270083_102270084delAC	uc003pqp.3	+						GRIK2_uc003pqn.2_Intron|GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	103543096	103543098	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103543096_103543098delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104070257	104070257	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104070257delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	105034063	105034063	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105034063delT								None (None upstream) : HACE1 (141905 downstream)																																			---	---	---	---
PREP	5550	broad.mit.edu	37	6	105759225	105759225	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105759225delC	uc003prc.2	-							NM_002726	NP_002717			prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	105963579	105963580	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105963579_105963580insT								PREP (112610 upstream) : PRDM1 (570615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106050456	106050459	+	IGR	DEL	TCTA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106050456_106050459delTCTA								PREP (199487 upstream) : PRDM1 (483736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106254246	106254247	+	IGR	INS	-	CA	CA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106254246_106254247insCA								PREP (403277 upstream) : PRDM1 (279948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106459992	106459993	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106459992_106459993delAC								PREP (609023 upstream) : PRDM1 (74202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	107289891	107289891	+	IGR	DEL	T	-	-	rs111532264		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107289891delT								MIR587 (57796 upstream) : C6orf203 (59516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	107444080	107444080	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107444080delA								BEND3 (8444 upstream) : PDSS2 (29681 downstream)																																			---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107523586	107523586	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107523586delA	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
SCML4	256380	broad.mit.edu	37	6	108076968	108076968	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108076968delA	uc010kdf.2	-						SCML4_uc003prz.3_Intron|SCML4_uc011eam.1_Intron|SCML4_uc003psa.3_Intron	NM_198081	NP_932347			sex comb on midleg-like 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)														---	---	---	---
SEC63	11231	broad.mit.edu	37	6	108214924	108214924	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108214924delT	uc003psc.3	-						SEC63_uc003psb.3_Intron	NM_007214	NP_009145			SEC63-like protein						protein folding|protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|receptor activity|unfolded protein binding			ovary(1)|skin(1)	2		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)														---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109191792	109191792	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109191792delG	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507			armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)														---	---	---	---
PPIL6	285755	broad.mit.edu	37	6	109748282	109748282	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109748282delA	uc003ptg.3	-						PPIL6_uc010kdo.2_Intron|PPIL6_uc010kdp.2_Intron	NM_173672	NP_775943			peptidylprolyl isomerase-like 6 isoform 1						protein folding		peptidyl-prolyl cis-trans isomerase activity				0		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)														---	---	---	---
AKD1	221264	broad.mit.edu	37	6	109818584	109818589	+	Intron	DEL	CTCTCA	-	-	rs139514272	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109818584_109818589delCTCTCA	uc003ptn.2	-						AKD1_uc011eas.1_Intron	NM_001145128	NP_001138600			adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
GPR6	2830	broad.mit.edu	37	6	110301119	110301120	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110301119_110301120insC	uc011eaw.1	+	2	984_985	c.804_805insC	c.(802-807)CCACCCfs	p.P268fs	GPR6_uc011eav.1_Frame_Shift_Ins_p.P283fs|GPR6_uc003ptu.2_Frame_Shift_Ins_p.P268fs	NM_005284	NP_005275	P46095	GPR6_HUMAN	G protein-coupled receptor 6	268_269	Cytoplasmic (Potential).					integral to plasma membrane					0		all_cancers(87;1.64e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;2.83e-05)|all_lung(197;0.00016)|Lung NSC(302;0.000318)|Colorectal(196;0.0488)		BRCA - Breast invasive adenocarcinoma(108;8.01e-05)|Epithelial(106;8.76e-05)|all cancers(137;0.000197)|OV - Ovarian serous cystadenocarcinoma(136;0.0307)														---	---	---	---
WASF1	8936	broad.mit.edu	37	6	110423573	110423574	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110423573_110423574insA	uc003ptv.1	-						WASF1_uc003ptw.1_Intron|WASF1_uc003ptx.1_Intron|WASF1_uc003pty.1_Intron	NM_003931	NP_003922			Wiskott-Aldrich syndrome protein family member						actin filament polymerization|cellular component movement	actin cytoskeleton	actin binding				0		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)														---	---	---	---
CDK19	23097	broad.mit.edu	37	6	110962849	110962850	+	Intron	INS	-	AAGAAAGG	AAGAAAGG	rs148405572	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110962849_110962850insAAGAAAGG	uc003puh.1	-						CDK19_uc003pui.1_Intron|CDK19_uc011eax.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CDK19	23097	broad.mit.edu	37	6	111108186	111108186	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111108186delA	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	111377607	111377607	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111377607delT								GSTM2P1 (8850 upstream) : SLC16A10 (31174 downstream)																																			---	---	---	---
FYN	2534	broad.mit.edu	37	6	112025372	112025372	+	Intron	DEL	T	-	-	rs67511839		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112025372delT	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron|FYN_uc010kdy.1_5'Flank	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	112917920	112917920	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112917920delG								RFPL4B (245422 upstream) : None (None downstream)																																			---	---	---	---
MARCKS	4082	broad.mit.edu	37	6	114181210	114181210	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114181210delA	uc003pvy.3	+	2	849	c.454delA	c.(454-456)AAAfs	p.K152fs		NM_002356	NP_002347	P29966	MARCS_HUMAN	myristoylated alanine-rich protein kinase C	152	Calmodulin-binding (PSD).				energy reserve metabolic process|regulation of insulin secretion	actin cytoskeleton|plasma membrane	actin filament binding|calmodulin binding				0		all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198)		Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	115174939	115174939	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115174939delT								HS3ST5 (511399 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115263259	115263259	+	IGR	DEL	C	-	-	rs67347646		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115263259delC								HS3ST5 (599719 upstream) : FRK (999434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115762963	115762963	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115762963delA								None (None upstream) : FRK (499730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115806947	115806947	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115806947delT								None (None upstream) : FRK (455746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116058648	116058651	+	IGR	DEL	CACA	-	-	rs112275057		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116058648_116058651delCACA								None (None upstream) : FRK (204042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116235127	116235128	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116235127_116235128insT								None (None upstream) : FRK (27565 downstream)																																			---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117706684	117706684	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117706684delA	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935			proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117761584	117761584	+	Intron	DEL	A	-	-	rs71763591		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117761584delA	uc003pxq.1	-							NM_001017408	NP_001017408			golgi associated PDZ and coiled-coil motif						apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding			ovary(1)	1		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)				O	ROS1	glioblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	6	117936012	117936013	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117936012_117936013delAA								GOPC (12331 upstream) : NUS1 (60604 downstream)																																			---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118472285	118472286	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118472285_118472286insA	uc003pxx.3	+							NM_001029858	NP_001025029			solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	119012163	119012163	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119012163delA	uc003pya.1	-						C6orf204_uc003pyc.2_Intron	NM_206921	NP_996804			chromosome 6 open reading frame 204 isoform b							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)														---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121563198	121563198	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121563198delA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943			hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)														---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121600547	121600547	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121600547delA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943			hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)														---	---	---	---
GJA1	2697	broad.mit.edu	37	6	121761354	121761355	+	Intron	DEL	TT	-	-	rs3840370		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121761354_121761355delTT	uc003pyr.2	+						GJA1_uc011ebo.1_Intron|GJA1_uc011ebp.1_Intron	NM_000165	NP_000156			connexin 43						cell-cell signaling|cellular membrane organization|gap junction assembly|heart development|muscle contraction|positive regulation of I-kappaB kinase/NF-kappaB cascade	connexon complex|Golgi-associated vesicle membrane|integral to plasma membrane|membrane raft	ion transmembrane transporter activity|signal transducer activity			ovary(2)	2				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	121822834	121822835	+	IGR	INS	-	T	T	rs142424180	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121822834_121822835insT								GJA1 (51962 upstream) : HSF2 (897861 downstream)																																			---	---	---	---
PKIB	5570	broad.mit.edu	37	6	122983627	122983627	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122983627delT	uc003pyz.2	+						PKIB_uc003pza.2_Intron|PKIB_uc003pzb.2_Intron|PKIB_uc003pzc.2_Intron	NM_181794	NP_861459			cAMP-dependent protein kinase inhibitor beta								cAMP-dependent protein kinase inhibitor activity				0				GBM - Glioblastoma multiforme(226;0.164)														---	---	---	---
FABP7	2173	broad.mit.edu	37	6	123101679	123101679	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123101679delT	uc003pzf.2	+						FABP7_uc003pzd.2_Intron|FABP7_uc003pze.1_3'UTR	NM_001446	NP_001437			fatty acid binding protein 7, brain						negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	126783679	126783680	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126783679_126783680delCA	uc003qaq.1	-						CENPW_uc003qap.3_Intron					Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127016049	127016050	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127016049_127016050insT	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127338168	127338169	+	Intron	INS	-	TA	TA	rs10678256		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127338168_127338169insTA	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127683600	127683600	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127683600delA								ECHDC1 (18846 upstream) : C6orf174 (75952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127953809	127953809	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127953809delA								C6orf58 (40851 upstream) : THEMIS (75537 downstream)																																			---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128319794	128319794	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128319794delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129217555	129217556	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129217555_129217556delTT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129651744	129651745	+	Intron	DEL	TT	-	-	rs149171723		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129651744_129651745delTT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129706404	129706404	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129706404delG	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129796506	129796506	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129796506delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129909689	129909689	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129909689delC	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131199492	131199492	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131199492delA	uc003qch.2	-						EPB41L2_uc003qce.1_Intron|EPB41L2_uc003qcf.1_Intron|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron|EPB41L2_uc003qcj.1_5'Flank	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131276835	131276836	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131276835_131276836delAA	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	131768108	131768108	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131768108delG								AKAP7 (163435 upstream) : ARG1 (126257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132090500	132090501	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132090500_132090501insT								ENPP3 (21951 upstream) : ENPP1 (38655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132444630	132444630	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132444630delA								CTGF (172112 upstream) : MOXD1 (172565 downstream)																																			---	---	---	---
VNN3	55350	broad.mit.edu	37	6	133055258	133055258	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133055258delA	uc003qdp.2	-						VNN3_uc010kfs.2_Intron|VNN3_uc011ecl.1_Intron|VNN3_uc011ecm.1_Intron|VNN3_uc011ecn.1_Intron|VNN3_uc010kfu.2_Intron|VNN3_uc010kfv.2_Intron|VNN3_uc010kfw.2_Intron|VNN3_uc010kfx.2_Intron|VNN3_uc010kfy.2_Intron|VNN3_uc010kfz.2_Intron	NM_078625	NP_523239			SubName: Full=PAGEL-beta;												0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00242)|GBM - Glioblastoma multiforme(226;0.0168)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133599244	133599244	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133599244delT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134707148	134707159	+	IGR	DEL	GAAGGAAGGAAG	-	-	rs66858982		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134707148_134707159delGAAGGAAGGAAG								SGK1 (67952 upstream) : ALDH8A1 (531370 downstream)																																			---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	135861930	135861930	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135861930delA	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron|C6orf217_uc003qgm.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
BCLAF1	9774	broad.mit.edu	37	6	136582364	136582364	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136582364delA	uc003qgx.1	-						BCLAF1_uc011edb.1_Intron|BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Intron|BCLAF1_uc011edc.1_Intron|BCLAF1_uc011edd.1_Intron|BCLAF1_uc011ede.1_Intron	NM_014739	NP_055554			BCL2-associated transcription factor 1 isoform						induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136883493	136883494	+	Intron	DEL	TT	-	-	rs11322947		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136883493_136883494delTT	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136904967	136904967	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136904967delT	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
PEX7	5191	broad.mit.edu	37	6	137190527	137190528	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137190527_137190528delGT	uc003qhd.2	+						PEX7_uc010kgx.2_Intron	NM_000288	NP_000279			peroxisomal biogenesis factor 7						ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)														---	---	---	---
NHSL1	57224	broad.mit.edu	37	6	138750712	138750712	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138750712delA	uc003qhx.2	-						NHSL1_uc011edp.1_Intron	NM_020464	NP_065197			NHS-like 1 isoform 1												0																OREG0017693	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CITED2	10370	broad.mit.edu	37	6	139694105	139694105	+	3'UTR	DEL	T	-	-	rs10708981		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139694105delT	uc003qip.1	-	2						NM_006079	NP_006070			Cbp/p300-interacting transactivator, with						adrenal cortex formation|anti-apoptosis|cell proliferation|determination of left/right symmetry|heart development|liver development|negative regulation of cell migration|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell cycle|positive regulation of cell-cell adhesion|positive regulation of male gonad development|positive regulation of peroxisome proliferator activated receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of organ formation|response to estrogen stimulus|response to fluid shear stress|response to hypoxia|sex determination	cytoplasm|nuclear chromatin|nucleus	chromatin binding|LBD domain binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity				0	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140121919	140121920	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140121919_140121920insT	uc003qir.2	+											Homo sapiens, clone IMAGE:5557975, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140545464	140545465	+	IGR	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140545464_140545465insAC								CITED2 (849679 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	142041683	142041684	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142041683_142041684insA	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142759336	142759336	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142759336delT	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron|GPR126_uc011edv.1_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143090598	143090598	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143090598delT	uc003qjd.2	-							NM_006734	NP_006725			human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143469957	143469957	+	Intron	DEL	A	-	-	rs75465637		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143469957delA	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron|AIG1_uc011edw.1_Intron|AIG1_uc003qjg.2_Intron	NM_016108	NP_057192			androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)														---	---	---	---
LTV1	84946	broad.mit.edu	37	6	144181842	144181842	+	Intron	DEL	A	-	-	rs138724144	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144181842delA	uc003qjs.2	+						LTV1_uc003qju.1_Intron|C6orf94_uc010khj.2_Intron	NM_032860	NP_116249			LTV1 homolog											ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	145029206	145029206	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145029206delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	145093031	145093031	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145093031delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	148091391	148091391	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148091391delT								SAMD5 (200234 upstream) : SASH1 (572338 downstream)																																			---	---	---	---
UST	10090	broad.mit.edu	37	6	149326140	149326141	+	Intron	INS	-	T	T	rs145839547		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149326140_149326141insT	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
UST	10090	broad.mit.edu	37	6	149358451	149358451	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149358451delT	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149808515	149808515	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149808515delA	uc010kic.2	-						ZC3H12D_uc003qmm.2_5'Flank|ZC3H12D_uc010kid.2_5'Flank	NM_139126				peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149856948	149856948	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149856948delA	uc003qmo.1	-						PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Intron	NM_139126	NP_624311			peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150103892	150103892	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150103892delA	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	151475923	151475923	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151475923delA								MTHFD1L (52903 upstream) : AKAP12 (85211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	151943913	151943913	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151943913delA								C6orf97 (1586 upstream) : ESR1 (67718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	151946369	151946369	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151946369delA								C6orf97 (4042 upstream) : ESR1 (65262 downstream)																																			---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152241011	152241012	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152241011_152241012delAC	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Intron|ESR1_uc011eex.1_Intron	NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152783720	152783720	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152783720delT	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_3'UTR|SYNE1_uc003qow.2_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152793572	152793572	+	Intron	DEL	T	-	-	rs4331993		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152793572delT	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154904788	154904789	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154904788_154904789delAA								CNKSR3 (73035 upstream) : RBM16 (149723 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155170215	155170215	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155170215delT	uc003qqb.2	+							NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155318138	155318139	+	Intron	DEL	AT	-	-	rs138748666		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155318138_155318139delAT	uc003qqb.2	+							NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155575539	155575539	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155575539delC	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron|TIAM2_uc003qqh.2_Intron|uc003qqi.1_RNA	NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	158195314	158195315	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158195314_158195315delGA								ZDHHC14 (100338 upstream) : SNX9 (48979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	158726357	158726358	+	IGR	DEL	GT	-	-	rs112329118		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158726357_158726358delGT								GTF2H5 (105991 upstream) : TULP4 (7334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	159547985	159547986	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159547985_159547986delTT								TAGAP (81801 upstream) : FNDC1 (42443 downstream)																																			---	---	---	---
WTAP	9589	broad.mit.edu	37	6	160164678	160164678	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160164678delT	uc003qsl.2	+						WTAP_uc010kjx.2_Intron|WTAP_uc003qsk.2_Intron|WTAP_uc003qsm.1_Intron|WTAP_uc003qsn.2_Intron	NM_004906	NP_004897			Wilms' tumour 1-associating protein isoform 1						cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)														---	---	---	---
MRPL18	29074	broad.mit.edu	37	6	160219059	160219059	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160219059delT	uc003qsw.3	+						MRPL18_uc010kkb.2_Intron|PNLDC1_uc003qsx.1_5'Flank|PNLDC1_uc003qsy.1_5'Flank	NM_014161	NP_054880			mitochondrial ribosomal protein L18 precursor						rRNA transport|translation	mitochondrial ribosome	5S rRNA binding|structural constituent of ribosome				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160427238	160427239	+	Intron	INS	-	C	C	rs138795126	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160427238_160427239insC	uc003qta.2	+							NM_000876	NP_000867			insulin-like growth factor 2 receptor precursor						receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160793735	160793736	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160793735_160793736insT	uc003qti.2	+						SLC22A3_uc011efx.1_Intron	NM_021977	NP_068812			solute carrier family 22 member 3							integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)														---	---	---	---
LPAL2	80350	broad.mit.edu	37	6	160887595	160887595	+	RNA	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160887595delT	uc003qtj.2	-	10		c.1960delA				NR_028093				Homo sapiens cDNA FLJ43922 fis, clone TESTI4012406.												0		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)														---	---	---	---
LPA	4018	broad.mit.edu	37	6	160953129	160953129	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160953129delA	uc003qtl.2	-							NM_005577	NP_005568			lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)													---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163596776	163596777	+	Intron	INS	-	AGGAGG	AGGAGG	rs5881509		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163596776_163596777insAGGAGG	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron|uc011egg.1_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
QKI	9444	broad.mit.edu	37	6	163899920	163899920	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163899920delA	uc003qui.2	+	3	945	c.394delA	c.(394-396)AAAfs	p.K132fs	QKI_uc003que.2_Frame_Shift_Del_p.K132fs|QKI_uc003quf.2_Frame_Shift_Del_p.K132fs|QKI_uc003qug.2_Frame_Shift_Del_p.K132fs|QKI_uc003quh.2_Frame_Shift_Del_p.K132fs|QKI_uc003quj.2_Frame_Shift_Del_p.K132fs	NM_006775	NP_006766	Q96PU8	QKI_HUMAN	quaking homolog, KH domain RNA binding isoform	132	KH.				mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	164816487	164816487	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164816487delT								QKI (821595 upstream) : C6orf118 (876668 downstream)																																			---	---	---	---
C6orf118	168090	broad.mit.edu	37	6	165720404	165720405	+	Intron	INS	-	TG	TG	rs145859741	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165720404_165720405insTG	uc003qum.3	-						C6orf118_uc011egi.1_Intron	NM_144980	NP_659417			hypothetical protein LOC168090												0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)														---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	165977377	165977378	+	Intron	DEL	AA	-	-	rs71653280		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165977377_165977378delAA	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652			phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)													---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167156685	167156686	+	Intron	INS	-	C	C	rs149519272	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167156685_167156686insC	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167175881	167175882	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167175881_167175882delTG	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
CCR6	1235	broad.mit.edu	37	6	167416821	167416821	+	5'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167416821delT	uc003qvl.2	+	3					FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvj.2_Intron|FGFR1OP_uc003qvk.2_Intron	NM_031409	NP_113597			chemokine (C-C motif) receptor 6						cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	168052216	168052217	+	IGR	INS	-	TG	TG	rs149093424		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168052216_168052217insTG								TCP10 (254218 upstream) : C6orf123 (133004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168131809	168131810	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168131809_168131810delAA								TCP10 (333811 upstream) : C6orf123 (53411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168584308	168584308	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168584308delT								FRMD1 (104469 upstream) : DACT2 (123278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168801074	168801074	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168801074delA								DACT2 (80672 upstream) : SMOC2 (40957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168823847	168823848	+	IGR	DEL	CG	-	-	rs2763268		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168823847_168823848delCG								DACT2 (103445 upstream) : SMOC2 (18183 downstream)																																			---	---	---	---
WDR27	253769	broad.mit.edu	37	6	169964801	169964802	+	Intron	INS	-	GA	GA	rs147733878	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169964801_169964802insGA	uc003qwx.2	-						WDR27_uc003qwv.1_Intron|WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron					RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)														---	---	---	---
WDR27	253769	broad.mit.edu	37	6	170098504	170098505	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170098504_170098505delAC	uc003qwx.2	-						WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron|WDR27_uc011egw.1_Intron|WDR27_uc010kkx.2_Intron					RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)														---	---	---	---
DLL1	28514	broad.mit.edu	37	6	170592276	170592276	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170592276delC	uc003qxm.2	-							NM_005618	NP_005609			delta-like 1 precursor						cell communication|cell fate determination|hemopoiesis|Notch receptor processing|Notch signaling pathway|regulation of cell adhesion	extracellular region|integral to plasma membrane	calcium ion binding|Notch binding			lung(4)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)														---	---	---	---
PSMB1	5689	broad.mit.edu	37	6	170857592	170857593	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170857592_170857593delAA	uc011ehe.1	-						PSMB1_uc003qxq.2_Intron|PSMB1_uc003qxr.2_Intron	NM_002793	NP_002784			proteasome beta 1 subunit precursor						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cell junction|cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)													---	---	---	---
SUN1	23353	broad.mit.edu	37	7	858508	858508	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:858508delT	uc011jvp.1	+						SUN1_uc010ksa.1_Intron|SUN1_uc003sje.1_Intron|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron	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																		---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2404086	2404086	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2404086delG	uc003slx.2	+	6	1162	c.1079delG	c.(1078-1080)TGGfs	p.W360fs	EIF3B_uc003sly.2_Frame_Shift_Del_p.W360fs|EIF3B_uc003slz.1_Frame_Shift_Del_p.W321fs|EIF3B_uc003sma.2_Frame_Shift_Del_p.W88fs	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,	360	Sufficient for interaction with EIF3E.|WD 1.				regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)														---	---	---	---
CARD11	84433	broad.mit.edu	37	7	3039522	3039523	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3039522_3039523delTT	uc003smv.2	-							NM_032415	NP_115791			caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
FOXK1	221937	broad.mit.edu	37	7	4697208	4697208	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4697208delA	uc003sna.1	+							NM_001037165	NP_001032242			forkhead box K1						cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5196779	5196779	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5196779delA								LOC389458 (83926 upstream) : WIPI2 (33056 downstream)																																			---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5444748	5444748	+	Intron	DEL	A	-	-	rs112000838		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5444748delA	uc003soi.3	-						TNRC18_uc010ksx.1_Intron|TNRC18_uc003sok.1_Intron	NM_001080495	NP_001073964			trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)														---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5448286	5448286	+	Intron	DEL	A	-	-	rs61635186	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5448286delA	uc003soi.3	-						TNRC18_uc010ksx.1_Intron|TNRC18_uc003sok.1_Intron	NM_001080495	NP_001073964			trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5471500	5471501	+	IGR	DEL	AC	-	-	rs72179962		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5471500_5471501delAC								TNRC18 (6455 upstream) : FBXL18 (43928 downstream)																																			---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5729959	5729960	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5729959_5729960delAA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron|RNF216_uc003spa.1_RNA	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
AIMP2	7965	broad.mit.edu	37	7	6052639	6052640	+	Intron	DEL	AA	-	-	rs143685042		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6052639_6052640delAA	uc003spo.2	+							NM_006303	NP_006294			aminoacyl tRNA synthetase complex-interacting						apoptosis|cell differentiation|multicellular organismal development|tRNA aminoacylation for protein translation	cytosol|nucleus	protein binding			ovary(1)	1																		---	---	---	---
RAC1	5879	broad.mit.edu	37	7	6439959	6439959	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6439959delT	uc003spx.2	+						RAC1_uc003spw.2_Intron	NM_006908	NP_008839			ras-related C3 botulinum toxin substrate 1						actin filament polymerization|apoptosis|axon guidance|cell motility|cell-matrix adhesion|induction of apoptosis by extracellular signals|inflammatory response|lamellipodium assembly|localization within membrane|negative regulation of interleukin-23 production|negative regulation of receptor-mediated endocytosis|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of lamellipodium assembly|positive regulation of Rho protein signal transduction|regulation of cell migration|regulation of defense response to virus by virus|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|ruffle organization|small GTPase mediated signal transduction|T cell costimulation|viral reproduction	cytosol|melanosome|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity|thioesterase binding			lung(2)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Pravastatin(DB00175)|Simvastatin(DB00641)													---	---	---	---
RAC1	5879	broad.mit.edu	37	7	6442157	6442158	+	3'UTR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6442157_6442158delAA	uc003spx.2	+	6					RAC1_uc003spw.2_3'UTR	NM_006908	NP_008839			ras-related C3 botulinum toxin substrate 1						actin filament polymerization|apoptosis|axon guidance|cell motility|cell-matrix adhesion|induction of apoptosis by extracellular signals|inflammatory response|lamellipodium assembly|localization within membrane|negative regulation of interleukin-23 production|negative regulation of receptor-mediated endocytosis|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of lamellipodium assembly|positive regulation of Rho protein signal transduction|regulation of cell migration|regulation of defense response to virus by virus|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|ruffle organization|small GTPase mediated signal transduction|T cell costimulation|viral reproduction	cytosol|melanosome|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity|thioesterase binding			lung(2)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Pravastatin(DB00175)|Simvastatin(DB00641)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	6600001	6600002	+	IGR	INS	-	T	T	rs67127957		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6600001_6600002insT								GRID2IP (8934 upstream) : ZDHHC4 (17063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	6605655	6605655	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6605655delT								GRID2IP (14588 upstream) : ZDHHC4 (11410 downstream)																																			---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7440319	7440319	+	Intron	DEL	A	-	-	rs34102862		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7440319delA	uc003src.1	-						COL28A1_uc011jxe.1_Intron	NM_001037763	NP_001032852			collagen, type XXVIII precursor						cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	9957859	9957860	+	IGR	INS	-	G	G	rs141737395	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9957859_9957860insG								PER4 (282412 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10735648	10735648	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10735648delC								None (None upstream) : NDUFA4 (237167 downstream)																																			---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11059718	11059718	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11059718delT	uc003sry.1	+						PHF14_uc011jxi.1_Intron|PHF14_uc003srz.2_Intron|PHF14_uc011jxj.1_Intron	NM_014660	NP_055475			PHD finger protein 14 isoform 2								zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14530576	14530577	+	Intron	DEL	TT	-	-	rs67652801		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14530576_14530577delTT	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_Intron|DGKB_uc011jxu.1_Intron	NM_004080	NP_004071			diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)													---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15353778	15353778	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15353778delA	uc003stb.1	-							NM_001004320	NP_001004320			transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	15649001	15649002	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15649001_15649002insA								TMEM195 (47361 upstream) : MEOX2 (1837 downstream)																																			---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20194102	20194103	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20194102_20194103insT	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439			putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21895856	21895856	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21895856delA	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	22661424	22661425	+	IGR	INS	-	AT	AT	rs150423998	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22661424_22661425insAT								MGC87042 (121626 upstream) : IL6 (104078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	23520217	23520218	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23520217_23520218insC								IGF2BP3 (10222 upstream) : RPS2P32 (9789 downstream)																																			---	---	---	---
C7orf46	340277	broad.mit.edu	37	7	23738918	23738919	+	Intron	INS	-	G	G	rs142028325	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23738918_23738919insG	uc003swo.3	+						C7orf46_uc003swq.3_Intron|C7orf46_uc003swr.3_Intron|C7orf46_uc003swp.3_Intron|C7orf46_uc010kup.2_Intron	NM_199136	NP_954587			hypothetical protein LOC340277 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25060018	25060018	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25060018delA								OSBPL3 (40258 upstream) : CYCS (98259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25835828	25835828	+	IGR	DEL	A	-	-	rs35541376		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25835828delA								NPVF (567723 upstream) : MIR148A (153711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26268441	26268441	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26268441delT								CBX3 (15467 upstream) : SNX10 (63074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26424918	26424918	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26424918delG								SNX10 (10981 upstream) : LOC441204 (13421 downstream)																																			---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26872856	26872857	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26872856_26872857insA	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29537108	29537108	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29537108delT	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron|CHN2_uc010kvg.2_Intron|CHN2_uc010kvh.2_Intron|CHN2_uc010kvi.2_Intron|CHN2_uc010kve.2_Intron|CHN2_uc003taa.2_Intron|CHN2_uc010kvf.2_Intron|CHN2_uc010kvj.2_Intron|CHN2_uc010kvk.2_Intron|CHN2_uc010kvl.2_Intron|CHN2_uc010kvm.2_Intron|CHN2_uc011jzv.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
SCRN1	9805	broad.mit.edu	37	7	29994603	29994603	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29994603delT	uc010kvp.2	-						SCRN1_uc011jzy.1_Intron|SCRN1_uc003tak.2_Intron|SCRN1_uc011jzz.1_Intron|SCRN1_uc011kaa.1_Intron|SCRN1_uc011jzw.1_Intron|SCRN1_uc011jzx.1_Intron	NM_001145515	NP_001138987			secernin 1 isoform c						exocytosis|proteolysis	cytoplasm|nuclear membrane	dipeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30565749	30565749	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30565749delG	uc003tbd.2	-											Homo sapiens full length insert cDNA clone ZC66C07.																														---	---	---	---
CRHR2	1395	broad.mit.edu	37	7	30694783	30694783	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30694783delG	uc003tbn.2	-						CRHR2_uc010kvw.1_Intron|CRHR2_uc010kvx.1_Intron|CRHR2_uc010kvy.1_Intron|CRHR2_uc003tbo.2_Intron|CRHR2_uc003tbp.2_Intron	NM_001883	NP_001874			corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	33076071	33076072	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33076071_33076072delTT	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron|uc003tdl.1_RNA	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
BMPER	168667	broad.mit.edu	37	7	33977126	33977127	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33977126_33977127delGT	uc011kap.1	+							NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
HERPUD2	64224	broad.mit.edu	37	7	35709759	35709760	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35709759_35709760insA	uc003tet.2	-						HERPUD2_uc003tes.3_Intron	NM_022373	NP_071768			HERPUD family member 2						response to unfolded protein	integral to membrane				ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36056096	36056096	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36056096delG								SEPT7 (111181 upstream) : EEPD1 (136740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	37735418	37735419	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37735418_37735419insA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																														---	---	---	---
TARP	445347	broad.mit.edu	37	7	38335621	38335621	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38335621delT	uc003tge.1	-						uc003tfz.1_Intron|TARP_uc003tgf.1_Intron|TARP_uc003tgj.1_Intron|TARP_uc003tgh.1_Intron|TARP_uc003tgi.1_Intron|TARP_uc003tgg.1_Intron					Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.												0																		---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40117455	40117455	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40117455delA	uc003thh.3	+						CDK13_uc003thi.3_Intron|CDK13_uc003thj.2_Intron	NM_003718	NP_003709			cell division cycle 2-like 5 isoform 1						alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40337741	40337741	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40337741delG	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	41444090	41444090	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41444090delA								C7orf10 (543733 upstream) : INHBA (284513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42831527	42831527	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42831527delA								GLI3 (554909 upstream) : C7orf25 (117347 downstream)																																			---	---	---	---
C7orf25	79020	broad.mit.edu	37	7	42966271	42966271	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42966271delA	uc010kxr.2	-						PSMA2_uc003thy.2_Intron|PSMA2_uc010kxt.2_Intron|PSMA2_uc003thz.1_Intron	NM_001099858	NP_001093328			hypothetical protein LOC79020 a											skin(1)	1																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43274110	43274110	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43274110delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44416365	44416366	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44416365_44416366insC								CAMK2B (51135 upstream) : NUDCD3 (5601 downstream)																																			---	---	---	---
DDX56	54606	broad.mit.edu	37	7	44610647	44610648	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44610647_44610648insT	uc003tlg.2	-						DDX56_uc003tle.2_Intron|DDX56_uc003tlf.2_Intron|DDX56_uc003tlh.2_Intron|DDX56_uc010kyg.2_Intron|DDX56_uc010kyh.1_Intron	NM_019082	NP_061955			DEAD (Asp-Glu-Ala-Asp) box polypeptide 56						rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44644856	44644856	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44644856delA	uc003tln.2	+						OGDH_uc003tlm.2_5'Flank|OGDH_uc011kbx.1_5'Flank|OGDH_uc011kby.1_5'Flank	NM_002541	NP_002532			oxoglutarate dehydrogenase isoform 1 precursor						glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	45975848	45975848	+	IGR	DEL	C	-	-	rs34616821	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45975848delC								IGFBP3 (14977 upstream) : None (None downstream)																																			---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47890691	47890692	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47890691_47890692delAC	uc003tny.1	-							NM_138295	NP_612152			polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47901793	47901793	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47901793delA	uc003tny.1	-							NM_138295	NP_612152			polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
ZPBP	11055	broad.mit.edu	37	7	50043834	50043834	+	Intron	DEL	T	-	-	rs71756643		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50043834delT	uc003tou.2	-						ZPBP_uc011kci.1_Intron|ZPBP_uc010kyw.2_Intron	NM_007009	NP_008940			zona pellucida binding protein isoform 1						binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	52204886	52204887	+	IGR	INS	-	AGG	AGG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52204886_52204887insAGG								COBL (820371 upstream) : POM121L12 (898462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52987209	52987210	+	IGR	INS	-	A	A	rs141272630	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52987209_52987210insA								None (None upstream) : POM121L12 (116139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53571084	53571085	+	IGR	INS	-	T	T	rs113757422		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53571084_53571085insT								POM121L12 (466467 upstream) : HPVC1 (697832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54604896	54604897	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54604896_54604897insT								HPVC1 (334782 upstream) : VSTM2A (5122 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55191521	55191522	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55191521_55191522delTG	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron|EGFR_uc011kco.1_Intron	NM_005228	NP_005219			epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55780173	55780174	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55780173_55780174insA								FKBP9L (7913 upstream) : SEPT14 (81063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56316266	56316267	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56316266_56316267delCA								PSPH (132176 upstream) : DKFZp434L192 (247649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56776556	56776557	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56776556_56776557delTG								DKFZp434L192 (211579 upstream) : ZNF479 (410771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61749684	61749684	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61749684delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61763050	61763050	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61763050delA								None (None upstream) : LOC643955 (988622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61765778	61765778	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61765778delA								None (None upstream) : LOC643955 (985894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61910112	61910113	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61910112_61910113insT								None (None upstream) : LOC643955 (841559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62476043	62476044	+	IGR	DEL	TC	-	-	rs66464406		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62476043_62476044delTC								None (None upstream) : LOC643955 (275628 downstream)																																	OREG0018084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	7	62579295	62579295	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62579295delA								None (None upstream) : LOC643955 (172377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62692288	62692288	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62692288delA								None (None upstream) : LOC643955 (59384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62706803	62706803	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62706803delA								None (None upstream) : LOC643955 (44869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62728438	62728438	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62728438delA								None (None upstream) : LOC643955 (23234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63466581	63466581	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63466581delT								LOC100287704 (654430 upstream) : ZNF727 (39240 downstream)																																			---	---	---	---
ZNF273	10793	broad.mit.edu	37	7	64348585	64348586	+	Intron	INS	-	GCT	GCT	rs137940981	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64348585_64348586insGCT	uc003ttl.2	+						uc003ttk.1_Intron	NM_021148	NP_066971			zinc finger protein 273						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(55;0.0295)|all_lung(88;0.0691)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	64395133	64395133	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64395133delT								ZNF273 (3180 upstream) : ZNF117 (39697 downstream)																																			---	---	---	---
ZNF117	51351	broad.mit.edu	37	7	64446743	64446743	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64446743delA	uc003ttr.2	-							NM_015852	NP_056936			zinc finger protein 117							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)																---	---	---	---
STAG3L4	64940	broad.mit.edu	37	7	66770959	66770959	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66770959delT	uc003tvt.3	+						STAG3L4_uc010laj.2_Intron	NM_022906	NP_075057			stromal antigen 3-like 4												0		Lung NSC(55;0.0839)|all_lung(88;0.181)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	68297943	68297944	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68297943_68297944delTT								None (None upstream) : AUTS2 (765961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68815860	68815860	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68815860delT								None (None upstream) : AUTS2 (248045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68883788	68883788	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68883788delT								None (None upstream) : AUTS2 (180117 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70011775	70011776	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70011775_70011776delAA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	71145595	71145601	+	Intron	DEL	CCCTCTC	-	-	rs148790962		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71145595_71145601delCCCTCTC	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72040751	72040751	+	Intron	DEL	A	-	-	rs72347331		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72040751delA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
POM121	9883	broad.mit.edu	37	7	72409038	72409038	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72409038delT	uc003twk.2	+						POM121_uc003twj.2_Intron|POM121_uc010lam.1_Intron	NM_172020	NP_742017			nuclear pore membrane protein 121						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)																---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72860110	72860110	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72860110delA	uc003tyc.2	-							NM_032408	NP_115784			bromodomain adjacent to zinc finger domain, 1B						ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	73052944	73052947	+	IGR	DEL	TTTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73052944_73052947delTTTG								MLXIPL (14074 upstream) : VPS37D (29227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	73058975	73058975	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73058975delC								MLXIPL (20105 upstream) : VPS37D (23199 downstream)																																			---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73182656	73182657	+	Intron	INS	-	T	T	rs11465063		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73182656_73182657insT	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73981670	73981670	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73981670delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																OREG0018121	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74105135	74105135	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74105135delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74122205	74122205	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74122205delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|uc003uaz.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74172387	74172388	+	Intron	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74172387_74172388insC	uc003uau.2	+						GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|GTF2I_uc003uba.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
WBSCR16	81554	broad.mit.edu	37	7	74470283	74470283	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74470283delT	uc003ubr.2	-						WBSCR16_uc010lca.2_Intron|WBSCR16_uc010lcb.1_Intron	NM_030798	NP_110425			Williams-Beuren syndrome chromosome region 16												0																		---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75068666	75068666	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75068666delT	uc010lde.1	-						POM121C_uc003udk.3_Intron					Homo sapiens POM121-2 mRNA for nuclear pore membrane protein 121-2, partial cds.						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0																		---	---	---	---
CCL24	6369	broad.mit.edu	37	7	75442903	75442903	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75442903delC	uc011kga.1	-							NM_002991	NP_002982			small inducible cytokine A24 precursor						cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity				0																		---	---	---	---
YWHAG	7532	broad.mit.edu	37	7	75990616	75990617	+	5'Flank	INS	-	AAAAAAAAAAA	AAAAAAAAAAA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75990616_75990617insAAAAAAAAAAA	uc011kgj.1	-							NM_012479	NP_036611			tyrosine 3-monooxygenase/tryptophan						G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	76006455	76006458	+	IGR	DEL	AAAG	-	-	rs71799935		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76006455_76006458delAAAG								YWHAG (18113 upstream) : SRCRB4D (12189 downstream)																																			---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76053177	76053177	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76053177delA	uc003ufd.3	+						ZP3_uc003ufc.3_Intron	NM_001110354	NP_001103824			zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76054009	76054010	+	5'Flank	INS	-	A	A	rs76164389		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76054009_76054010insA	uc003ufd.3	+						ZP3_uc003ufc.3_Intron	NM_001110354	NP_001103824			zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	76683932	76683933	+	IGR	INS	-	GA	GA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76683932_76683933insGA								LOC100132832 (1577 upstream) : CCDC146 (68001 downstream)																																			---	---	---	---
CCDC146	57639	broad.mit.edu	37	7	76809593	76809594	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76809593_76809594delAC	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930			coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)																---	---	---	---
PTPN12	5782	broad.mit.edu	37	7	77247668	77247669	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77247668_77247669delTT	uc003ugh.2	+						PTPN12_uc011kgp.1_Intron|PTPN12_uc011kgq.1_Intron|PTPN12_uc010lds.2_Intron	NM_002835	NP_002826			protein tyrosine phosphatase, non-receptor type							soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
PHTF2	57157	broad.mit.edu	37	7	77494098	77494098	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77494098delT	uc003ugs.3	+						PHTF2_uc003ugo.3_Intron|PHTF2_uc003ugp.2_Intron|PHTF2_uc003ugq.3_Intron|PHTF2_uc010ldv.2_Intron|PHTF2_uc003ugr.3_Intron|PHTF2_uc003ugt.3_Intron|PHTF2_uc003ugu.3_Intron	NM_001127357	NP_001120829			putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77996417	77996418	+	Intron	INS	-	ACAC	ACAC	rs144020618	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77996417_77996418insACAC	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	79467378	79467378	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79467378delA								MAGI2 (384488 upstream) : GNAI1 (296762 downstream)																																			---	---	---	---
CD36	948	broad.mit.edu	37	7	80042033	80042035	+	Intron	DEL	CTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80042033_80042035delCTT	uc003uhc.2	+							NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	82179802	82179803	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82179802_82179803delAA								CACNA2D1 (106771 upstream) : PCLO (203518 downstream)																																			---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83591153	83591153	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83591153delA	uc003uhz.2	-							NM_006080	NP_006071			semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	83980383	83980386	+	IGR	DEL	ACAC	-	-	rs72465895		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83980383_83980386delACAC								SEMA3A (156166 upstream) : SEMA3D (644488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	87119766	87119766	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87119766delA								ABCB4 (14747 upstream) : ABCB1 (13182 downstream)																																			---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87306303	87306304	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87306303_87306304insA	uc003uiz.1	-						ABCB1_uc003uja.1_Intron|ABCB1_uc010lei.1_Intron|RUNDC3B_uc011khd.1_Intron|RUNDC3B_uc003ujb.2_Intron|RUNDC3B_uc011khe.1_Intron|RUNDC3B_uc003ujc.2_Intron|RUNDC3B_uc003ujd.2_Intron	NM_000927	NP_000918			ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87674697	87674697	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87674697delT	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87772153	87772153	+	Intron	DEL	A	-	-	rs144525827		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87772153delA	uc003ujn.2	+						ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
SRI	6717	broad.mit.edu	37	7	87846632	87846632	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87846632delT	uc003ujq.1	-						SRI_uc011khg.1_Intron|SRI_uc003ujr.1_Intron|SRI_uc011khh.1_Intron|SRI_uc010lej.1_Intron	NM_003130	NP_003121			sorcin isoform a						heart development|intracellular sequestering of iron ion|muscle organ development|regulation of action potential|regulation of heart contraction|regulation of striated muscle contraction|signal transduction	sarcoplasmic reticulum membrane	calcium channel regulator activity|calcium ion binding|receptor binding			upper_aerodigestive_tract(1)	1	Esophageal squamous(14;0.00202)																	---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88571844	88571845	+	Intron	INS	-	TT	TT	rs139004943	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88571844_88571845insTT	uc011khi.1	+							NM_181646	NP_857597			zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89463259	89463260	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89463259_89463260delAA								ZNF804B (496915 upstream) : DPY19L2P4 (285454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89491627	89491627	+	IGR	DEL	G	-	-	rs34003276		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89491627delG								ZNF804B (525283 upstream) : DPY19L2P4 (257087 downstream)																																			---	---	---	---
STEAP1	26872	broad.mit.edu	37	7	89782843	89782843	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89782843delT	uc003ujx.2	+						STEAP1_uc010lem.2_5'Flank	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	89946406	89946406	+	IGR	DEL	T	-	-	rs35976683		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89946406delT								C7orf63 (6031 upstream) : GTPBP10 (23284 downstream)																																			---	---	---	---
GTPBP10	85865	broad.mit.edu	37	7	89982117	89982117	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89982117delT	uc003ukm.1	+						GTPBP10_uc003uki.1_Intron|GTPBP10_uc003ukj.1_Intron|GTPBP10_uc003ukk.1_Intron|GTPBP10_uc003ukl.1_Intron|GTPBP10_uc003ukn.1_Intron|GTPBP10_uc003uko.1_Intron	NM_033107	NP_149098			GTP-binding protein 10 isoform 2						ribosome biogenesis	chromosome|nucleolus	GTP binding|GTPase activity|magnesium ion binding				0																OREG0003797	type=REGULATORY REGION|Gene=BC021573|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90189304	90189304	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90189304delA	uc003ukt.1	+							NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90280814	90280815	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90280814_90280815insT	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	91292971	91292971	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91292971delA								FZD1 (394840 upstream) : MTERF (138489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91336318	91336318	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91336318delA								FZD1 (438187 upstream) : MTERF (95142 downstream)																																			---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91722747	91722747	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91722747delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron|AKAP9_uc003ull.2_Intron	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
CDK6	1021	broad.mit.edu	37	7	92404239	92404240	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92404239_92404240insA	uc011khw.1	-						CDK6_uc010lez.2_Intron	NM_001259	NP_001250			cyclin-dependent kinase 6						cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)					T	MLLT10	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	7	93544427	93544428	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93544427_93544428insA								GNGT1 (3942 upstream) : GNG11 (6588 downstream)																																			---	---	---	---
COL1A2	1278	broad.mit.edu	37	7	94042505	94042505	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94042505delT	uc003ung.1	+						COL1A2_uc011kib.1_Intron	NM_000089	NP_000080			alpha 2 type I collagen precursor						axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)										HNSCC(75;0.22)			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94717224	94717224	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94717224delA	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120			protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95838523	95838524	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95838523_95838524delCA	uc003uof.3	-						SLC25A13_uc003uog.3_Intron|SLC25A13_uc011kik.1_Intron	NM_014251	NP_055066			solute carrier family 25, member 13 isoform 2						ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	96156176	96156176	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96156176delA								SLC25A13 (204717 upstream) : SHFM1 (146061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97038390	97038390	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97038390delA								ACN9 (227317 upstream) : TAC1 (322881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97252823	97252823	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97252823delA								ACN9 (441750 upstream) : TAC1 (108448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97689464	97689466	+	IGR	DEL	TTT	-	-	rs112507209		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97689464_97689466delTTT								OCM2 (70048 upstream) : LMTK2 (46731 downstream)																																			---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97752279	97752279	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97752279delT	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	98130674	98130674	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98130674delT								BAIAP2L1 (100247 upstream) : NPTX2 (115923 downstream)																																			---	---	---	---
ARPC1B	10095	broad.mit.edu	37	7	98985523	98985523	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98985523delA	uc003upz.2	+						ARPC1A_uc011kit.1_Intron|ARPC1B_uc003uqa.2_Intron|ARPC1B_uc003uqb.2_Intron|ARPC1B_uc003uqc.2_Intron|ARPC1B_uc003uqd.2_5'Flank	NM_005720	NP_005711			actin related protein 2/3 complex subunit 1B						cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton				0	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PTCD1	26024	broad.mit.edu	37	7	99032218	99032220	+	Intron	DEL	AAA	-	-	rs80240572		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99032218_99032220delAAA	uc003uqh.2	-						PTCD1_uc011kiw.1_Intron	NM_015545	NP_056360			pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99796752	99796753	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99796752_99796753delAA	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron|STAG3_uc003uub.1_5'Flank	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100687124	100687124	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100687124delT	uc003uxp.1	+						MUC17_uc010lho.1_Intron	NM_001040105	NP_001035194			mucin 17 precursor							extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)																	---	---	---	---
RABL5	64792	broad.mit.edu	37	7	100961801	100961801	+	Intron	DEL	A	-	-	rs67705526	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100961801delA	uc003uyl.2	-						RABL5_uc011kkk.1_Intron|RABL5_uc011kkl.1_Intron|RABL5_uc003uym.2_Intron|RABL5_uc010lhw.2_Intron|RABL5_uc011kkm.1_Intron	NM_022777	NP_073614			RAB, member RAS oncogene family-like 5 isoform								GTP binding				0	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101040670	101040670	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101040670delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101043634	101043634	+	Intron	DEL	A	-	-	rs55932051		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101043634delA	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101048779	101048779	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101048779delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101177936	101177937	+	Intron	DEL	AC	-	-	rs71854925		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101177936_101177937delAC	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
MYL10	93408	broad.mit.edu	37	7	101266001	101266001	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101266001delC	uc003uyr.2	-							NM_138403	NP_612412			myosin, light chain 10, regulatory							mitochondrion	calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	101286740	101286740	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101286740delT								MYL10 (14164 upstream) : CUX1 (172552 downstream)																																			---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101839857	101839857	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101839857delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
SPDYE2	441273	broad.mit.edu	37	7	102197800	102197800	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102197800delG	uc011kkx.1	+						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron|POLR2J3_uc011kkw.1_Intron|SPDYE2_uc003vaa.1_Intron	NM_001031618	NP_001026789			speedy homolog E2												0																		---	---	---	---
UPK3BL	100134938	broad.mit.edu	37	7	102219557	102219559	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102219557_102219559delTTT	uc003uzy.2	-											Homo sapiens cDNA FLJ50019 complete cds, highly similar to Ras GTPase-activating protein 4.							integral to membrane					0																		---	---	---	---
NAPEPLD	222236	broad.mit.edu	37	7	102772111	102772113	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102772111_102772113delAAA	uc003vbc.2	-						NAPEPLD_uc003vbd.2_Intron|NAPEPLD_uc011klj.1_Intron|NAPEPLD_uc003vbe.2_Intron|NAPEPLD_uc003vbf.2_Intron	NM_198990	NP_945341			N-acyl phosphatidylethanolamine phospholipase D						phospholipid catabolic process	membrane	metal ion binding			skin(1)	1																		---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104746457	104746457	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104746457delT	uc003vcm.2	+						MLL5_uc010ljc.2_Intron|MLL5_uc010lje.1_Intron|MLL5_uc010ljf.1_5'Flank|MLL5_uc010ljg.2_5'Flank|MLL5_uc010ljh.1_5'Flank	NM_182931	NP_891847			myeloid/lymphoid or mixed-lineage leukemia 5						cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105769061	105769067	+	IGR	DEL	AAAAAAA	-	-	rs67747079		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105769061_105769067delAAAAAAA								SYPL1 (16004 upstream) : NAMPT (119667 downstream)																																			---	---	---	---
SLC26A4	5172	broad.mit.edu	37	7	107350347	107350347	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107350347delG	uc003vep.2	+						SLC26A4_uc011kmb.1_Intron|SLC26A4_uc011kmc.1_Intron|SLC26A4_uc011kmd.1_Intron	NM_000441	NP_000432			pendrin						regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7														Pendred_syndrome				---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107406419	107406419	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107406419delT	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102			solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107407972	107407972	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107407972delT	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102			solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107571786	107571787	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107571786_107571787insA	uc003vew.2	-						LAMB1_uc003vev.2_Intron|LAMB1_uc003veu.2_5'Flank	NM_002291	NP_002282			laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107791048	107791048	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107791048delT	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron|NRCAM_uc003vez.2_Intron|NRCAM_uc003vfa.2_Intron|NRCAM_uc011kmj.1_Intron	NM_001037132	NP_001032209			neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5																		---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107891095	107891095	+	Intron	DEL	A	-	-	rs115207803	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107891095delA	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209			neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108109517	108109518	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108109517_108109518delAA								NRCAM (12691 upstream) : PNPLA8 (2553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108188801	108188801	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108188801delA								PNPLA8 (20196 upstream) : THAP5 (13872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	111309608	111309608	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111309608delT								IMMP2L (107070 upstream) : DOCK4 (56557 downstream)																																			---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111452014	111452014	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111452014delA	uc003vfx.2	-						DOCK4_uc003vfw.2_Intron|DOCK4_uc003vfy.2_Intron|uc003vfz.2_Intron	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111722452	111722452	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111722452delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
IFRD1	3475	broad.mit.edu	37	7	112097284	112097284	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112097284delA	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgi.2_3'UTR|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron	NM_001007245	NP_001007246			interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	112628158	112628158	+	IGR	DEL	A	-	-	rs5886638		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112628158delA								C7orf60 (48226 upstream) : GPR85 (92310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	113701492	113701493	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113701492_113701493delTG								PPP1R3A (142410 upstream) : FOXP2 (24889 downstream)																																			---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	113972168	113972169	+	Intron	DEL	CG	-	-	rs2694932	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113972168_113972169delCG	uc003vgv.1	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgt.1_Intron	NM_014491	NP_055306			forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	114353365	114353365	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114353365delA								FOXP2 (22273 upstream) : MDFIC (208844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	115016616	115016618	+	IGR	DEL	AAG	-	-	rs10557418		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115016616_115016618delAAG								MDFIC (357353 upstream) : TFEC (558584 downstream)																																			---	---	---	---
MET	4233	broad.mit.edu	37	7	116317042	116317043	+	Intron	INS	-	T	T	rs147075688		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116317042_116317043insT	uc003vij.2	+						MET_uc010lkh.2_Intron|MET_uc003vii.1_Intron|MET_uc010lkg.2_Intron	NM_000245	NP_000236			met proto-oncogene isoform b precursor						axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)					Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117284115	117284115	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117284115delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483			cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
Unknown	0	broad.mit.edu	37	7	117556990	117556990	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117556990delT								CTTNBP2 (43429 upstream) : NAA38 (267096 downstream)																																			---	---	---	---
KCND2	3751	broad.mit.edu	37	7	119989377	119989378	+	Intron	INS	-	ACAA	ACAA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119989377_119989378insACAA	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	120579144	120579144	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120579144delA								TSPAN12 (80967 upstream) : ING3 (11673 downstream)																																			---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120629717	120629717	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120629717delC	uc003vjq.3	+	2	489	c.42delC	c.(40-42)TGCfs	p.C14fs	C7orf58_uc003vjr.1_Frame_Shift_Del_p.C14fs|C7orf58_uc003vjs.3_Frame_Shift_Del_p.C14fs	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	14						endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)																	---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121022823	121022823	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121022823delT	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703			family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)																	---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121519761	121519761	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121519761delA	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron	NM_002851	NP_002842			protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
AASS	10157	broad.mit.edu	37	7	121738966	121738966	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121738966delA	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754			aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
AASS	10157	broad.mit.edu	37	7	121753508	121753508	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121753508delT	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754			aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	121790986	121790989	+	IGR	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121790986_121790989delTTTT								AASS (6642 upstream) : FEZF1 (150460 downstream)																																			---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122000911	122000911	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122000911delT	uc010lkp.2	-						CADPS2_uc011knx.1_Intron|CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123225689	123225690	+	IGR	INS	-	TG	TG	rs151270068	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123225689_123225690insTG								NDUFA5 (27731 upstream) : ASB15 (16231 downstream)																																			---	---	---	---
ASB15	142685	broad.mit.edu	37	7	123254294	123254294	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123254294delA	uc003vku.1	+						ASB15_uc003vkv.1_Intron|ASB15_uc003vkw.1_Intron	NM_080928	NP_563616			ankyrin repeat and SOCS box-containing 15						intracellular signal transduction					skin(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123930145	123930146	+	Intron	INS	-	T	T	rs149170456	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123930145_123930146insT	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																														---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126682001	126682001	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126682001delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
IMPDH1	3614	broad.mit.edu	37	7	128038457	128038457	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128038457delG	uc011kol.1	-						IMPDH1_uc011kom.1_Intron|IMPDH1_uc003vmt.2_Intron|IMPDH1_uc003vmu.2_Intron|IMPDH1_uc003vmw.2_Intron|IMPDH1_uc011kon.1_Intron|IMPDH1_uc003vmv.2_Intron|IMPDH1_uc003vmx.2_Intron|IMPDH1_uc003vmy.2_Intron	NM_001142573	NP_001136045			inosine monophosphate dehydrogenase 1 isoform e						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)											OREG0018292	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
IMPDH1	3614	broad.mit.edu	37	7	128039741	128039742	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128039741_128039742delAA	uc011kol.1	-						IMPDH1_uc011kom.1_Intron|IMPDH1_uc003vmt.2_Intron|IMPDH1_uc003vmu.2_Intron|IMPDH1_uc003vmw.2_Intron|IMPDH1_uc011kon.1_Intron|IMPDH1_uc003vmv.2_Intron|IMPDH1_uc003vmx.2_Intron|IMPDH1_uc003vmy.2_Intron	NM_001142573	NP_001136045			inosine monophosphate dehydrogenase 1 isoform e						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)													---	---	---	---
UBE2H	7328	broad.mit.edu	37	7	129584591	129584592	+	Intron	DEL	CG	-	-	rs57052885		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129584591_129584592delCG	uc003vpf.1	-						UBE2H_uc003vpg.1_Intron	NM_003344	NP_003335			ubiquitin-conjugating enzyme E2H isoform 1						protein K11-linked ubiquitination|protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin-protein ligase activity			skin(1)	1	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130147428	130147428	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130147428delT	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	130504998	130504998	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130504998delT								KLF14 (86138 upstream) : MIR29A (56508 downstream)																																			---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130670092	130670093	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130670092_130670093insT	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131070103	131070104	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131070103_131070104delTT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	131299598	131299599	+	IGR	INS	-	A	A	rs77806172		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131299598_131299599insA								PODXL (58222 upstream) : PLXNA4 (508493 downstream)																																			---	---	---	---
AGBL3	340351	broad.mit.edu	37	7	134679031	134679031	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134679031delT	uc011kpw.1	+							NM_178563	NP_848658			carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135323163	135323165	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135323163_135323165delAAA	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135476195	135476203	+	IGR	DEL	TTTTTTTTT	-	-	rs72329465		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135476195_135476203delTTTTTTTTT								FAM180A (42601 upstream) : LUZP6 (135302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136047960	136047961	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136047960_136047961insT								LUZP6 (385756 upstream) : CHRM2 (505438 downstream)																																			---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137137627	137137627	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137137627delT	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137699044	137699045	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137699044_137699045insA	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137726955	137726955	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137726955delA	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137791279	137791279	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137791279delT	uc003vtz.2	+						AKR1D1_uc011kqe.1_Intron|AKR1D1_uc011kqf.1_Intron|AKR1D1_uc010lmy.1_Intron	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138269744	138269744	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138269744delA	uc003vuc.2	+	19					TRIM24_uc003vub.2_3'UTR	NM_015905	NP_056989			transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8																		---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138822525	138822525	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138822525delT	uc003vus.2	+						TTC26_uc003vuq.2_Intron|TTC26_uc011kqm.1_Intron|TTC26_uc003vur.3_Intron|TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202			tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1																		---	---	---	---
MRPS33	51650	broad.mit.edu	37	7	140710177	140710177	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140710177delA	uc003vwd.3	-						MRPS33_uc003vwe.3_Intron	NM_016071	NP_057155			mitochondrial ribosomal protein S33						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0	Melanoma(164;0.00956)																	---	---	---	---
EPHB6	2051	broad.mit.edu	37	7	142562309	142562309	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142562309delG	uc011kst.1	+	7	1538	c.751delG	c.(751-753)GGGfs	p.G251fs	EPHB6_uc011ksu.1_Frame_Shift_Del_p.G251fs|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	251	Extracellular (Potential).|Cys-rich.					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)																	---	---	---	---
TAS2R41	259287	broad.mit.edu	37	7	143175439	143175440	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143175439_143175440insT	uc003wdc.1	+	1	474_475	c.474_475insT	c.(472-477)GAATTTfs	p.E158fs	uc003wda.2_Intron	NM_176883	NP_795364	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	158_159	Extracellular (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			pancreas(1)|skin(1)	2	Melanoma(164;0.15)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	143658281	143658281	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143658281delA								OR2F1 (173 upstream) : OR6B1 (42809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145763116	145763118	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145763116_145763118delAAA								None (None upstream) : CNTNAP2 (50335 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146892530	146892530	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146892530delT	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	148347109	148347109	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148347109delA								C7orf33 (34158 upstream) : CUL1 (47897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	148625754	148625754	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148625754delT								EZH2 (44340 upstream) : MIR1975 (12826 downstream)																																			---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148873536	148873536	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148873536delT	uc003wfl.2	+						ZNF398_uc011kul.1_Intron|ZNF398_uc011kum.1_Intron	NM_170686	NP_733787			zinc finger 398 isoform a						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)															---	---	---	---
ZNF767	79970	broad.mit.edu	37	7	149295382	149295383	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149295382_149295383insT	uc003wfy.3	-						ZNF767_uc003wfx.2_Intron|ZNF767_uc011kuq.1_Intron	NR_027789				Homo sapiens cDNA FLJ12700 fis, clone NT2RP1000721.											central_nervous_system(1)	1	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	150248415	150248426	+	IGR	DEL	TGTGCACAGGAG	-	-	rs111495872		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150248415_150248426delTGTGCACAGGAG								GIMAP7 (30255 upstream) : GIMAP4 (16032 downstream)																																			---	---	---	---
GIMAP2	26157	broad.mit.edu	37	7	150384350	150384351	+	Intron	INS	-	TTTGTTTGTTTG	TTTGTTTGTTTG	rs146938233	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150384350_150384351insTTTGTTTGTTTG	uc003who.2	+						GIMAP1_uc003whp.2_Intron	NM_015660	NP_056475			GTPase, IMAP family member 2							integral to membrane	GTP binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
ABP1	26	broad.mit.edu	37	7	150554121	150554121	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150554121delC	uc003why.1	+	3	4781	c.563delC	c.(562-564)GCCfs	p.A188fs	ABP1_uc003whz.1_Frame_Shift_Del_p.A188fs|ABP1_uc003wia.1_Frame_Shift_Del_p.A188fs	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	188					amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
ABP1	26	broad.mit.edu	37	7	150558259	150558259	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150558259delC	uc003why.1	+	6	6436	c.2218delC	c.(2218-2220)CCCfs	p.P740fs	ABP1_uc003whz.1_Frame_Shift_Del_p.P740fs|ABP1_uc003wia.1_Frame_Shift_Del_p.P759fs	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	740					amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
SMARCD3	6604	broad.mit.edu	37	7	150952971	150952971	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150952971delT	uc003wjt.2	-						SMARCD3_uc003wju.2_Intron	NM_001003802	NP_001003802			SWI/SNF related, matrix associated, actin						cellular lipid metabolic process|chromatin modification|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
RHEB	6009	broad.mit.edu	37	7	151176970	151176971	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151176970_151176971insA	uc003wkh.1	-							NM_005614	NP_005605			Ras homolog enriched in brain precursor						cell cycle arrest|insulin receptor signaling pathway|positive regulation of TOR signaling cascade|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|metal ion binding|protein binding			large_intestine(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)														---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151544560	151544561	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151544560_151544561delCT	uc003wkk.2	-						PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287			AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151928866	151928866	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151928866delA	uc003wla.2	-						MLL3_uc003wkz.2_Intron	NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	7	152219335	152219336	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152219335_152219336insT								LOC100128822 (56707 upstream) : XRCC2 (124253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152687063	152687063	+	IGR	DEL	C	-	-	rs67745630		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152687063delC								ACTR3B (134600 upstream) : DPP6 (897356 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153902215	153902215	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153902215delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154501069	154501071	+	Intron	DEL	TTG	-	-	rs143055243	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154501069_154501071delTTG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	155379303	155379303	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155379303delT								CNPY1 (52764 upstream) : RBM33 (57900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155398892	155398892	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155398892delT								CNPY1 (72353 upstream) : RBM33 (38311 downstream)																																			---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155473256	155473256	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155473256delT	uc010lqk.1	+						RBM33_uc003wme.2_Intron	NM_053043	NP_444271			RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	155971312	155971313	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155971312_155971313insA								SHH (366345 upstream) : C7orf4 (361872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155977381	155977381	+	IGR	DEL	C	-	-	rs6969032	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155977381delC								SHH (372414 upstream) : C7orf4 (355804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	156367475	156367475	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156367475delA								C7orf4 (33680 upstream) : C7orf13 (63587 downstream)																																			---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156555695	156555696	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156555695_156555696delAA	uc003wmw.3	-						LMBR1_uc003wmv.3_Intron|LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron	NM_022458	NP_071903			limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156621733	156621733	+	Intron	DEL	A	-	-	rs112349840		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156621733delA	uc003wmw.3	-						LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron|LMBR1_uc010lqo.2_Intron	NM_022458	NP_071903			limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	156878623	156878623	+	IGR	DEL	A	-	-	rs35468473		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156878623delA								MNX1 (75276 upstream) : UBE3C (53032 downstream)																																			---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157790504	157790518	+	Intron	DEL	GGGAGATGAGTGCAC	-	-	rs59328428		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157790504_157790518delGGGAGATGAGTGCAC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	158105642	158105643	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158105642_158105643delGT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	158198142	158198142	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158198142delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158719676	158719676	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158719676delT	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	158999583	158999584	+	IGR	DEL	GG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158999583_158999584delGG								VIPR2 (61934 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	289133	289134	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:289133_289134insA								ZNF596 (91801 upstream) : FBXO25 (67674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1066812	1066812	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1066812delA	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1197216	1197217	+	IGR	INS	-	G	G	rs143735419	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1197216_1197217insG								ERICH1 (515990 upstream) : DLGAP2 (252352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1284020	1284020	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1284020delA								ERICH1 (602794 upstream) : DLGAP2 (165549 downstream)																																			---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2047898	2047899	+	Intron	INS	-	T	T	rs149139233	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2047898_2047899insT	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961			myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2221439	2221440	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2221439_2221440delCA								MYOM2 (128060 upstream) : CSMD1 (571436 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2837838	2837840	+	Intron	DEL	CTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2837838_2837840delCTC	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2890249	2890249	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2890249delC	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3015525	3015525	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3015525delA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3868119	3868120	+	Intron	INS	-	CA	CA	rs146560485	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3868119_3868120insCA	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	4985367	4985368	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4985367_4985368delTT								CSMD1 (133039 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5101736	5101736	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5101736delT								CSMD1 (249408 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6256876	6256876	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6256876delA								None (None upstream) : MCPH1 (7245 downstream)																																			---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6567241	6567241	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6567241delT	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6612417	6612417	+	Intron	DEL	T	-	-	rs71687580		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6612417delT	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9592868	9592868	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9592868delT	uc003wss.2	+						TNKS_uc011kww.1_Intron|TNKS_uc010lrt.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	11017902	11017903	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11017902_11017903delAA	uc003wtk.1	-							NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11120930	11120930	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11120930delA								XKR6 (62055 upstream) : MTMR9 (21070 downstream)																																			---	---	---	---
TDH	157739	broad.mit.edu	37	8	11217650	11217651	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11217650_11217651delAC	uc003wtq.1	+						TDH_uc003wts.1_Intron|TDH_uc003wtt.1_Intron	NR_001578				Homo sapiens mRNA for hypothetical protein (ORF1), clone vir17.												0																		---	---	---	---
BLK	640	broad.mit.edu	37	8	11355633	11355633	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11355633delT	uc003wty.2	+						BLK_uc003wtz.2_Intron|BLK_uc003wtx.2_Intron	NM_001715	NP_001706			B lymphoid tyrosine kinase						intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12752125	12752125	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12752125delA								LOC340357 (83215 upstream) : C8orf79 (51026 downstream)																																			---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14124941	14124941	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14124941delA	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14602716	14602717	+	Intron	INS	-	TG	TG	rs138151741	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14602716_14602717insTG	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
MSR1	4481	broad.mit.edu	37	8	15978192	15978193	+	Intron	DEL	TT	-	-	rs35356880		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15978192_15978193delTT	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron	NM_138715	NP_619729			macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	16054367	16054367	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16054367delT								MSR1 (4067 upstream) : FGF20 (795967 downstream)																																			---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17396271	17396271	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17396271delT	uc011kyc.1	+						SLC7A2_uc011kyd.1_5'Flank|SLC7A2_uc011kye.1_5'Flank	NM_001008539	NP_001008539			solute carrier family 7, member 2 isoform 2						cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17503685	17503686	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17503685_17503686delAA	uc003wxv.2	-						MTUS1_uc003wxt.2_Intron|MTUS1_uc011kyg.1_Intron|MTUS1_uc010lsy.2_Intron|MTUS1_uc003wxw.2_Intron|MTUS1_uc003wxs.2_Intron	NM_001001924	NP_001001924			mitochondrial tumor suppressor 1 isoform 1							Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18636895	18636895	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18636895delA	uc003wza.2	-						PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19065374	19065374	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19065374delA								PSD3 (194178 upstream) : SH2D4A (105833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20451440	20451441	+	IGR	INS	-	G	G	rs141055639	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20451440_20451441insG								LZTS1 (338637 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21335803	21335804	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21335803_21335804delCT								None (None upstream) : GFRA2 (213726 downstream)																																			---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21554574	21554592	+	Intron	DEL	GGGACCGAGGAGGGTAGAT	-	-	rs114961029	by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21554574_21554592delGGGACCGAGGAGGGTAGAT	uc003wzu.1	-						GFRA2_uc003wzv.1_Intron|GFRA2_uc003wzw.1_Intron	NM_001495	NP_001486			GDNF family receptor alpha 2 isoform a							anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)														---	---	---	---
BMP1	649	broad.mit.edu	37	8	22028439	22028439	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22028439delA	uc003xbg.2	+						BMP1_uc011kzb.1_Intron|BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_Intron|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120			bone morphogenetic protein 1 isoform 3						cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22165711	22165713	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22165711_22165713delTTT	uc003xbn.2	+						PIWIL2_uc011kzf.1_Intron|PIWIL2_uc010ltv.2_Intron	NM_018068	NP_060538			piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
SLC39A14	23516	broad.mit.edu	37	8	22273947	22273948	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22273947_22273948delTT	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903			solute carrier family 39 (zinc transporter),							endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)														---	---	---	---
EGR3	1960	broad.mit.edu	37	8	22545638	22545638	+	3'UTR	DEL	T	-	-	rs71726099		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22545638delT	uc003xcm.1	-	2					EGR3_uc011kzn.1_3'UTR|EGR3_uc011kzo.1_3'UTR	NM_004430	NP_004421			early growth response 3						circadian rhythm|muscle organ development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23329656	23329669	+	IGR	DEL	TGTGTGTGTGTGTC	-	-	rs2977450		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23329656_23329669delTGTGTGTGTGTGTC								ENTPD4 (14412 upstream) : SLC25A37 (56694 downstream)																																	OREG0018637	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NKX3-1	4824	broad.mit.edu	37	8	23539287	23539288	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23539287_23539288insT	uc011kzx.1	-						NKX3-1_uc003xdv.1_Intron	NM_006167	NP_006158			NK3 homeobox 1						negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24609585	24609585	+	IGR	DEL	T	-	-	rs33918172		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24609585delT								ADAM7 (225104 upstream) : NEFM (161689 downstream)																																			---	---	---	---
NEFL	4747	broad.mit.edu	37	8	24812020	24812020	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24812020delA	uc003xee.2	-							NM_006158	NP_006149			neurofilament, light polypeptide 68kDa						anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25199803	25199803	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25199803delT	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xeh.1_Intron|DOCK5_uc003xei.2_Intron|DOCK5_uc003xej.2_Intron	NM_024940	NP_079216			dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	28956895	28956895	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28956895delT	uc003xhh.3	-						KIF13B_uc011laz.1_5'Flank	NM_015254	NP_056069			kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29033568	29033568	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29033568delA	uc003xhh.3	-						KIF13B_uc003xhj.2_Intron|KIF13B_uc010lvf.1_Intron	NM_015254	NP_056069			kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30106987	30106987	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30106987delA								DCTN6 (65928 upstream) : RBPMS (134957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30125366	30125369	+	IGR	DEL	AAAA	-	-	rs112389683		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30125366_30125369delAAAA								DCTN6 (84307 upstream) : RBPMS (116575 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30316778	30316779	+	Intron	INS	-	T	T	rs68025839		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30316778_30316779insT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron|RBPMS_uc010lvh.1_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
UBXN8	7993	broad.mit.edu	37	8	30608867	30608867	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30608867delA	uc003xii.2	+						UBXN8_uc010lvi.2_Intron|UBXN8_uc011lbb.1_Intron|UBXN8_uc003xij.2_5'Flank	NM_005671	NP_005662			reproduction 8						single fertilization						0																		---	---	---	---
WRN	7486	broad.mit.edu	37	8	30922660	30922660	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30922660delT	uc003xio.3	+							NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32079551	32079554	+	Intron	DEL	ACAC	-	-	rs60839450		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32079551_32079554delACAC	uc003xip.2	+							NM_013962	NP_039256			neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32467181	32467184	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32467181_32467184delTTTT	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32524014	32524014	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32524014delA	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Intron|NRG1_uc003xiy.2_Intron|NRG1_uc010lvt.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32612095	32612095	+	Intron	DEL	A	-	-	rs76017751		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32612095delA	uc003xiv.2	+						NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33367554	33367554	+	Intron	DEL	A	-	-	rs79956819		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33367554delA	uc003xjl.3	-						C8orf41_uc003xjk.3_Intron|C8orf41_uc010lvv.2_Intron|C8orf41_uc003xjm.3_Intron|C8orf41_uc003xjn.1_Intron	NM_025115	NP_079391			hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33592983	33592984	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33592983_33592984delAA								DUSP26 (135544 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34239340	34239343	+	IGR	DEL	TCTA	-	-	rs71883571		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34239340_34239343delTCTA								DUSP26 (781901 upstream) : UNC5D (853632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34732162	34732162	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34732162delA								None (None upstream) : UNC5D (360813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34869245	34869246	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34869245_34869246delAG								None (None upstream) : UNC5D (223729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34976142	34976142	+	IGR	DEL	T	-	-	rs34323478		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34976142delT								None (None upstream) : UNC5D (116833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37120666	37120666	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37120666delA								KCNU1 (327025 upstream) : ZNF703 (432635 downstream)																																			---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	38990272	38990272	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38990272delT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron	NM_145004	NP_659441			a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41284227	41284227	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41284227delG								SFRP1 (117247 upstream) : GOLGA7 (63854 downstream)																																			---	---	---	---
ANK1	286	broad.mit.edu	37	8	41695388	41695388	+	Intron	DEL	A	-	-	rs74412962		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41695388delA	uc003xom.2	-							NM_001142446	NP_001135918			ankyrin 1 isoform 9						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
ANK1	286	broad.mit.edu	37	8	41748802	41748803	+	Intron	DEL	TT	-	-	rs111612663		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41748802_41748803delTT	uc003xom.2	-							NM_001142446	NP_001135918			ankyrin 1 isoform 9						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41941821	41941821	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41941821delT								MYST3 (32316 upstream) : AP3M2 (68643 downstream)																																			---	---	---	---
POLB	5423	broad.mit.edu	37	8	42207508	42207508	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42207508delT	uc003xoz.1	+						POLB_uc003xpa.1_Intron|POLB_uc011lcs.1_Intron	NM_002690	NP_002681			DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)								DNA_polymerases_(catalytic_subunits)					---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42765500	42765500	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42765500delT	uc003xpr.2	+						HOOK3_uc010lxq.1_Intron	NM_032410	NP_115786			golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
HGSNAT	138050	broad.mit.edu	37	8	43013596	43013597	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43013596_43013597insT	uc003xpx.3	+							NM_152419	NP_689632			heparan-alpha-glucosaminide N-acetyltransferase						lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	43354451	43354451	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43354451delT								POTEA (136123 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	48076457	48076457	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48076457delA								BEYLA (309050 upstream) : KIAA0146 (97085 downstream)																																			---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48835627	48835629	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48835627_48835629delTTT	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	8	49920658	49920658	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49920658delT								SNAI2 (86670 upstream) : C8orf22 (64245 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51090919	51090920	+	Intron	DEL	TT	-	-	rs112121506		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51090919_51090920delTT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840			syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51205018	51205018	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51205018delT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840			syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	52005578	52005580	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52005578_52005580delTTT								SNTG1 (300151 upstream) : PXDNL (226564 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52252040	52252040	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52252040delA	uc003xqu.3	-						PXDNL_uc003xqt.3_Intron	NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	54442759	54442759	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54442759delT								OPRK1 (278565 upstream) : ATP6V1H (185357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54465510	54465511	+	IGR	DEL	TG	-	-	rs3030935		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54465510_54465511delTG								OPRK1 (301316 upstream) : ATP6V1H (162605 downstream)																																			---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54910902	54910902	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54910902delT	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_Intron	NM_006756	NP_006747			transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)					T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	8	55302105	55302105	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55302105delT								MRPL15 (241031 upstream) : SOX17 (68390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55705409	55705409	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55705409delA								RP1 (22878 upstream) : XKR4 (309608 downstream)																																			---	---	---	---
SDR16C5	195814	broad.mit.edu	37	8	57233410	57233410	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57233410delA	uc003xsy.1	-						SDR16C5_uc010lyk.1_5'Flank|SDR16C5_uc010lyl.1_5'Flank	NM_138969	NP_620419			epidermal retinal dehydrogenase 2						detection of light stimulus involved in visual perception|keratinocyte proliferation|retinal metabolic process|retinol metabolic process	endoplasmic reticulum membrane|integral to membrane|integral to membrane of membrane fraction	binding|retinol dehydrogenase activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	58425807	58425808	+	IGR	DEL	AC	-	-	rs111688974		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58425807_58425808delAC								C8orf71 (228519 upstream) : FAM110B (481305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60217943	60217943	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60217943delC								TOX (186176 upstream) : CA8 (883480 downstream)																																			---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61471393	61471393	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61471393delT	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61735360	61735360	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61735360delA	uc003xue.2	+						CHD7_uc003xuf.2_Intron	NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	65134118	65134118	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65134118delA								None (None upstream) : MIR124-2 (157588 downstream)																																			---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65527975	65527975	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65527975delG	uc003xvj.2	-							NM_004820	NP_004811			cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)																---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66695083	66695083	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66695083delA	uc003xvq.2	-						PDE7A_uc003xvr.2_Intron|PDE7A_uc003xvp.2_Intron	NM_002604	NP_002595			phosphodiesterase 7A isoform b							cell fraction|cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding				0			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
DNAJC5B	85479	broad.mit.edu	37	8	66964201	66964201	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66964201delT	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096			DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68049609	68049609	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68049609delA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	68319249	68319249	+	IGR	DEL	A	-	-	rs75255829		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68319249delA								ARFGEF1 (63337 upstream) : CPA6 (15157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	69741757	69741757	+	IGR	DEL	T	-	-	rs72028274		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69741757delT								C8orf34 (10501 upstream) : SULF1 (637102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	69753623	69753626	+	IGR	DEL	GTGT	-	-	rs34634691		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69753623_69753626delGTGT								C8orf34 (22367 upstream) : SULF1 (625233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71829711	71829711	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71829711delT								XKR9 (181535 upstream) : EYA1 (279959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72659168	72659168	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72659168delA								EYA1 (384701 upstream) : MSC (94609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	73203209	73203210	+	Intron	INS	-	T	T	rs891536	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73203209_73203210insT	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																														---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74559173	74559174	+	Intron	INS	-	ACAC	ACAC	rs142043134	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74559173_74559174insACAC	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.1_Intron	NM_014393	NP_055208			staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74897026	74897027	+	IGR	DEL	TT	-	-	rs11555178		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74897026_74897027delTT								TMEM70 (2015 upstream) : LY96 (6560 downstream)																																			---	---	---	---
LY96	23643	broad.mit.edu	37	8	74939176	74939176	+	Intron	DEL	T	-	-	rs34219418		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74939176delT	uc003yad.2	+							NM_015364	NP_056179			MD-2 protein precursor						cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)															---	---	---	---
JPH1	56704	broad.mit.edu	37	8	75149365	75149365	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75149365delA	uc003yae.2	-						JPH1_uc003yaf.2_Intron	NM_020647	NP_065698			junctophilin 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	76002965	76002966	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76002965_76002966delCA								CRISPLD1 (56174 upstream) : HNF4G (317217 downstream)																																			---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76463609	76463609	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76463609delT	uc003yaq.2	+						HNF4G_uc003yar.2_Intron	NM_004133	NP_004124			hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	76851233	76851233	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76851233delA								HNF4G (372174 upstream) : LOC100192378 (671882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79087610	79087610	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79087610delT								None (None upstream) : PKIA (340726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79763633	79763633	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79763633delC								IL7 (45875 upstream) : STMN2 (759747 downstream)																																			---	---	---	---
HEY1	23462	broad.mit.edu	37	8	80679388	80679388	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80679388delA	uc003ybm.2	-						HEY1_uc010lzq.2_5'Flank|HEY1_uc003ybl.2_Intron	NM_012258	NP_036390			hairy/enhancer-of-split related with YRPW motif						angiogenesis|negative regulation of Notch signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|Notch signaling pathway|transcription, DNA-dependent	nucleus	DNA binding|protein binding			lung(3)	3	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	80796047	80796050	+	IGR	DEL	TCTC	-	-	rs67217941	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80796047_80796050delTCTC								HEY1 (115949 upstream) : MRPS28 (35046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81229155	81229155	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81229155delT								TPD52 (145319 upstream) : ZBTB10 (168699 downstream)																																			---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81407650	81407653	+	Intron	DEL	TTTT	-	-	rs73257152	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81407650_81407653delTTTT	uc003ybx.3	+						ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Intron|ZBTB10_uc010lzt.2_Intron	NM_001105539	NP_001099009			zinc finger and BTB domain containing 10 isoform						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81527140	81527140	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81527140delT								ZBTB10 (92532 upstream) : ZNF704 (23629 downstream)																																			---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81589494	81589494	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81589494delT	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
FABP5	2171	broad.mit.edu	37	8	82196888	82196888	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82196888delT	uc003yca.1	+	4						NM_001444	NP_001435			fatty acid binding protein 5						epidermis development	cytoplasm	fatty acid binding|protein binding|transporter activity				0	Lung NSC(7;3.57e-05)|all_lung(9;0.00011)		Epithelial(68;0.102)															---	---	---	---
SNX16	64089	broad.mit.edu	37	8	82721675	82721675	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82721675delA	uc011lft.1	-						SNX16_uc003ycn.2_Intron|SNX16_uc003yco.2_Intron	NM_022133	NP_071416			sorting nexin 16 isoform a						cell communication|early endosome to late endosome transport|endosome to lysosome transport|protein targeting to lysosome	early endosome membrane|extrinsic to endosome membrane|late endosome membrane|lysosome	identical protein binding|phosphatidylinositol binding			ovary(1)|pancreas(1)	2																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85736980	85736980	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85736980delA	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron|RALYL_uc003ycu.3_Intron|RALYL_uc003ycv.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	85939102	85939102	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85939102delA								RALYL (105031 upstream) : LRRCC1 (80275 downstream)																																			---	---	---	---
C8orf59	401466	broad.mit.edu	37	8	86129455	86129455	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86129455delT	uc010mac.1	-						C8orf59_uc003ydd.2_Intron|C8orf59_uc010mad.1_Intron|C8orf59_uc003yde.2_Intron|C8orf59_uc011lfu.1_Intron	NM_001099670	NP_001093140			hypothetical protein LOC401466												0																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86193740	86193740	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86193740delT	uc003ydg.2	+	7					CA13_uc003ydf.1_Intron	NM_198584	NP_940986			carbonic anhydrase XIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	86533914	86533914	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86533914delA								CA2 (140193 upstream) : REXO1L1 (34650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88562498	88562498	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88562498delT								CNBD1 (167543 upstream) : DCAF4L2 (320475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88714056	88714056	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88714056delA								CNBD1 (319101 upstream) : DCAF4L2 (168917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88834181	88834181	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88834181delC								CNBD1 (439226 upstream) : DCAF4L2 (48792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88904406	88904406	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88904406delT								DCAF4L2 (18110 upstream) : MMP16 (145056 downstream)																																			---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89176538	89176538	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89176538delA	uc003yeb.3	-						MMP16_uc003yec.2_Intron	NM_005941	NP_005932			matrix metalloproteinase 16 isoform 1						collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8																		---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90936586	90936586	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90936586delT	uc003yeg.2	+						OSGIN2_uc003yeh.2_Intron	NM_004337	NP_004328			oxidative stress induced growth inhibitor family						germ cell development|meiosis						0			BRCA - Breast invasive adenocarcinoma(11;0.0344)															---	---	---	---
DECR1	1666	broad.mit.edu	37	8	91056917	91056917	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91056917delT	uc003yek.1	+						DECR1_uc011lgc.1_Intron|DECR1_uc011lgd.1_Intron	NM_001359	NP_001350			2,4-dienoyl CoA reductase 1 precursor						fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	91379671	91379671	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91379671delT								CALB1 (271984 upstream) : TMEM64 (254552 downstream)																																			---	---	---	---
LRRC69	100130742	broad.mit.edu	37	8	92217990	92217990	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92217990delA	uc010mal.1	+						LRRC69_uc003yev.1_Intron|LRRC69_uc003yew.1_Intron	NM_001129890	NP_001123362			leucine rich repeat containing 69												0																		---	---	---	---
SLC26A7	115111	broad.mit.edu	37	8	92365045	92365045	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92365045delA	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|SLC26A7_uc003yez.2_Intron|SLC26A7_uc003yfa.2_Intron	NM_052832	NP_439897			solute carrier family 26, member 7 isoform a							basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93073151	93073154	+	Intron	DEL	GAGA	-	-	rs35094638		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93073151_93073154delGAGA	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	93659287	93659288	+	IGR	DEL	GT	-	-	rs62518739		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93659287_93659288delGT								RUNX1T1 (551581 upstream) : C8orf83 (236577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94165502	94165502	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94165502delA	uc003yft.1	-											Homo sapiens cDNA clone IMAGE:30557893.																														---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95884379	95884379	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95884379delT	uc003yhb.2	+						INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96359042	96359042	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96359042delT								C8orf37 (77605 upstream) : GDF6 (795518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97220202	97220202	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97220202delA								GDF6 (47182 upstream) : UQCRB (19108 downstream)																																			---	---	---	---
PGCP	10404	broad.mit.edu	37	8	98097613	98097614	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98097613_98097614delAA	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100199236	100199236	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100199236delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yit.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yix.1_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
SNX31	169166	broad.mit.edu	37	8	101607543	101607543	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101607543delT	uc003yjr.2	-						SNX31_uc011lha.1_Intron|SNX31_uc011lhb.1_Intron	NM_152628	NP_689841			sorting nexin 31						cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	102349541	102349541	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102349541delT								ZNF706 (131581 upstream) : NACAP1 (24481 downstream)																																			---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103281412	103281412	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103281412delA	uc003ykr.1	-						UBR5_uc003yks.1_Intron|UBR5_uc003ykq.2_5'Flank	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103543207	103543207	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103543207delT								UBR5 (118712 upstream) : ODF1 (20641 downstream)																																			---	---	---	---
KLF10	7071	broad.mit.edu	37	8	103665676	103665676	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103665676delA	uc011lhk.1	-						KLF10_uc011lhj.1_Intron	NM_005655	NP_005646			Kruppel-like factor 10 isoform a						cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)															---	---	---	---
AZIN1	51582	broad.mit.edu	37	8	103846502	103846502	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103846502delA	uc003ykx.2	-						AZIN1_uc003yky.2_Intron	NM_015878	NP_056962			ornithine decarboxylase antizyme inhibitor						polyamine biosynthetic process|regulation of cellular amino acid metabolic process	cytosol	catalytic activity|protein binding				0	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	104013489	104013489	+	IGR	DEL	A	-	-	rs67513038		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104013489delA								AZIN1 (137092 upstream) : ATP6V1C1 (19759 downstream)																																			---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104082417	104082417	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104082417delT	uc003ykz.3	+	13					ATP6V1C1_uc010mbz.2_3'UTR|ATP6V1C1_uc003yla.2_3'UTR|ATP6V1C1_uc011lhl.1_3'UTR	NM_001695	NP_001686			ATPase, H+ transporting, lysosomal V1 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|plasma membrane|proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism				0	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	106218791	106218792	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106218791_106218792insT								LRP12 (617571 upstream) : ZFPM2 (112355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107216927	107216927	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107216927delA								ZFPM2 (400162 upstream) : OXR1 (65546 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107691426	107691426	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107691426delT	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc003ymg.1_Intron|OXR1_uc003ymi.1_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	109596061	109596061	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109596061delT								TTC35 (96925 upstream) : TMEM74 (23019 downstream)																																			---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110478776	110478776	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110478776delA	uc003yne.2	+							NM_177531	NP_803875			fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
EBAG9	9166	broad.mit.edu	37	8	110567215	110567215	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110567215delT	uc003ynf.2	+						EBAG9_uc010mcn.1_Intron|EBAG9_uc003yng.2_Intron	NM_198120	NP_936056			estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	112211362	112211369	+	IGR	DEL	ACACACAC	-	-	rs13258565		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112211362_112211369delACACACAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112710722	112710723	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112710722_112710723insA								None (None upstream) : CSMD3 (524438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112739838	112739841	+	IGR	DEL	GAGA	-	-	rs34943985		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112739838_112739841delGAGA								None (None upstream) : CSMD3 (495320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112969302	112969303	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112969302_112969303insT								None (None upstream) : CSMD3 (265858 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113266307	113266307	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113266307delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113292375	113292375	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113292375delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113382960	113382960	+	Intron	DEL	T	-	-	rs76799004		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113382960delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113521023	113521023	+	Intron	DEL	T	-	-	rs145770099		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113521023delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113540691	113540691	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113540691delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113702411	113702411	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113702411delT	uc003ynu.2	-						CSMD3_uc003yns.2_5'Flank|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114202915	114202916	+	Intron	DEL	TT	-	-	rs113068906		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114202915_114202916delTT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114207456	114207459	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114207456_114207459delTTTT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114237577	114237577	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114237577delT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114265701	114265701	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114265701delT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116010907	116010908	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116010907_116010908delTT								None (None upstream) : TRPS1 (409817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116735374	116735374	+	IGR	DEL	A	-	-	rs150790204		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116735374delA								TRPS1 (54146 upstream) : EIF3H (921682 downstream)																																			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117696790	117696790	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117696790delT	uc003yoa.2	-						EIF3H_uc003yob.2_Intron|EIF3H_uc011lhz.1_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
MED30	90390	broad.mit.edu	37	8	118533318	118533318	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118533318delG	uc003yoj.2	+						MED30_uc011lib.1_Intron	NM_080651	NP_542382			TRAP/Mediator complex component TRAP25						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding				0	all_cancers(13;3.41e-25)|Lung NSC(37;3.02e-05)|Ovarian(258;0.00163)		STAD - Stomach adenocarcinoma(47;0.0266)															---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118992933	118992933	+	Intron	DEL	G	-	-	rs55724989		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118992933delG	uc003yok.1	-							NM_000127	NP_000118			exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	8	119152518	119152518	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119152518delT								EXT1 (28460 upstream) : SAMD12 (49177 downstream)																																			---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119401961	119401961	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119401961delA	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119539097	119539097	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119539097delG	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120788929	120788929	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120788929delA	uc003you.2	-							NM_003184	NP_003175			TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121215953	121215953	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121215953delA	uc003yox.2	+	9	1148	c.883delA	c.(883-885)AAAfs	p.K295fs	COL14A1_uc003yoy.2_5'UTR|COL14A1_uc010mde.1_5'UTR	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	295	VWFA 1.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121228754	121228754	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121228754delT	uc003yox.2	+						COL14A1_uc003yoy.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121280557	121280558	+	Intron	DEL	TA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121280557_121280558delTA	uc003yox.2	+						COL14A1_uc003yoz.2_5'Flank	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
MTBP	27085	broad.mit.edu	37	8	121502681	121502681	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121502681delT	uc003ypc.1	+							NM_022045	NP_071328			Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121767383	121767384	+	Intron	DEL	TG	-	-	rs71661409		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121767383_121767384delTG	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301			basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121786787	121786787	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121786787delA	uc010mdg.2	-						SNTB1_uc003ype.2_Intron|uc003ypf.1_Intron	NM_021021	NP_066301			basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122087800	122087800	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122087800delA								SNTB1 (263491 upstream) : HAS2 (537471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122169985	122169986	+	IGR	INS	-	GT	GT	rs145430419	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122169985_122169986insGT								SNTB1 (345676 upstream) : HAS2 (455285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122195285	122195285	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122195285delA								SNTB1 (370976 upstream) : HAS2 (429986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122322817	122322817	+	IGR	DEL	T	-	-	rs13261167	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122322817delT								SNTB1 (498508 upstream) : HAS2 (302454 downstream)																																			---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122640781	122640781	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122640781delT	uc003yph.2	-							NM_005328	NP_005319			hyaluronan synthase 2							integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122902593	122902593	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122902593delT								HAS2AS (245660 upstream) : ZHX2 (891308 downstream)																																			---	---	---	---
C8orf76	84933	broad.mit.edu	37	8	124240860	124240860	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124240860delA	uc003yqc.1	-						C8orf76_uc003yqd.2_Intron	NM_032847	NP_116236			hypothetical protein LOC84933								binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124359727	124359727	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124359727delA	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron|ATAD2_uc003yqj.2_Intron	NM_014109	NP_054828			ATPase family, AAA domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
FBXO32	114907	broad.mit.edu	37	8	124516682	124516682	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124516682delC	uc003yqr.2	-						FBXO32_uc003yqq.2_Intron|FBXO32_uc010mdk.2_Intron	NM_058229	NP_478136			F-box only protein 32 isoform 1											skin(3)|breast(2)|lung(1)	6	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125212423	125212423	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125212423delA								FER1L6 (80122 upstream) : TMEM65 (110738 downstream)																																			---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126059687	126059688	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126059687_126059688delTT	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron|KIAA0196_uc003yru.1_Intron	NM_014846	NP_055661			strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126325345	126325347	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126325345_126325347delAAA	uc003yrw.2	+							NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	126963981	126963981	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126963981delT	uc003yry.2	-											Homo sapiens mRNA; cDNA DKFZp686L20185 (from clone DKFZp686L20185).																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	127234368	127234368	+	IGR	DEL	T	-	-	rs34773237		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127234368delT								TRIB1 (783726 upstream) : FAM84B (330319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127408004	127408005	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127408004_127408005delAC								TRIB1 (957362 upstream) : FAM84B (156682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127463641	127463641	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127463641delA								None (None upstream) : FAM84B (101046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127609937	127609937	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127609937delT								FAM84B (39471 upstream) : LOC727677 (692125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128101672	128101674	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128101672_128101674delAAA								FAM84B (531206 upstream) : LOC727677 (200388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128720053	128720054	+	Intron	INS	-	AC	AC	rs140521095	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128720053_128720054insAC	uc003ysg.2	-											Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
PVT1	5820	broad.mit.edu	37	8	128933004	128933004	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128933004delA	uc010mdq.2	+						PVT1_uc003ysl.2_Intron|PVT1_uc010mdp.1_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	129135016	129135017	+	IGR	DEL	TT	-	-	rs34982323		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129135016_129135017delTT								PVT1 (21518 upstream) : MIR1208 (27345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129938419	129938419	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129938419delC								MIR1208 (775985 upstream) : GSDMC (822024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130634456	130634457	+	IGR	INS	-	G	G	rs151263405	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130634456_130634457insG								None (None upstream) : GSDMC (125986 downstream)																																			---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131199667	131199668	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131199667_131199668delTT	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131226960	131226962	+	Intron	DEL	AAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131226960_131226962delAAG	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	131432202	131432204	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131432202_131432204delTTT								ASAP1 (17986 upstream) : ADCY8 (360344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	131769758	131769759	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131769758_131769759insA								ASAP1 (355542 upstream) : ADCY8 (22789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132459741	132459742	+	IGR	INS	-	AG	AG	rs143802535	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132459741_132459742insAG								ADCY8 (406906 upstream) : EFR3A (456617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132832728	132832729	+	IGR	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132832728_132832729delAT								ADCY8 (779893 upstream) : EFR3A (83630 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133184450	133184450	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133184450delA	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	133701943	133701944	+	IGR	DEL	GT	-	-	rs72438064		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133701943_133701944delGT								LRRC6 (14130 upstream) : TMEM71 (20250 downstream)																																			---	---	---	---
PHF20L1	51105	broad.mit.edu	37	8	133811435	133811436	+	Intron	INS	-	A	A	rs2244885	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133811435_133811436insA	uc003ytt.2	+						PHF20L1_uc003ytr.2_Intron|PHF20L1_uc010mdv.2_Intron|PHF20L1_uc003yts.2_Intron|PHF20L1_uc011lja.1_Intron|PHF20L1_uc003ytu.1_Intron|PHF20L1_uc003ytq.2_3'UTR	NM_016018	NP_057102			PHD finger protein 20-like 1 isoform 1								nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134446830	134446831	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134446830_134446831insC								NDRG1 (137283 upstream) : ST3GAL1 (20260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134885112	134885113	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134885112_134885113insA								ST3GAL1 (300929 upstream) : ZFAT (604920 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135592200	135592204	+	Intron	DEL	AAAAA	-	-	rs149153004		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135592200_135592204delAAAAA	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	135968391	135968391	+	IGR	DEL	A	-	-	rs111809328		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135968391delA								MIR30D (151203 upstream) : LOC286094 (277983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136062912	136062912	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136062912delG								MIR30D (245724 upstream) : LOC286094 (183462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136125823	136125823	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136125823delA								MIR30D (308635 upstream) : LOC286094 (120551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136240060	136240060	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136240060delG								MIR30D (422872 upstream) : LOC286094 (6314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136365044	136365045	+	IGR	INS	-	T	T	rs56126545		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136365044_136365045insT								LOC286094 (53085 upstream) : KHDRBS3 (104671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137871650	137871650	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137871650delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138014483	138014483	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138014483delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138514444	138514445	+	IGR	DEL	GT	-	-	rs72273086		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138514444_138514445delGT								None (None upstream) : FAM135B (627823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138680948	138680949	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138680948_138680949insA								None (None upstream) : FAM135B (461319 downstream)																																			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139225751	139225753	+	Intron	DEL	TTT	-	-	rs144088044		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139225751_139225753delTTT	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996			hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139472181	139472181	+	Intron	DEL	C	-	-	rs34811937		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139472181delC	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996			hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139918902	139918902	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139918902delT	uc003yvd.2	-							NM_152888	NP_690848			collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140402885	140402885	+	IGR	DEL	A	-	-	rs141543225		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140402885delA								COL22A1 (476649 upstream) : KCNK9 (210197 downstream)																																			---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140656965	140656966	+	Intron	INS	-	A	A	rs1990899	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140656965_140656966insA	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685			potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)															---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140675069	140675069	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140675069delG	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685			potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)															---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141082648	141082650	+	Intron	DEL	GAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141082648_141082650delGAG	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141407485	141407486	+	Intron	INS	-	AAAC	AAAC	rs146913147	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141407485_141407486insAAAC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141683205	141683206	+	Intron	DEL	TT	-	-	rs34388720		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141683205_141683206delTT	uc003yvu.2	-						PTK2_uc011ljp.1_Intron|PTK2_uc003yvo.2_Intron|PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
MIR1302-7	100302147	broad.mit.edu	37	8	142867905	142867905	+	5'Flank	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142867905delG	hsa-mir-1302-7|MI0006368	-																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	144225188	144225195	+	IGR	DEL	GATGGATG	-	-	rs72299534		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144225188_144225195delGATGGATG								C8orf31 (89468 upstream) : LY6H (14137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144264074	144264075	+	IGR	INS	-	GTGTGT	GTGTGT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144264074_144264075insGTGTGT								LY6H (22021 upstream) : GPIHBP1 (30993 downstream)																																			---	---	---	---
TOP1MT	116447	broad.mit.edu	37	8	144441413	144441414	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144441413_144441414insA	uc011lkd.1	-						TOP1MT_uc011lke.1_Intron|uc003yya.2_Intron	NM_052963	NP_443195			mitochondrial topoisomerase I precursor						DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)													---	---	---	---
ZNF707	286075	broad.mit.edu	37	8	144780324	144780324	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144780324delA	uc011lkq.1	+						BREA2_uc010mfj.1_RNA	NM_173831				zinc finger protein 707						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(1)	1	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;5.6e-41)|Epithelial(56;1.02e-39)|all cancers(56;9.65e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	144836304	144836304	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144836304delA								FAM83H (20390 upstream) : SCRIB (36786 downstream)																																			---	---	---	---
NFKBIL2	4796	broad.mit.edu	37	8	145668200	145668200	+	Intron	DEL	C	-	-	rs760474		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145668200delC	uc011llg.1	-							NM_013432	NP_038460			NF-kappa-B inhibitor-like protein 2						cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)															---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145813039	145813044	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145813039_145813044delTTTTTT	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
ZNF250	58500	broad.mit.edu	37	8	146112292	146112292	+	Intron	DEL	A	-	-	rs72451532		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146112292delA	uc003zeq.3	-						COMMD5_uc010mgf.2_Intron|ZNF250_uc003zer.3_Intron|ZNF250_uc010mgg.2_Intron	NM_021061	NP_066405			zinc finger protein 250 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	146152877	146152878	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146152877_146152878insA								COMMD5 (26031 upstream) : ZNF16 (2868 downstream)																																			---	---	---	---
KANK1	23189	broad.mit.edu	37	9	569197	569198	+	Intron	INS	-	A	A	rs147405653	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:569197_569198insA	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron|KANK1_uc003zgo.1_Intron|KANK1_uc003zgp.1_5'Flank	NM_015158	NP_055973			KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)														---	---	---	---
DMRT1	1761	broad.mit.edu	37	9	922261	922261	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:922261delA	uc003zgv.2	+							NM_021951	NP_068770			doublesex and mab-3 related transcription factor						cell differentiation|male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	4037548	4037549	+	Intron	DEL	AC	-	-	rs56254712		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4037548_4037549delAC	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc003zhy.1_Intron|GLIS3_uc003zhz.1_Intron	NM_152629	NP_689842			GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
C9orf68	55064	broad.mit.edu	37	9	4622590	4622590	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4622590delC	uc011llz.1	-						C9orf68_uc003zik.2_Intron|C9orf68_uc003zil.2_Intron|C9orf68_uc010mhj.2_Intron|C9orf68_uc011lly.1_Intron	NM_001039395	NP_001034484			hypothetical protein LOC55064												0		Breast(48;0.0456)		GBM - Glioblastoma multiforme(50;0.0222)														---	---	---	---
AK3	50808	broad.mit.edu	37	9	4714096	4714097	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4714096_4714097delAC	uc003ziq.1	-						AK3_uc003zip.1_Intron|AK3_uc011lma.1_Intron|AK3_uc003zir.1_Intron	NM_016282	NP_057366			adenylate kinase 3						blood coagulation	mitochondrial matrix	ATP binding|GTP binding|nucleoside triphosphate adenylate kinase activity			ovary(2)	2	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0302)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5746106	5746106	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5746106delT	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_Intron|KIAA1432_uc003zjj.1_Intron	NM_020829	NP_065880			connexin 43-interacting protein 150 isoform a							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	5837161	5837161	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5837161delT								ERMP1 (4080 upstream) : MLANA (53748 downstream)																																			---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6761340	6761340	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6761340delT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc010mhw.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc010mhv.2_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6873941	6873942	+	Intron	INS	-	GAGA	GAGA	rs141740448	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6873941_6873942insGAGA	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc010mhw.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6917030	6917030	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6917030delT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6960870	6960871	+	Intron	INS	-	G	G	rs72545789		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6960870_6960871insG	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7128278	7128278	+	Intron	DEL	A	-	-	rs73403349	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7128278delA	uc003zkh.2	+						KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	7638240	7638240	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7638240delT								KDM4C (462593 upstream) : C9orf123 (158253 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	10053769	10053769	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10053769delT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11704413	11704414	+	IGR	DEL	TG	-	-	rs35197691		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11704413_11704414delTG								None (None upstream) : TYRP1 (988972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	14534543	14534544	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14534543_14534544delGA								NFIB (220598 upstream) : ZDHHC21 (20937 downstream)																																			---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14857376	14857376	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14857376delT	uc003zlm.2	-						FREM1_uc010mic.2_Intron	NM_144966	NP_659403			FRAS1 related extracellular matrix 1 precursor						cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	15067603	15067603	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15067603delA	uc003zln.1	-											Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
TTC39B	158219	broad.mit.edu	37	9	15171900	15171900	+	3'UTR	DEL	A	-	-	rs71654661		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15171900delA	uc003zlr.1	-	20					TTC39B_uc003zlq.1_3'UTR|TTC39B_uc011lmp.1_3'UTR|TTC39B_uc010mie.1_3'UTR|TTC39B_uc011lmq.1_3'UTR|TTC39B_uc011lmr.1_3'UTR|TTC39B_uc003zlp.1_3'UTR	NM_152574	NP_689787			tetratricopeptide repeat domain 39B								binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	16374147	16374147	+	IGR	DEL	T	-	-	rs79537523		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16374147delT								C9orf93 (402252 upstream) : BNC2 (35355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	17993995	17993995	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17993995delT								SH3GL2 (196875 upstream) : ADAMTSL1 (480109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18926280	18926280	+	IGR	DEL	A	-	-	rs112287521		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18926280delA								ADAMTSL1 (15335 upstream) : FAM154A (1613 downstream)																																			---	---	---	---
HAUS6	54801	broad.mit.edu	37	9	19094440	19094440	+	Intron	DEL	A	-	-	rs112198354		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19094440delA	uc003znk.2	-						HAUS6_uc003znl.1_5'Flank	NM_017645	NP_060115			HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2																		---	---	---	---
ACER2	340485	broad.mit.edu	37	9	19398019	19398019	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19398019delG	uc003znx.1	+											Homo sapiens PP11646 mRNA, complete cds.						ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2																		---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20346394	20346395	+	3'UTR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20346394_20346395delAA	uc003zoe.2	-	11					MLLT3_uc011lne.1_3'UTR|MLLT3_uc011lnf.1_3'UTR	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	9	21184558	21184558	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21184558delT								IFNA21 (17899 upstream) : IFNA4 (2060 downstream)																																			---	---	---	---
MTAP	4507	broad.mit.edu	37	9	22028213	22028214	+	Intron	DEL	AT	-	-	rs142048183		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22028213_22028214delAT	uc003zpi.1	+						CDKN2BAS_uc010miw.1_Intron|CDKN2BAS_uc010mix.1_Intron|CDKN2BAS_uc003zpm.2_Intron	NM_002451	NP_002442			5'-methylthioadenosine phosphorylase						nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)													---	---	---	---
ELAVL2	1993	broad.mit.edu	37	9	23731001	23731001	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23731001delA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423			ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	26182740	26182743	+	IGR	DEL	TTTT	-	-	rs76732306		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26182740_26182743delTTTT								TUSC1 (503884 upstream) : C9orf82 (657941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26511596	26511596	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26511596delA								TUSC1 (832740 upstream) : C9orf82 (329088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26594915	26594915	+	IGR	DEL	T	-	-	rs77439432		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26594915delT								TUSC1 (916059 upstream) : C9orf82 (245769 downstream)																																			---	---	---	---
IFT74	80173	broad.mit.edu	37	9	27002933	27002933	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27002933delT	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_Intron|IFT74_uc003zqg.3_Intron|LRRC19_uc003zqh.2_Intron	NM_001099223	NP_001092693			coiled-coil domain containing 2 isoform a							cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27208346	27208347	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27208346_27208347delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	28834020	28834021	+	IGR	DEL	TT	-	-	rs72282538		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28834020_28834021delTT								LINGO2 (114717 upstream) : MIR876 (29603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29368086	29368086	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29368086delT								MIR873 (479133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30198305	30198306	+	IGR	INS	-	G	G	rs142328331	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30198305_30198306insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30494924	30494924	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30494924delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30551379	30551379	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30551379delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31942755	31942755	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31942755delT								None (None upstream) : ACO1 (441846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	32917694	32917695	+	IGR	DEL	CA	-	-	rs13289533		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32917694_32917695delCA								TMEM215 (128497 upstream) : APTX (54914 downstream)																																			---	---	---	---
APTX	54840	broad.mit.edu	37	9	33023220	33023222	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33023220_33023222delTTT	uc003zrz.2	-						DNAJA1_uc003zsd.1_5'Flank|DNAJA1_uc011lnt.1_5'Flank	NM_175071	NP_778241			aprataxin isoform d						cell death|double-strand break repair|regulation of protein stability|response to hydrogen peroxide|single strand break repair	chromatin|nucleolus|nucleoplasm	chromatin binding|damaged DNA binding|DNA 5'-adenosine monophosphate hydrolase activity|double-stranded DNA binding|double-stranded RNA binding|phosphoglycolate phosphatase activity|phosphoprotein binding|polynucleotide 3'-phosphatase activity|protein N-terminus binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
UBAP1	51271	broad.mit.edu	37	9	34206581	34206581	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34206581delA	uc003ztx.2	+						UBAP1_uc010mka.1_Intron|UBAP1_uc003zty.2_Intron|UBAP1_uc011loi.1_Intron|UBAP1_uc011loj.1_Intron	NM_016525	NP_057609			ubiquitin associated protein 1							cytoplasm					0			LUSC - Lung squamous cell carcinoma(29;0.00272)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	34351708	34351708	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34351708delA								NUDT2 (8013 upstream) : KIAA1161 (17200 downstream)																																			---	---	---	---
C9orf24	84688	broad.mit.edu	37	9	34390137	34390137	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34390137delT	uc003zuh.1	-							NM_032596	NP_115985			testes development-related NYD-SP22 isoform 1											ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34918406	34918406	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34918406delA								C9orf144 (79823 upstream) : KIAA1045 (39115 downstream)																																			---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34997369	34997369	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34997369delA	uc003zvt.2	+	4					DNAJB5_uc003zvs.2_3'UTR|DNAJB5_uc011los.1_3'UTR	NM_012266	NP_036398			DnaJ (Hsp40) homolog, subfamily B, member 5						protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
GNE	10020	broad.mit.edu	37	9	36249476	36249477	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36249476_36249477delAG	uc010mlh.2	-						CLTA_uc003zzf.1_Intron|GNE_uc010mlg.2_5'Flank|GNE_uc011lpl.1_Intron|GNE_uc010mli.2_Intron|GNE_uc010mlj.2_Intron	NM_005476	NP_005467			UDP-N-acetylglucosamine-2-epimerase/N-						cell adhesion|lipopolysaccharide biosynthetic process|N-acetylneuraminate metabolic process|UDP-N-acetylglucosamine metabolic process		ATP binding|N-acylmannosamine kinase activity|UDP-N-acetylglucosamine 2-epimerase activity				0			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	36443722	36443722	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36443722delA								RNF38 (42527 upstream) : MELK (129183 downstream)																																			---	---	---	---
MELK	9833	broad.mit.edu	37	9	36676229	36676230	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36676229_36676230delTT	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606			maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	38120892	38120893	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38120892_38120893delAA								SHB (51682 upstream) : ALDH1B1 (271809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	44742109	44742110	+	IGR	INS	-	TG	TG	rs145005151	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44742109_44742110insTG								None (None upstream) : FAM27C (248126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	45362789	45362791	+	IGR	DEL	TTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:45362789_45362791delTTC								FAM27C (371298 upstream) : FAM27A (364238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66466800	66466800	+	RNA	DEL	G	-	-	rs139943429	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66466800delG	uc004aec.2	+	3		c.1433delG								Homo sapiens, clone IMAGE:5213378, mRNA.																														---	---	---	---
LOC442421	442421	broad.mit.edu	37	9	66496434	66496434	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66496434delC	uc004aee.1	+						LOC442421_uc004aed.1_5'Flank					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	66527855	66527855	+	Intron	DEL	A	-	-	rs5897901		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66527855delA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	66821222	66821223	+	IGR	DEL	CT	-	-	rs112498295		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66821222_66821223delCT								LOC442421 (318195 upstream) : AQP7P1 (433044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67337092	67337092	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67337092delT								AQP7P1 (47600 upstream) : FAM27B (455838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68409971	68409972	+	5'Flank	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68409971_68409972delTC	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68412348	68412348	+	RNA	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68412348delA	uc004aew.1	+	2		c.510delA			uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68473056	68473056	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68473056delT								FAM27B (678867 upstream) : MIR1299 (529183 downstream)																																			---	---	---	---
ANKRD20A4	728747	broad.mit.edu	37	9	69391298	69391299	+	Intron	INS	-	TA	TA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69391298_69391299insTA	uc004afn.2	+						ANKRD20A4_uc010mnw.1_Intron	NM_001098805	NP_001092275			ankyrin repeat domain 20 family, member A4												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	69811095	69811095	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69811095delA								LOC100133920 (146146 upstream) : FOXD4L5 (364614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69817826	69817827	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69817826_69817827insA								LOC100133920 (152877 upstream) : FOXD4L5 (357882 downstream)																																			---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70969933	70969933	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70969933delA	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71852905	71852905	+	Intron	DEL	T	-	-	rs73450890	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71852905delT	uc004ahe.2	+						TJP2_uc011lrs.1_Intron|TJP2_uc011lrt.1_Intron|TJP2_uc004ahd.2_Intron|TJP2_uc004ahf.2_Intron|TJP2_uc011lru.1_Intron|TJP2_uc011lrv.1_Intron	NM_004817	NP_004808			tight junction protein 2 (zona occludens 2)						cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	71906836	71906837	+	IGR	INS	-	A	A	rs74351800		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71906836_71906837insA								TJP2 (36718 upstream) : FAM189A2 (32651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	74154766	74154766	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74154766delA								TRPM3 (92946 upstream) : TMEM2 (143516 downstream)																																			---	---	---	---
TMC1	117531	broad.mit.edu	37	9	75186239	75186239	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75186239delA	uc004aiz.1	+							NM_138691	NP_619636			transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1																		---	---	---	---
TMC1	117531	broad.mit.edu	37	9	75315168	75315169	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75315168_75315169delAA	uc004aiz.1	+						TMC1_uc010moz.1_Intron|TMC1_uc004aja.1_Intron|TMC1_uc004ajb.1_Intron|TMC1_uc004ajc.1_Intron|TMC1_uc010mpa.1_Intron	NM_138691	NP_619636			transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	76091073	76091073	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76091073delT								ANXA1 (305766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	77523612	77523612	+	IGR	DEL	A	-	-	rs75109213		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77523612delA								TRPM6 (20602 upstream) : C9orf40 (37888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78282842	78282842	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78282842delA								OSTF1 (520729 upstream) : PCSK5 (222718 downstream)																																			---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78799576	78799576	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78799576delT	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	78925697	78925697	+	5'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78925697delA	uc004akc.1	+	2										Homo sapiens cDNA FLJ16215 fis, clone CTONG2025610, moderately similar to PC6B.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	79142876	79142876	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79142876delG								GCNT1 (20546 upstream) : PRUNE2 (83417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83620662	83620662	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83620662delA								None (None upstream) : TLE1 (577938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84364524	84364528	+	Intron	DEL	TTCCT	-	-	rs60770857		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84364524_84364528delTTCCT	uc004amc.2	+						uc004amd.2_Intron					Homo sapiens cDNA clone IMAGE:4813482.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	84474614	84474615	+	IGR	INS	-	CA	CA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84474614_84474615insCA								TLE1 (171018 upstream) : FLJ43950 (53737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85718553	85718553	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85718553delA								RASEF (40510 upstream) : FRMD3 (139352 downstream)																																			---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86584096	86584096	+	3'UTR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86584096delC	uc004ang.3	-	17					HNRNPK_uc011lsw.1_3'UTR|HNRNPK_uc004and.3_3'UTR|HNRNPK_uc004ank.3_3'UTR|HNRNPK_uc004anf.3_3'UTR|HNRNPK_uc004anh.3_3'UTR|HNRNPK_uc011lsx.1_3'UTR|HNRNPK_uc004ani.3_3'UTR|HNRNPK_uc004anj.3_3'UTR|HNRNPK_uc004ann.3_3'UTR|HNRNPK_uc004anl.3_3'UTR|HNRNPK_uc004anm.3_3'UTR	NM_031262	NP_112552			heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86584370	86584370	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86584370delA	uc004ang.3	-						HNRNPK_uc011lsw.1_Intron|HNRNPK_uc004and.3_Intron|HNRNPK_uc004ank.3_Intron|HNRNPK_uc004anf.3_Intron|HNRNPK_uc004anh.3_Intron|HNRNPK_uc011lsx.1_Intron|HNRNPK_uc004ani.3_Intron|HNRNPK_uc004anj.3_Intron|HNRNPK_uc004ann.3_Intron|HNRNPK_uc004anl.3_Intron|HNRNPK_uc004anm.3_Intron	NM_031262	NP_112552			heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	86693417	86693417	+	Intron	DEL	A	-	-	rs34077830		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86693417delA	uc004ant.2	+											Homo sapiens mRNA; cDNA DKFZp779O1559 (from clone DKFZp779O1559).																														---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87320330	87320330	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87320330delT	uc004aoa.1	+						NTRK2_uc004anv.1_Intron|NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron|NTRK2_uc011lsz.1_Intron|NTRK2_uc011lta.1_Intron|NTRK2_uc004aob.1_Intron|NTRK2_uc011ltb.1_Intron	NM_001018064	NP_001018074			neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16															TSP Lung(25;0.17)			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87618979	87618980	+	Intron	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87618979_87618980delGA	uc004aoa.1	+						NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074			neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16															TSP Lung(25;0.17)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87858136	87858136	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87858136delC								NTRK2 (219631 upstream) : AGTPBP1 (303319 downstream)																																			---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88667264	88667264	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88667264delT	uc004aol.2	-						GOLM1_uc010mqd.1_Intron|GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89518442	89518443	+	IGR	INS	-	AC	AC	rs141312181	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89518442_89518443insAC								ZCCHC6 (549064 upstream) : GAS1 (40836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89875500	89875507	+	Intron	DEL	AAAAAAAA	-	-	rs142686931		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89875500_89875507delAAAAAAAA	uc004apb.1	-											Homo sapiens cDNA clone IMAGE:30346008.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	90685115	90685116	+	IGR	INS	-	T	T	rs145969978	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90685115_90685116insT								CDK20 (95448 upstream) : SPIN1 (317724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90956747	90956748	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90956747_90956748insA								CDK20 (367080 upstream) : SPIN1 (46092 downstream)																																			---	---	---	---
SHC3	53358	broad.mit.edu	37	9	91664886	91664889	+	Intron	DEL	AATT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91664886_91664889delAATT	uc004aqg.2	-							NM_016848	NP_058544			src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	91901151	91901151	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91901151delT								SHC3 (107469 upstream) : CKS2 (24962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92994753	92994753	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92994753delT								LOC100129066 (660079 upstream) : DIRAS2 (377361 downstream)																																			---	---	---	---
AUH	549	broad.mit.edu	37	9	93977809	93977809	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93977809delT	uc004arf.3	-						AUH_uc004arg.3_Intron	NM_001698	NP_001689			AU RNA binding protein/enoyl-Coenzyme A						branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0																		---	---	---	---
C9orf44	158314	broad.mit.edu	37	9	94907351	94907351	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94907351delT	uc004arp.1	+							NR_027341				Homo sapiens cDNA FLJ13600 fis, clone PLACE1009947.												0																		---	---	---	---
IARS	3376	broad.mit.edu	37	9	95003101	95003101	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95003101delA	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron	NM_013417	NP_038203			isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)													---	---	---	---
ANKRD19	138649	broad.mit.edu	37	9	95582886	95582886	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95582886delT	uc011lua.1	+						ANKRD19_uc004ass.2_Intron|ANKRD19_uc004asr.3_Intron					SubName: Full=ANKRD19 protein; SubName: Full=cDNA FLJ77364, highly similar to Homo sapiens ankyrin repeat domain 19 (ANKRD19), mRNA; SubName: Full=Ankyrin repeat domain 19, isoform CRA_a;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	96883727	96883727	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96883727delA								PTPDC1 (11591 upstream) : MIRLET7A1 (54512 downstream)																																			---	---	---	---
FANCC	2176	broad.mit.edu	37	9	97961594	97961606	+	Intron	DEL	CTGCAGCCCCACC	-	-	rs66565473		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97961594_97961606delCTGCAGCCCCACC	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127			Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)						D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	9	98175401	98175401	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98175401delT								FANCC (95410 upstream) : PTCH1 (29865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98855295	98855295	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98855295delT	uc004avy.3	+						uc004avz.2_5'Flank					Homo sapiens cDNA clone IMAGE:3638298.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	98910246	98910246	+	IGR	DEL	A	-	-	rs139074595		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98910246delA								NCRNA00092 (126209 upstream) : HSD17B3 (87343 downstream)																																			---	---	---	---
HIATL2	84278	broad.mit.edu	37	9	99760171	99760171	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99760171delT	uc004aws.2	-							NR_002894				RecName: Full=Hippocampus abundant transcript-like protein 2;												0																		---	---	---	---
TRIM14	9830	broad.mit.edu	37	9	100849763	100849763	+	Frame_Shift_Del	DEL	G	-	-	rs144459488	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100849763delG	uc004ayd.2	-	6	1336	c.1318delC	c.(1318-1320)CGGfs	p.R440fs	TRIM14_uc004ayf.1_Frame_Shift_Del_p.R347fs|TRIM14_uc011luz.1_Frame_Shift_Del_p.R218fs|TRIM14_uc011lva.1_Frame_Shift_Del_p.R221fs|TRIM14_uc004ayg.1_Frame_Shift_Del_p.R440fs|TRIM14_uc004ayh.1_Frame_Shift_Del_p.R440fs|TRIM14_uc004ayi.1_Intron|TRIM14_uc004ayj.1_Frame_Shift_Del_p.R347fs	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha	440	B30.2/SPRY.			RLRPRDDLDRLGVFLDYEAGVLAFYDVTGGMSHLHTFRATF QEPLYPALRLWEGAISIPRLP -> ACGPATTSTGSASSWT TRPASSPSTT (in Ref. 2; BAA09478).		cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101148165	101148166	+	Intron	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101148165_101148166delGA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	102150441	102150441	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102150441delA								SEC61B (157541 upstream) : NR4A3 (433696 downstream)																																			---	---	---	---
TMEFF1	8577	broad.mit.edu	37	9	103323835	103323835	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103323835delT	uc004baz.1	+						TMEFF1_uc004bay.1_Intron	NM_003692	NP_003683			transmembrane protein with EGF-like and two						multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	103682593	103682593	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103682593delT								MURC (332422 upstream) : LPPR1 (108438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106099169	106099169	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106099169delA								CYLC2 (318399 upstream) : SMC2 (757372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106444867	106444868	+	IGR	INS	-	G	G	rs138180475	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106444867_106444868insG								CYLC2 (664097 upstream) : SMC2 (411673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107292915	107292915	+	IGR	DEL	A	-	-	rs5899601		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107292915delA								OR13C4 (3425 upstream) : OR13C3 (5136 downstream)																																			---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108235432	108235432	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108235432delA	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108300871	108300871	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108300871delT	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108695144	108695144	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108695144delA								TMEM38B (157700 upstream) : ZNF462 (930234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110289903	110289904	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110289903_110289904insT								KLF4 (37856 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111042711	111042714	+	IGR	DEL	CACA	-	-	rs10532816		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111042711_111042714delCACA								KLF4 (790664 upstream) : ACTL7B (574157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111209087	111209087	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111209087delA								KLF4 (957040 upstream) : ACTL7B (407784 downstream)																																			---	---	---	---
IKBKAP	8518	broad.mit.edu	37	9	111665955	111665955	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111665955delA	uc004bdm.3	-						IKBKAP_uc004bdl.2_Intron|IKBKAP_uc011lwc.1_Intron|IKBKAP_uc010mtq.2_Intron	NM_003640	NP_003631			inhibitor of kappa light polypeptide gene						immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7																		---	---	---	---
C9orf5	23731	broad.mit.edu	37	9	111869017	111869017	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111869017delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401			hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)														---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112762223	112762223	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112762223delT	uc004bei.2	+						PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034			A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113275445	113275446	+	Intron	DEL	TT	-	-	rs75490536		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113275445_113275446delTT	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_Intron|SVEP1_uc004bev.2_Intron	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113445250	113445250	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113445250delT	uc004bey.2	+						MUSK_uc004bex.2_Intron	NM_005592	NP_005583			skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114135312	114135312	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114135312delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115851594	115851595	+	IGR	DEL	GC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115851594_115851595delGC								ZFP37 (32598 upstream) : C9orf110 (15411 downstream)																																			---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116226354	116226354	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116226354delG	uc004bhq.2	+						RGS3_uc004bhr.2_Intron|RGS3_uc004bhs.2_Intron	NM_144488	NP_652759			regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117038016	117038016	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117038016delC	uc011lxl.1	+	37	3685	c.3685delC	c.(3685-3687)CCCfs	p.P1229fs	COL27A1_uc004bii.2_RNA	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	1229	Collagen-like 10.|Pro-rich.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	117647516	117647517	+	IGR	INS	-	G	G	rs139275481	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117647516_117647517insG								TNFSF15 (79108 upstream) : TNFSF8 (17607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118368435	118368435	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118368435delT								DEC1 (203512 upstream) : C9orf27 (282111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118709721	118709722	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118709721_118709722insA								C9orf27 (22344 upstream) : PAPPA (206349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118749514	118749514	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118749514delT								C9orf27 (62137 upstream) : PAPPA (166557 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119576835	119576835	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119576835delA	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	120381304	120381304	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120381304delA								ASTN2 (203987 upstream) : TLR4 (85156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	123101493	123101493	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123101493delA								MIR147 (94165 upstream) : CDK5RAP2 (49655 downstream)																																			---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123151585	123151585	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123151585delA	uc004bkf.2	-						CDK5RAP2_uc010mvi.2_Intron|CDK5RAP2_uc004bke.2_Intron|CDK5RAP2_uc004bkg.2_Intron|CDK5RAP2_uc011lxw.1_Intron|CDK5RAP2_uc011lxx.1_Intron|CDK5RAP2_uc011lxy.1_Intron|CDK5RAP2_uc011lxz.1_Intron|CDK5RAP2_uc011lya.1_Intron	NM_018249	NP_060719			CDK5 regulatory subunit associated protein 2						brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
PSMD5	5711	broad.mit.edu	37	9	123595492	123595493	+	Intron	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123595492_123595493delGA	uc004bko.2	-						PSMD5_uc011lye.1_Intron	NM_005047	NP_005038			proteasome 26S non-ATPase subunit 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding				0																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124074857delA	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168			gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124351674	124351674	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124351674delT	uc004bln.2	+							NM_032552	NP_115941			disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	125425831	125425831	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125425831delG								OR1L1 (906 upstream) : OR1L3 (11578 downstream)																																			---	---	---	---
STRBP	55342	broad.mit.edu	37	9	126030153	126030153	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126030153delC	uc004bns.2	-						STRBP_uc004bnt.2_Intron|STRBP_uc004bnu.2_Intron|STRBP_uc004bnv.2_Intron	NM_018387	NP_060857			spermatid perinuclear RNA binding protein						multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126150776	126150776	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126150776delA	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc010mwh.1_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126344438	126344438	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126344438delA	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127360949	127360949	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127360949delC	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591			nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
RPL35	11224	broad.mit.edu	37	9	127620948	127620949	+	Intron	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127620948_127620949insC	uc004boy.1	-							NM_007209	NP_009140			ribosomal protein L35						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	mRNA binding|protein binding|structural constituent of ribosome			ovary(1)	1				GBM - Glioblastoma multiforme(294;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	129039063	129039064	+	5'Flank	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129039063_129039064delCA	uc004bqf.1	-											Homo sapiens cDNA clone IMAGE:5259303.																														---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129787977	129787977	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129787977delT	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451			Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130053433	130053433	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130053433delT	uc011mae.1	+						GARNL3_uc011mad.1_Intron	NM_032293	NP_115669			GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130062292	130062292	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130062292delT	uc011mae.1	+						GARNL3_uc011mad.1_Intron	NM_032293	NP_115669			GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130420530	130420530	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130420530delC	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130446502	130446503	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130446502_130446503delTG	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
SLC27A4	10999	broad.mit.edu	37	9	131116023	131116023	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131116023delT	uc004but.2	+						SLC27A4_uc004buu.2_Intron	NM_005094	NP_005085			solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0																		---	---	---	---
ZER1	10444	broad.mit.edu	37	9	131514607	131514609	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131514607_131514609delTTT	uc004bwa.1	-							NM_006336	NP_006327			zyg-11 homolog B (C. elegans)-like						ATP hydrolysis coupled proton transport|regulation of ubiquitin-protein ligase activity	Cul2-RING ubiquitin ligase complex|vacuolar proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
DOLPP1	57171	broad.mit.edu	37	9	131843361	131843361	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131843361delC	uc004bxc.2	+						DOLPP1_uc004bxd.2_5'Flank|DOLPP1_uc004bxe.2_5'Flank	NM_020438	NP_065171			dolichyl pyrophosphate phosphatase 1 isoform a						dolichyl diphosphate biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to endoplasmic reticulum membrane	dolichyldiphosphatase activity			skin(1)	1																OREG0003930	type=REGULATORY REGION|Gene=DOLPP1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
Unknown	0	broad.mit.edu	37	9	132283703	132283703	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132283703delT								C9orf106 (198821 upstream) : C9orf50 (90803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132335179	132335179	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132335179delC	uc004bya.1	+											Homo sapiens cDNA clone IMAGE:4812570.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	132338294	132338295	+	Intron	DEL	AC	-	-	rs34824868		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132338294_132338295delAC	uc004bya.1	+											Homo sapiens cDNA clone IMAGE:4812570.																														---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132737138	132737138	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132737138delA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132751216	132751217	+	Intron	DEL	TA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132751216_132751217delTA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
GPR107	57720	broad.mit.edu	37	9	132848815	132848815	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132848815delT	uc004bze.2	+						GPR107_uc004bzb.2_Intron|GPR107_uc004bzc.3_Intron|GPR107_uc011mbx.1_Intron|GPR107_uc004bzd.2_Intron	NM_001136557	NP_001130029			G protein-coupled receptor 107 isoform 1							integral to membrane				upper_aerodigestive_tract(1)	1		Ovarian(14;0.000531)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	133286583	133286583	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133286583delC	uc004bzj.2	+											RecName: Full=Hemicentin-2.; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	133438420	133438420	+	IGR	DEL	T	-	-	rs34572418		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133438420delT								ASS1 (61760 upstream) : LOC100272217 (14319 downstream)																																			---	---	---	---
NUP214	8021	broad.mit.edu	37	9	134049354	134049355	+	Intron	DEL	TT	-	-	rs79169508		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134049354_134049355delTT	uc004cag.2	+						NUP214_uc004cah.2_Intron|NUP214_uc004cai.2_Intron|NUP214_uc004caf.1_Intron|NUP214_uc010mzf.2_Intron	NM_005085	NP_005076			nucleoporin 214kDa						carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)				T	DEK|SET|ABL1	AML|T-ALL								---	---	---	---
POMT1	10585	broad.mit.edu	37	9	134397371	134397372	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134397371_134397372delAG	uc004cav.2	+						POMT1_uc004cax.2_Intron|POMT1_uc011mcj.1_Intron|POMT1_uc004cau.2_Intron|POMT1_uc004caw.2_Intron|POMT1_uc011mck.1_Intron|POMT1_uc011mcl.1_Intron|POMT1_uc011mcm.1_Intron	NM_007171	NP_009102			protein-O-mannosyltransferase 1 isoform a						multicellular organismal development|protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135158204	135158205	+	Intron	INS	-	T	T	rs143064436	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135158204_135158205insT	uc004cbk.2	-						SETX_uc004cbj.2_Intron|SETX_uc010mzt.2_Intron	NM_015046	NP_055861			senataxin						cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
DDX31	64794	broad.mit.edu	37	9	135500889	135500890	+	Intron	DEL	AA	-	-	rs75372078		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135500889_135500890delAA	uc004cbq.1	-						DDX31_uc010mzu.1_Intron	NM_022779	NP_073616			DEAD (Asp-Glu-Ala-Asp) box polypeptide 31							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)														---	---	---	---
TSC1	7248	broad.mit.edu	37	9	135782303	135782304	+	Intron	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135782303_135782304delAT	uc004cca.2	-						TSC1_uc004ccb.3_Intron|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_Intron|TSC1_uc011mcs.1_Intron	NM_000368	NP_000359			tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding	p.?(1)		lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)				D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136653454	136653454	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136653454delG	uc004ces.2	-						VAV2_uc004cer.2_Intron|VAV2_uc004cet.1_Intron	NM_001134398	NP_001127870			vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	136879833	136879833	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136879833delT								VAV2 (22387 upstream) : NCRNA00094 (10728 downstream)																																			---	---	---	---
KIAA0649	9858	broad.mit.edu	37	9	138379371	138379372	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138379371_138379372insT	uc004cfr.1	+	4	3564_3565	c.3015_3016insT	c.(3013-3018)AGCTTCfs	p.S1005fs		NM_014811	NP_055626	Q5T8A7	K0649_HUMAN	1A6/DRIM (down-regulated in metastasis)	1005_1006						nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(145;6.91e-08)|Epithelial(140;4.69e-07)|all cancers(34;9.33e-06)														---	---	---	---
KCNT1	57582	broad.mit.edu	37	9	138649260	138649260	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138649260delG	uc011mdq.1	+						KCNT1_uc011mdr.1_Intron|KCNT1_uc010nbf.2_Intron|KCNT1_uc004cgo.1_Intron	NM_020822	NP_065873			potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)														---	---	---	---
KCNT1	57582	broad.mit.edu	37	9	138679898	138679899	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138679898_138679899delTC	uc011mdq.1	+						KCNT1_uc011mdr.1_Intron|KCNT1_uc010nbf.2_Intron	NM_020822	NP_065873			potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)														---	---	---	---
MAMDC4	158056	broad.mit.edu	37	9	139749363	139749363	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139749363delC	uc004cjs.2	+						MAMDC4_uc011mej.1_Intron	NM_206920	NP_996803			apical early endosomal glycoprotein precursor						protein transport	integral to membrane				breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1)	7	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)														---	---	---	---
MAMDC4	158056	broad.mit.edu	37	9	139754985	139754986	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139754985_139754986delAA	uc004cjs.2	+						MAMDC4_uc011mej.1_Intron	NM_206920	NP_996803			apical early endosomal glycoprotein precursor						protein transport	integral to membrane				breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1)	7	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)														---	---	---	---
MAN1B1	11253	broad.mit.edu	37	9	140002788	140002788	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140002788delG	uc004cld.2	+						MAN1B1_uc011mep.1_3'UTR|MAN1B1_uc010ncc.2_Intron|MAN1B1_uc004clf.1_Intron|MAN1B1_uc004clg.1_Intron	NM_016219	NP_057303			alpha 1,2-mannosidase						oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140249916	140249917	+	Intron	INS	-	G	G	rs150292386		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140249916_140249917insG	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron|EXD3_uc004cmq.1_Intron|EXD3_uc010ncg.1_Intron	NM_017820	NP_060290			exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
C9orf167	54863	broad.mit.edu	37	9	140340898	140340899	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140340898_140340899insA	uc011mew.1	+											Homo sapiens cDNA FLJ20385 fis, clone KAIA4085.						chaperone mediated protein folding requiring cofactor	integral to membrane	ATP binding|nucleoside-triphosphatase activity			pancreas(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.137)	OV - Ovarian serous cystadenocarcinoma(145;9.07e-05)|Epithelial(140;0.000728)														---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140396079	140396079	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140396079delC	uc004cnf.2	-						C9orf167_uc011mew.1_Intron|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499			patatin-like phospholipase domain containing 7						lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140700894	140700895	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140700894_140700895delTT	uc011mfc.1	+							NM_024757	NP_079033			euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)														---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140960903	140960904	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140960903_140960904delAG	uc004cog.2	+						CACNA1B_uc004coi.2_Intron	NM_000718	NP_000709			calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	765788	765789	+	IGR	INS	-	A	A	rs147379822	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:765788_765789insA								DIP2C (30180 upstream) : LARP4B (89695 downstream)																																			---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1230936	1230936	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1230936delG	uc009xhq.2	-	9	2282	c.1908delC	c.(1906-1908)CCCfs	p.P636fs	ADARB2_uc009xhp.2_Frame_Shift_Del_p.P20fs|ADARB2_uc001igl.3_5'UTR|ADARB2_uc001igm.3_Frame_Shift_Del_p.P145fs	NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2	636	A to I editase.				mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	2250937	2250938	+	IGR	INS	-	AG	AG	rs145423285	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2250937_2250938insAG								ADARB2 (471219 upstream) : PFKP (858814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4501371	4501371	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4501371delT								KLF6 (673898 upstream) : LOC100216001 (120073 downstream)																																			---	---	---	---
AKR1C1	1645	broad.mit.edu	37	10	5019873	5019873	+	Intron	DEL	T	-	-	rs75268655		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5019873delT	uc001iho.2	+						AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc001ihq.2_Intron	NM_001353	NP_001344			aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)													---	---	---	---
ASB13	79754	broad.mit.edu	37	10	5684553	5684553	+	Intron	DEL	A	-	-	rs12268809	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5684553delA	uc001iig.2	-						ASB13_uc001iii.2_Intron|ASB13_uc001iih.2_Intron|ASB13_uc009xic.2_Intron	NM_024701	NP_078977			ankyrin repeat and SOCS box-containing protein						intracellular signal transduction		protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(2;9.59e-09)														---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5772380	5772380	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5772380delT	uc001iij.2	+						C10orf18_uc001iik.2_5'Flank	NM_017782	NP_060252			hypothetical protein LOC54906											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FBXO18	84893	broad.mit.edu	37	10	5978590	5978591	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5978590_5978591insT	uc001iis.2	+						FBXO18_uc001iir.2_Intron|FBXO18_uc009xig.2_Intron|FBXO18_uc001iit.2_Intron	NM_178150	NP_835363			F-box only protein, helicase, 18 isoform 2						DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7627789	7627790	+	Intron	DEL	AA	-	-	rs75428263		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7627789_7627790delAA	uc001ijq.2	-						ITIH5_uc001ijp.2_Intron|ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046			inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	8066918	8066919	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8066918_8066919delGA								TAF3 (10205 upstream) : FLJ45983 (25494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8848562	8848562	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8848562delA								GATA3 (731400 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9809698	9809698	+	IGR	DEL	A	-	-	rs78320462		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9809698delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	11699132	11699132	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11699132delA								USP6NL (45453 upstream) : ECHDC3 (85224 downstream)																																			---	---	---	---
UCMA	221044	broad.mit.edu	37	10	13265252	13265252	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13265252delA	uc001imd.2	-							NM_145314	NP_660357			upper zone of growth plate and cartilage matrix							proteinaceous extracellular matrix					0																		---	---	---	---
PRPF18	8559	broad.mit.edu	37	10	13653882	13653883	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13653882_13653883delTT	uc001imp.2	+						PRPF18_uc001imq.2_Intron	NM_003675	NP_003666			PRP18 pre-mRNA processing factor 18 homolog						mRNA processing|RNA splicing	nuclear speck|spliceosomal complex				central_nervous_system(1)	1																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	13751856	13751856	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13751856delT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497			FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15701107	15701107	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15701107delT	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	15768168	15768168	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15768168delG								ITGA8 (6398 upstream) : FAM188A (52007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16351806	16351806	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16351806delA								FAM188A (449287 upstream) : PTER (127161 downstream)																																			---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16825364	16825365	+	Intron	DEL	TT	-	-	rs71846718		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16825364_16825365delTT	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron|RSU1_uc001ion.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17078021	17078021	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17078021delA	uc001ioo.2	-							NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	19322196	19322197	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19322196_19322197delTT								ARL5B (355256 upstream) : PLXDC2 (783175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19555078	19555078	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19555078delT								ARL5B (588138 upstream) : PLXDC2 (550294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20958745	20958746	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20958745_20958746delAA								PLXDC2 (389630 upstream) : NEBL (110159 downstream)																																			---	---	---	---
C10orf140	387640	broad.mit.edu	37	10	21807470	21807470	+	5'Flank	DEL	A	-	-	rs111265769		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21807470delA	uc010qcs.1	-						C10orf140_uc009xkd.2_5'UTR					SubName: Full=cDNA FLJ56186;							nucleus	nucleotide binding			ovary(1)	1																		---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21861546	21861546	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21861546delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21875206	21875207	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21875206_21875207delTT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21879274	21879274	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21879274delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	10	22749730	22749730	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22749730delC								SPAG6 (43192 upstream) : PIP4K2A (74037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	23445390	23445390	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23445390delA								MSRB2 (34449 upstream) : PTF1A (36070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	23978045	23978046	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23978045_23978046delTT								OTUD1 (246737 upstream) : KIAA1217 (5629 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24827439	24827440	+	Intron	INS	-	AG	AG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24827439_24827440insAG	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc001irw.2_Intron|KIAA1217_uc001irz.2_Intron|KIAA1217_uc001irx.2_Intron|KIAA1217_uc001iry.2_Intron	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	25069929	25069930	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25069929_25069930insT								ARHGAP21 (57332 upstream) : PRTFDC1 (67624 downstream)																																			---	---	---	---
PRTFDC1	56952	broad.mit.edu	37	10	25147403	25147403	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25147403delT	uc001ise.1	-						PRTFDC1_uc010qdd.1_Intron|PRTFDC1_uc001isf.1_Intron|PRTFDC1_uc009xkm.1_Intron	NM_020200	NP_064585			phosphoribosyl transferase domain containing 1						adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP salvage|grooming behavior|hypoxanthine metabolic process|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity			ovary(1)	1																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26439700	26439700	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26439700delT	uc001isn.2	+						MYO3A_uc009xko.1_Intron|MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129			myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
RAB18	22931	broad.mit.edu	37	10	27822550	27822550	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27822550delA	uc001itv.2	+						RAB18_uc001itw.2_Intron|RAB18_uc010qdq.1_Intron|RAB18_uc010qdr.1_Intron	NM_021252	NP_067075			RAB18, member RAS oncogene family						endocytosis|protein transport|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction	intracellular|plasma membrane	ATP binding|GTP binding|GTPase activity|transcription factor binding				0																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28270269	28270269	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28270269delA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron|ARMC4_uc010qdu.1_Intron	NM_018076	NP_060546			armadillo repeat containing 4								binding			ovary(4)|skin(2)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	29169047	29169047	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29169047delT								BAMBI (197179 upstream) : LYZL1 (408943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29187879	29187879	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29187879delT								BAMBI (216011 upstream) : LYZL1 (390111 downstream)																																			---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29760116	29760116	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29760116delC	uc001iut.1	-	31	6339	c.5586delG	c.(5584-5586)GGGfs	p.G1862fs	LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Frame_Shift_Del_p.G776fs|SVIL_uc001iuu.1_Frame_Shift_Del_p.G1436fs	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1862	Gelsolin-like 3.				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	30180428	30180429	+	IGR	DEL	TT	-	-	rs113723333		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30180428_30180429delTT								SVIL (154564 upstream) : KIAA1462 (121300 downstream)																																			---	---	---	---
ZNF438	220929	broad.mit.edu	37	10	31200368	31200368	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31200368delA	uc010qdz.1	-						ZNF438_uc001ivn.2_Intron|ZNF438_uc010qdy.1_Intron|ZNF438_uc001ivo.3_Intron|ZNF438_uc009xlg.2_Intron|ZNF438_uc001ivp.3_Intron|ZNF438_uc010qea.1_Intron|ZNF438_uc010qeb.1_Intron|ZNF438_uc010qec.1_Intron	NM_182755	NP_877432			zinc finger protein 438 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)																---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31765065	31765065	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31765065delA	uc001ivs.3	+						ZEB1_uc001ivr.3_Intron|ZEB1_uc010qee.1_Intron|ZEB1_uc010qef.1_Intron|ZEB1_uc009xlh.1_Intron|ZEB1_uc009xli.1_Intron|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_Intron|ZEB1_uc001ivt.3_Intron|ZEB1_uc001ivu.3_Intron|ZEB1_uc001ivv.3_Intron|ZEB1_uc010qeh.1_Intron|ZEB1_uc009xll.2_Intron|ZEB1_uc009xlm.1_Intron|ZEB1_uc009xln.1_Intron|ZEB1_uc009xlo.1_Intron|ZEB1_uc009xlp.2_Intron	NM_030751	NP_110378			zinc finger E-box binding homeobox 1 isoform b						cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)																---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31776770	31776770	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31776770delT	uc001ivs.3	+						ZEB1_uc001ivr.3_Intron|ZEB1_uc010qee.1_Intron|ZEB1_uc010qef.1_Intron|ZEB1_uc009xlh.1_Intron|ZEB1_uc009xli.1_Intron|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_Intron|ZEB1_uc001ivt.3_Intron|ZEB1_uc001ivu.3_Intron|ZEB1_uc001ivv.3_Intron|ZEB1_uc010qeh.1_Intron|ZEB1_uc009xll.2_Intron|ZEB1_uc009xlm.1_Intron|ZEB1_uc009xln.1_Intron|ZEB1_uc009xlo.1_Intron|ZEB1_uc009xlp.2_Intron	NM_030751	NP_110378			zinc finger E-box binding homeobox 1 isoform b						cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	32050699	32050702	+	IGR	DEL	AGGA	-	-	rs112430684		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32050699_32050702delAGGA								ZEB1 (232572 upstream) : ARHGAP12 (44523 downstream)																																			---	---	---	---
ARHGAP12	94134	broad.mit.edu	37	10	32142978	32142979	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32142978_32142979insA	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757			Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	33746849	33746849	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33746849delT								NRP1 (122843 upstream) : PARD3 (653249 downstream)																																			---	---	---	---
CUL2	8453	broad.mit.edu	37	10	35363433	35363434	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35363433_35363434delTT	uc001ixv.2	-						CUL2_uc009xma.2_5'Flank|CUL2_uc010qer.1_5'Flank|CUL2_uc001ixw.2_Intron|CUL2_uc010qes.1_Intron	NM_003591	NP_003582			cullin 2						cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3																		---	---	---	---
FZD8	8325	broad.mit.edu	37	10	35930413	35930414	+	5'Flank	DEL	GG	-	-	rs78405338	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35930413_35930414delGG	uc001iyz.1	-							NM_031866	NP_114072			frizzled 8 precursor						axonogenesis|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|T cell differentiation in thymus|vasculature development	cell projection|Golgi apparatus|integral to membrane|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	35956408	35956410	+	IGR	DEL	CAT	-	-	rs150869536		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35956408_35956410delCAT								FZD8 (26046 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36778026	36778027	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36778026_36778027insT								FZD8 (847664 upstream) : ANKRD30A (636758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37028321	37028321	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37028321delT								None (None upstream) : ANKRD30A (386464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37893025	37893028	+	IGR	DEL	TAGA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37893025_37893028delTAGA								ANKRD30A (371530 upstream) : ZNF248 (197419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38428209	38428210	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38428209_38428210delTT								ZNF37A (15933 upstream) : LOC100129055 (36389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39118900	39118900	+	IGR	DEL	G	-	-	rs74192178		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39118900delG								LOC399744 (377820 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42706720	42706720	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42706720delA								None (None upstream) : LOC441666 (120595 downstream)																																			---	---	---	---
RET	5979	broad.mit.edu	37	10	43599969	43599969	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43599969delA	uc001jal.2	+						RET_uc001jak.1_Intron|RET_uc010qez.1_5'Flank	NM_020975	NP_066124			ret proto-oncogene isoform a						homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development	integral to membrane	ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity			thyroid(404)|adrenal_gland(20)|lung(9)|large_intestine(5)|breast(4)|ovary(4)|central_nervous_system(3)|urinary_tract(1)|NS(1)	451		Ovarian(717;0.0423)			Sunitinib(DB01268)		1	T|Mis|N|F	H4|PRKAR1A|NCOA4|PCM1|GOLGA5|TRIM33|KTN1|TRIM27|HOOK3	medullary thyroid| papillary thyroid|pheochromocytoma	medullary thyroid| papillary thyroid|pheochromocytoma	Hirschsprung disease		Multiple_Endocrine_Neoplasia_type_2B|Multiple_Endocrine_Neoplasia_type_2A|Familial_Medullary_Thyroid_Carcinoma				---	---	---	---
ZNF487	642819	broad.mit.edu	37	10	43942699	43942699	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43942699delT	uc010qfb.1	+							NR_026693				SubName: Full=cDNA FLJ52643, weakly similar to Zinc finger protein 11B;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	44773186	44773186	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44773186delT								HNRNPA3P1 (487321 upstream) : CXCL12 (92421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45061169	45061170	+	IGR	INS	-	A	A	rs137946280	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45061169_45061170insA								CXCL12 (180627 upstream) : TMEM72 (345594 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47094139	47094139	+	Intron	DEL	C	-	-	rs28590570	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47094139delC	uc001jed.3	-											Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47105946	47105947	+	Intron	INS	-	AG	AG	rs148390482		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47105946_47105947insAG	uc001jed.3	-						uc001jef.2_Intron					Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47113799	47113800	+	Intron	INS	-	AAGA	AAGA	rs143332868	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47113799_47113800insAAGA	uc001jed.3	-						uc001jef.2_Intron					Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
ANTXRL	195977	broad.mit.edu	37	10	47693694	47693695	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47693694_47693695delAA	uc001jel.2	+							NR_003601				Homo sapiens cDNA FLJ32754 fis, clone TESTI2001671.												0																		---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49632499	49632499	+	Intron	DEL	T	-	-	rs78072348		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49632499delT	uc009xnz.2	+						MAPK8_uc001jgl.2_Intron|MAPK8_uc001jgm.2_Intron|MAPK8_uc001jgo.2_Intron|MAPK8_uc009xoa.2_Intron|MAPK8_uc001jgn.2_Intron|MAPK8_uc010qgk.1_Intron|MAPK8_uc001jgp.2_Intron|MAPK8_uc001jgq.2_Intron	NM_139047	NP_620635			mitogen-activated protein kinase 8 isoform JNK1						activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)														---	---	---	---
C10orf71	118461	broad.mit.edu	37	10	50530449	50530449	+	5'UTR	DEL	A	-	-	rs141182587		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50530449delA	uc010qgp.1	+	3						NM_199459	NP_955629			hypothetical protein LOC118461 isoform 2												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	51008050	51008051	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51008050_51008051delTT								OGDHL (37625 upstream) : PARG (18276 downstream)																																			---	---	---	---
ASAH2	56624	broad.mit.edu	37	10	52005194	52005194	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52005194delA	uc001jjd.2	-	2	148	c.148delT	c.(148-150)TCAfs	p.S50fs	ASAH2_uc009xos.2_Frame_Shift_Del_p.S50fs	NM_019893	NP_063946	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase 2 isoform a	50	Lumenal (Potential).				apoptosis|ceramide metabolic process|signal transduction	integral to membrane|mitochondrion|plasma membrane	ceramidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	52024834	52024834	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52024834delA								ASAH2 (16464 upstream) : SGMS1 (40512 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	56038337	56038337	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56038337delA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	57726099	57726100	+	IGR	INS	-	AGA	AGA	rs147755546	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57726099_57726100insAGA								PCDH15 (338397 upstream) : ZWINT (391099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59275990	59275990	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59275990delA								None (None upstream) : IPMK (679628 downstream)																																			---	---	---	---
BICC1	80114	broad.mit.edu	37	10	60546935	60546935	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60546935delA	uc001jki.1	+							NM_001080512	NP_001073981			bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	63296182	63296182	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63296182delC								TMEM26 (82974 upstream) : C10orf107 (126537 downstream)																																			---	---	---	---
C10orf107	219621	broad.mit.edu	37	10	63479206	63479206	+	Intron	DEL	A	-	-	rs112605805		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63479206delA	uc010qik.1	+							NM_173554	NP_775825			hypothetical protein LOC219621												0	Prostate(12;0.016)																	---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63757035	63757035	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63757035delA	uc001jlt.1	+						ARID5B_uc010qil.1_Intron	NM_032199	NP_115575			AT rich interactive domain 5B (MRF1-like)						liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64159513	64159513	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64159513delA	uc001jly.3	+	5	1296	c.1234delA	c.(1234-1236)AAAfs	p.K412fs	ZNF365_uc001jmb.3_Intron|ZNF365_uc001jmc.2_Intron|ZNF365_uc001jlz.3_Frame_Shift_Del_p.K397fs|ZNF365_uc001jma.3_RNA	NM_014951	NP_055766	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform A	Error:Variant_position_missing_in_Q70YC4_after_alignment										ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64977095	64977095	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64977095delA	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc001jmp.1_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	65184356	65184357	+	Intron	INS	-	C	C	rs143782011	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65184356_65184357insC	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
REEP3	221035	broad.mit.edu	37	10	65357668	65357668	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65357668delA	uc001jmt.2	+						REEP3_uc009xpl.1_Intron	NM_001001330	NP_001001330			receptor accessory protein 3							integral to membrane					0	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
REEP3	221035	broad.mit.edu	37	10	65370835	65370835	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65370835delA	uc001jmt.2	+							NM_001001330	NP_001001330			receptor accessory protein 3							integral to membrane					0	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	65960349	65960350	+	IGR	INS	-	ACACACAC	ACACACAC	rs145986355	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65960349_65960350insACACACAC								REEP3 (578378 upstream) : ANXA2P3 (624935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66058504	66058504	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66058504delA								REEP3 (676533 upstream) : ANXA2P3 (526781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66746767	66746767	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66746767delT								ANXA2P3 (160133 upstream) : CTNNA3 (932958 downstream)																																			---	---	---	---
SIRT1	23411	broad.mit.edu	37	10	69668900	69668900	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69668900delT	uc001jnd.2	+						SIRT1_uc010qis.1_Intron|SIRT1_uc009xpp.2_Intron|SIRT1_uc001jne.2_Intron	NM_012238	NP_036370			sirtuin 1 isoform a						apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0																		---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70156582	70156583	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70156582_70156583insT	uc001job.2	-	4	784_785	c.457_458insA	c.(457-459)ATGfs	p.M153fs	RUFY2_uc001jnz.1_RNA|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Frame_Shift_Ins_p.M60fs|RUFY2_uc001jod.1_Frame_Shift_Ins_p.M118fs|RUFY2_uc009xpv.1_Frame_Shift_Ins_p.M1fs|RUFY2_uc001joe.1_Frame_Shift_Ins_p.M118fs	NM_017987	NP_060457	Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain-containing 2 isoform a	167	RUN.					nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
SLC25A16	8034	broad.mit.edu	37	10	70262472	70262472	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70262472delA	uc001joi.2	-						SLC25A16_uc010qix.1_Intron|SLC25A16_uc010qiy.1_Intron|SLC25A16_uc001joj.2_Intron	NM_152707	NP_689920			solute carrier family 25, member 16						coenzyme biosynthetic process|pantothenate metabolic process	integral to membrane|mitochondrial inner membrane	binding|solute:solute antiporter activity				0																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70434501	70434501	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70434501delA	uc001jok.3	+							NM_030625	NP_085128			CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
STOX1	219736	broad.mit.edu	37	10	70586532	70586532	+	5'Flank	DEL	A	-	-	rs35705908		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70586532delA	uc001jos.2	+						STOX1_uc001jor.2_5'Flank|STOX1_uc009xpy.2_5'Flank|STOX1_uc001joq.2_5'Flank	NM_001130161	NP_001123633			storkhead box 1 isoform a							cytoplasm|nucleolus	DNA binding			kidney(1)|skin(1)	2																		---	---	---	---
STOX1	219736	broad.mit.edu	37	10	70614480	70614481	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70614480_70614481insT	uc001jos.2	+						STOX1_uc001jor.2_Intron|STOX1_uc009xpy.2_Intron|STOX1_uc001joq.2_Intron	NM_001130161	NP_001123633			storkhead box 1 isoform a							cytoplasm|nucleolus	DNA binding			kidney(1)|skin(1)	2																		---	---	---	---
STOX1	219736	broad.mit.edu	37	10	70641631	70641631	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70641631delT	uc001jos.2	+						STOX1_uc001jor.2_Intron|STOX1_uc009xpy.2_Intron|STOX1_uc001joq.2_Intron	NM_001130161	NP_001123633			storkhead box 1 isoform a							cytoplasm|nucleolus	DNA binding			kidney(1)|skin(1)	2																		---	---	---	---
DDX21	9188	broad.mit.edu	37	10	70728709	70728709	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70728709delT	uc001jov.1	+						DDX21_uc001jow.1_Intron	NM_004728	NP_004719			DEAD (Asp-Glu-Ala-Asp) box polypeptide 21							nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3																		---	---	---	---
SUPV3L1	6832	broad.mit.edu	37	10	70946081	70946082	+	Intron	INS	-	A	A	rs78362222		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70946081_70946082insA	uc001jpe.1	+						SUPV3L1_uc010qjd.1_Intron	NM_003171	NP_003162			suppressor of var1, 3-like 1 precursor						DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2																		---	---	---	---
SUPV3L1	6832	broad.mit.edu	37	10	70967472	70967472	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70967472delT	uc001jpe.1	+						SUPV3L1_uc010qjd.1_Intron	NM_003171	NP_003162			suppressor of var1, 3-like 1 precursor						DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71128472	71128472	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71128472delG	uc001jpl.3	+						HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron|HK1_uc001jpj.3_Intron|HK1_uc001jpk.3_Intron|HK1_uc009xqd.2_Intron	NM_000188	NP_000179			hexokinase 1 isoform HKI						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72837370	72837370	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72837370delC								PCBD1 (188829 upstream) : UNC5B (134928 downstream)																																			---	---	---	---
SPOCK2	9806	broad.mit.edu	37	10	73849928	73849929	+	5'Flank	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73849928_73849929delTT	uc001jso.1	-						SPOCK2_uc001jsp.2_5'Flank|SPOCK2_uc010qjs.1_5'Flank|SPOCK2_uc010qjt.1_5'Flank	NM_014767	NP_055582			sparc/osteonectin, cwcv and kazal-like domains						extracellular matrix organization|regulation of cell differentiation|signal transduction|synapse assembly	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73940733	73940733	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73940733delT	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
FAM149B1	317662	broad.mit.edu	37	10	74948492	74948492	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74948492delA	uc009xqz.2	+						FAM149B1_uc010qkf.1_Intron|FAM149B1_uc001jtq.2_Intron	NM_173348	NP_775483			hypothetical protein LOC317662												0																		---	---	---	---
TTC18	118491	broad.mit.edu	37	10	75106402	75106402	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75106402delA	uc009xrc.2	-						TTC18_uc001jty.2_Intron|TTC18_uc009xrd.1_Intron	NM_145170	NP_660153			tetratricopeptide repeat domain 18								binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75550634	75550634	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75550634delT	uc009xrl.2	+						KIAA0913_uc001jve.2_Intron|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_5'Flank|KIAA0913_uc001jvi.2_5'Flank|KIAA0913_uc010qkr.1_5'Flank|KIAA0913_uc001jvj.2_5'Flank	NM_015037	NP_055852			hypothetical protein LOC23053								zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75560546	75560546	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75560546delC	uc009xrl.2	+						KIAA0913_uc001jve.2_Intron|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_Intron|KIAA0913_uc001jvi.2_Intron|KIAA0913_uc010qkr.1_Intron|KIAA0913_uc001jvj.2_Intron|KIAA0913_uc009xrn.1_3'UTR	NM_015037	NP_055852			hypothetical protein LOC23053								zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
VCL	7414	broad.mit.edu	37	10	75775450	75775450	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75775450delT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
VCL	7414	broad.mit.edu	37	10	75818648	75818649	+	Intron	INS	-	GT	GT	rs148608729	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75818648_75818649insGT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	77419120	77419120	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77419120delT								MIR606 (106809 upstream) : C10orf11 (123399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77474498	77474499	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77474498_77474499insT								MIR606 (162187 upstream) : C10orf11 (68020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	79418198	79418199	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79418198_79418199insA								KCNMA1 (20621 upstream) : DLG5 (132352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	79717808	79717809	+	IGR	DEL	TT	-	-	rs67780193		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79717808_79717809delTT								LOC100128292 (28226 upstream) : POLR3A (18097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	81358867	81358868	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81358867_81358868insA								SFTPA2 (38704 upstream) : SFTPA1 (11844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	81407284	81407284	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81407284delA								SFTPA1 (32083 upstream) : LOC650623 (35447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82095303	82095304	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82095303_82095304insT								MAT1A (45869 upstream) : DYDC1 (560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83041409	83041409	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83041409delA								SH2D4B (635093 upstream) : NRG3 (593661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85605586	85605587	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85605586_85605587insT								NRG3 (858651 upstream) : GHITM (293598 downstream)																																			---	---	---	---
C10orf99	387695	broad.mit.edu	37	10	85940301	85940301	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85940301delC	uc001kcu.2	+							NM_207373	NP_997256			hypothetical protein LOC387695 precursor							extracellular region				pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86871056	86871056	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86871056delT								FAM190B (592780 upstream) : GRID1 (488256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87167367	87167367	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87167367delT								FAM190B (889091 upstream) : GRID1 (191945 downstream)																																			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87372492	87372492	+	Intron	DEL	A	-	-	rs11296422		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87372492delA	uc001kdl.1	-						GRID1_uc009xsu.1_Intron|GRID1_uc010qmf.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	88178354	88178354	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88178354delG								GRID1 (52104 upstream) : WAPAL (16660 downstream)																																			---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88630538	88630538	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88630538delT	uc001kdy.2	+							NM_004329	NP_004320			bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8								Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88738540	88738540	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88738540delA	uc001kee.2	+							NM_133447	NP_597704			ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
GLUD1	2746	broad.mit.edu	37	10	88820205	88820205	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88820205delT	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262			glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
FAM35A	54537	broad.mit.edu	37	10	88946668	88946668	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88946668delA	uc001kei.3	+						FAM35A_uc001kej.3_Intron	NM_019054	NP_061927			hypothetical protein LOC54537											ovary(2)|skin(2)	4																		---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89671685	89671685	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89671685delT	uc001kfb.2	+							NM_000314	NP_000305			phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.Y27fs*1(2)|p.?(2)|p.V54fs*29(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89725294	89725294	+	3'UTR	DEL	T	-	-	rs1044487		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89725294delT	uc001kfb.2	+	10						NM_000314	NP_000305			phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	90378470	90378471	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90378470_90378471insT								LIPJ (11738 upstream) : LIPF (45623 downstream)																																			---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90682146	90682146	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90682146delA	uc001kfk.2	+	10	1630	c.1207delA	c.(1207-1209)AAAfs	p.K403fs	STAMBPL1_uc010qmx.1_Frame_Shift_Del_p.K403fs|STAMBPL1_uc009xto.2_RNA|STAMBPL1_uc001kfl.2_Frame_Shift_Del_p.K403fs|STAMBPL1_uc001kfn.2_Frame_Shift_Del_p.K237fs	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	403							metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91277238	91277238	+	Intron	DEL	T	-	-	rs75606778		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91277238delT	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
PANK1	53354	broad.mit.edu	37	10	91370222	91370222	+	Intron	DEL	A	-	-	rs10709875		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91370222delA	uc001kgp.1	-						PANK1_uc001kgn.1_Intron|PANK1_uc001kgo.1_Intron|PANK1_uc009xtu.1_Intron	NM_148977	NP_683878			pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	91575237	91575238	+	IGR	DEL	TT	-	-	rs75290984		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91575237_91575238delTT								KIF20B (40537 upstream) : HTR7 (925340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	92305349	92305349	+	IGR	DEL	A	-	-	rs75491416		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92305349delA								KIF20B (770649 upstream) : HTR7 (195229 downstream)																																			---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93601903	93601903	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93601903delT	uc001khp.2	+							NM_025235	NP_079511			tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741816	93741816	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741816delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
IDE	3416	broad.mit.edu	37	10	94267428	94267428	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94267428delA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
IDE	3416	broad.mit.edu	37	10	94281819	94281819	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94281819delA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	94485076	94485077	+	IGR	INS	-	TG	TG	rs10568596		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94485076_94485077insTG								HHEX (29670 upstream) : EXOC6 (105858 downstream)																																			---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95125918	95125919	+	Intron	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95125918_95125919delAC	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479			myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95963678	95963678	+	Intron	DEL	G	-	-	rs67443568		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95963678delG	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)																---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95987002	95987002	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95987002delA	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)																---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96112579	96112579	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96112579delA	uc001kjq.1	-						NOC3L_uc009xuk.1_Intron	NM_022451	NP_071896			nucleolar complex associated 3 homolog							nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)																---	---	---	---
TBC1D12	23232	broad.mit.edu	37	10	96275829	96275830	+	Intron	INS	-	C	C	rs139023120	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96275829_96275830insC	uc001kjr.2	+							NM_015188	NP_056003			TBC1 domain family, member 12							intracellular	Rab GTPase activator activity				0		Colorectal(252;0.0429)																---	---	---	---
CYP2C9	1559	broad.mit.edu	37	10	96731595	96731596	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96731595_96731596insA	uc001kka.3	+						CYP2C9_uc009xut.2_Intron	NM_000771	NP_000762			cytochrome P450, family 2, subfamily C,						exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(4)|ovary(2)	6		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	96932998	96932999	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96932998_96932999insT								CYP2C8 (103744 upstream) : C10orf129 (20958 downstream)																																			---	---	---	---
BLNK	29760	broad.mit.edu	37	10	97951973	97951973	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97951973delA	uc001kls.3	-						BLNK_uc001kme.3_Intron|BLNK_uc001klt.3_Intron|BLNK_uc009xvc.2_Intron|BLNK_uc001klu.3_Intron|BLNK_uc001klv.3_Intron|BLNK_uc001klw.3_Intron|BLNK_uc001klx.3_Intron|BLNK_uc001kly.3_Intron|BLNK_uc001klz.3_Intron|BLNK_uc001kma.3_Intron|BLNK_uc001kmb.3_Intron|BLNK_uc001kmc.3_Intron|BLNK_uc001kmd.3_Intron|BLNK_uc009xvd.2_Intron	NM_013314	NP_037446			B-cell linker isoform 1						B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(2)	2		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)														---	---	---	---
DNTT	1791	broad.mit.edu	37	10	98088796	98088797	+	Intron	INS	-	T	T	rs148988287	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98088796_98088797insT	uc001kmf.2	+						DNTT_uc001kmg.2_Intron	NM_004088	NP_004079			terminal deoxynucleotidyltransferase isoform 1						DNA modification	nucleus	DNA binding|DNA nucleotidylexotransferase activity|DNA-directed DNA polymerase activity|metal ion binding			ovary(1)	1		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)														---	---	---	---
TLL2	7093	broad.mit.edu	37	10	98274478	98274478	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98274478delT	uc001kml.1	-						TLL2_uc009xvf.1_5'Flank	NM_012465	NP_036597			tolloid-like 2 precursor						cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)														---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98312908	98312908	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98312908delA	uc001kmm.3	-						TM9SF3_uc010qot.1_Intron|TM9SF3_uc001kmn.1_5'Flank	NM_020123	NP_064508			transmembrane 9 superfamily member 3 precursor							integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)														---	---	---	---
PIK3AP1	118788	broad.mit.edu	37	10	98412330	98412330	+	Intron	DEL	A	-	-	rs79484028		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98412330delA	uc001kmq.2	-						PIK3AP1_uc001kmp.2_Intron	NM_152309	NP_689522			phosphoinositide-3-kinase adaptor protein 1							cytoplasm|plasma membrane				upper_aerodigestive_tract(3)|ovary(1)|skin(1)	5		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	98520138	98520138	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98520138delA								PIK3AP1 (39859 upstream) : MIR607 (68288 downstream)																																			---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98622964	98622967	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98622964_98622967delTTTT	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	NM_015652	NP_056467			hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98742363	98742363	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98742363delC	uc001kmv.2	+	1	1323	c.1216delC	c.(1216-1218)CCCfs	p.P406fs	C10orf12_uc009xvg.1_Frame_Shift_Del_p.P716fs	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	406										skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98819747	98819747	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98819747delG	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron	NM_003061	NP_003052			slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)														---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	99018291	99018291	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99018291delA	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99221731	99221731	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99221731delA	uc001kns.3	-						MMS19_uc001knq.2_5'Flank|MMS19_uc009xvs.2_Intron|MMS19_uc009xvt.2_Intron|MMS19_uc001knr.2_Intron|MMS19_uc010qox.1_Intron|MMS19_uc001knt.2_Intron|MMS19_uc001knu.1_Intron	NM_022362	NP_071757			MMS19 nucleotide excision repair homolog						chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)									Direct_reversal_of_damage|NER					---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99225437	99225437	+	Intron	DEL	T	-	-	rs79374790		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99225437delT	uc001kns.3	-						MMS19_uc009xvs.2_Intron|MMS19_uc009xvt.2_Intron|MMS19_uc001knr.2_Intron|MMS19_uc010qox.1_Intron|MMS19_uc001knt.2_Intron|MMS19_uc001knu.1_Intron	NM_022362	NP_071757			MMS19 nucleotide excision repair homolog						chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)									Direct_reversal_of_damage|NER					---	---	---	---
DNMBP	23268	broad.mit.edu	37	10	101643724	101643724	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101643724delT	uc001kqj.2	-						DNMBP_uc010qpl.1_Intron|DNMBP_uc001kqg.2_Intron|DNMBP_uc001kqh.2_Intron	NM_015221	NP_056036			dynamin binding protein						intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)														---	---	---	---
TLX1	3195	broad.mit.edu	37	10	102896746	102896747	+	3'UTR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102896746_102896747insC	uc001ksw.2	+	3						NM_005521	NP_005512			T-cell leukemia homeobox 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)				T	TRB@|TRD@	T-ALL								---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103766490	103766491	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103766490_103766491insT	uc009xwy.1	-							NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	103863819	103863819	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103863819delA								HPS6 (36027 upstream) : LDB1 (3508 downstream)																																			---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104140752	104140752	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104140752delA	uc001kux.1	+						GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
PSD	5662	broad.mit.edu	37	10	104176203	104176203	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104176203delC	uc001kvg.1	-	2	1120	c.593delG	c.(592-594)GGCfs	p.G198fs	PSD_uc001kvh.1_5'UTR|PSD_uc009xxd.1_Frame_Shift_Del_p.G198fs|PSD_uc001kvi.1_Frame_Shift_Del_p.G198fs|FBXL15_uc001kvj.1_5'Flank	NM_002779	NP_002770	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	198					regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|urinary_tract(1)	3				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)														---	---	---	---
ACTR1A	10121	broad.mit.edu	37	10	104258082	104258082	+	Intron	DEL	T	-	-	rs150610104		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104258082delT	uc001kvv.2	-						ACTR1A_uc010qqn.1_Intron|ACTR1A_uc010qqo.1_Intron	NM_005736	NP_005727			ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104334822	104334823	+	Intron	INS	-	C	C	rs10883740	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104334822_104334823insC	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron	NM_016169	NP_057253			suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)				D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				---	---	---	---
CYP17A1	1586	broad.mit.edu	37	10	104590294	104590295	+	3'UTR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104590294_104590295delAA	uc001kwg.2	-	8					C10orf26_uc009xxg.1_Intron	NM_000102	NP_000093			cytochrome P450, family 17						androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)													---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104620164	104620164	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104620164delT	uc001kwj.2	+						C10orf32_uc001kwh.2_Intron|C10orf32_uc001kwi.2_Intron	NM_020682	NP_065733			arsenic (+3 oxidation state) methyltransferase						arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104814053	104814054	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104814053_104814054insT	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)												OREG0020489	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105179557	105179557	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105179557delT	uc001kwy.1	+							NM_014976	NP_055791			programmed cell death 11						mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
CALHM2	51063	broad.mit.edu	37	10	105208932	105208932	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105208932delA	uc001kwz.2	-						CALHM2_uc001kxa.2_Intron|CALHM2_uc001kxc.2_Intron|CALHM2_uc001kxb.2_Intron|CALHM2_uc001kxd.1_3'UTR	NM_015916	NP_057000			calcium homeostasis modulator 2							integral to membrane				skin(1)	1																		---	---	---	---
SLK	9748	broad.mit.edu	37	10	105757343	105757343	+	Intron	DEL	T	-	-	rs112853283		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105757343delT	uc001kxo.1	+						SLK_uc001kxp.1_Intron	NM_014720	NP_055535			serine/threonine kinase 2						apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106578171	106578171	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106578171delT	uc001kyi.1	+							NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	107445676	107445676	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107445676delT								SORCS3 (420683 upstream) : SORCS1 (887746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107624668	107624669	+	IGR	INS	-	AGGA	AGGA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107624668_107624669insAGGA								SORCS3 (599675 upstream) : SORCS1 (708753 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108346170	108346171	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108346170_108346171delTT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108414613	108414614	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108414613_108414614delTT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	110518330	110518331	+	IGR	INS	-	GT	GT	rs139030687	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110518330_110518331insGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111724306	111724306	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111724306delA	uc001kyr.1	-											Homo sapiens mRNA; cDNA DKFZp686J1229 (from clone DKFZp686J1229).																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	111925099	111925099	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111925099delT								ADD3 (29779 upstream) : MXI1 (42264 downstream)																																			---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115376611	115376611	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115376611delT	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326			nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	115819306	115819306	+	IGR	DEL	A	-	-	rs71473023		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115819306delA								ADRB1 (12641 upstream) : C10orf118 (62668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	115868683	115868683	+	IGR	DEL	T	-	-	rs113693647		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115868683delT								ADRB1 (62018 upstream) : C10orf118 (13291 downstream)																																			---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116302348	116302349	+	Intron	INS	-	GAAGGAGGAA	GAAGGAGGAA	rs145911227	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116302348_116302349insGAAGGAGGAA	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc009xyo.2_Intron	NM_002313	NP_002304			actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116449505	116449506	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116449505_116449506insA	uc001lbz.1	-											Homo sapiens cDNA FLJ25105 fis, clone CBR01442.						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
FAM160B1	57700	broad.mit.edu	37	10	116603484	116603484	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116603484delT	uc001lcb.2	+						FAM160B1_uc001lcc.2_Intron	NM_020940	NP_065991			hypothetical protein LOC57700 isoform a											lung(1)	1																		---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117078033	117078033	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117078033delT	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186			attractin-like 1 precursor							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)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117378023	117378023	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117378023delT	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186			attractin-like 1 precursor							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)														---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118451344	118451344	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118451344delC	uc001lct.2	-						HSPA12A_uc001lcu.2_Intron	NM_025015	NP_079291			heat shock 70kDa protein 12A								ATP binding			ovary(1)	1				all cancers(201;0.0158)														---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118465255	118465255	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118465255delT	uc001lct.2	-						HSPA12A_uc001lcu.2_Intron	NM_025015	NP_079291			heat shock 70kDa protein 12A								ATP binding			ovary(1)	1				all cancers(201;0.0158)														---	---	---	---
CASC2	255082	broad.mit.edu	37	10	119891522	119891522	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119891522delA	uc001ldm.3	+						CASC2_uc009xzc.2_Intron	NR_026939				Homo sapiens mRNA for IGM1 protein.												0																		---	---	---	---
EIF3A	8661	broad.mit.edu	37	10	120803411	120803411	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120803411delA	uc001ldu.2	-						EIF3A_uc010qsu.1_Intron|EIF3A_uc009xzg.1_Intron	NM_003750	NP_003741			eukaryotic translation initiation factor 3,						formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121017445	121017445	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121017445delT	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299			G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)														---	---	---	---
TIAL1	7073	broad.mit.edu	37	10	121335341	121335341	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121335341delA	uc001lei.1	-						TIAL1_uc001leh.1_Intron|TIAL1_uc001lej.1_Intron|TIAL1_uc001lek.1_Intron|TIAL1_uc009xzi.1_Intron	NM_003252	NP_003243			TIA-1 related protein isoform 1						apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	122861334	122861334	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122861334delA								WDR11 (192299 upstream) : FGFR2 (376511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123190809	123190809	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123190809delT								WDR11 (521774 upstream) : FGFR2 (47036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123465034	123465034	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123465034delG								FGFR2 (107062 upstream) : ATE1 (37592 downstream)																																			---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124379705	124379705	+	Intron	DEL	T	-	-	rs72298879		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124379705delT	uc001lgk.1	+						DMBT1_uc001lgl.1_Intron|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Intron|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yab.1_Intron|DMBT1_uc009yac.1_5'Flank	NM_007329	NP_015568			deleted in malignant brain tumors 1 isoform b						epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	124574892	124574895	+	IGR	DEL	TCCT	-	-	rs113811365		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124574892_124574895delTCCT								FLJ46361 (17731 upstream) : CUZD1 (16780 downstream)																																			---	---	---	---
BUB3	9184	broad.mit.edu	37	10	124917510	124917510	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124917510delA	uc001lhe.2	+						BUB3_uc009yah.2_Intron|BUB3_uc001lhf.3_Intron|BUB3_uc001lhd.2_Intron|BUB3_uc010qud.1_Intron	NM_004725	NP_004716			budding uninhibited by benzimidazoles 3 isoform						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|attachment of spindle microtubules to kinetochore|cell division|meiosis|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	condensed chromosome kinetochore|cytosol|nucleus	protein binding			ovary(1)	1		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)																---	---	---	---
BUB3	9184	broad.mit.edu	37	10	124920172	124920172	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124920172delT	uc001lhe.2	+						BUB3_uc009yah.2_Intron|BUB3_uc001lhf.3_Intron|BUB3_uc001lhd.2_Intron|BUB3_uc010qud.1_Intron	NM_004725	NP_004716			budding uninhibited by benzimidazoles 3 isoform						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|attachment of spindle microtubules to kinetochore|cell division|meiosis|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	condensed chromosome kinetochore|cytosol|nucleus	protein binding			ovary(1)	1		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)																---	---	---	---
GPR26	2849	broad.mit.edu	37	10	125433437	125433438	+	Intron	INS	-	TCT	TCT	rs145117660	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125433437_125433438insTCT	uc001lhh.2	+							NM_153442	NP_703143			G protein-coupled receptor 26						activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	125931662	125931663	+	IGR	INS	-	C	C	rs146599338	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125931662_125931663insC								CHST15 (78456 upstream) : OAT (154209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	126038712	126038712	+	IGR	DEL	T	-	-	rs111455013		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126038712delT								CHST15 (185506 upstream) : OAT (47160 downstream)																																			---	---	---	---
OAT	4942	broad.mit.edu	37	10	126086392	126086392	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126086392delA	uc001lhp.2	-	10					OAT_uc001lhq.2_RNA|OAT_uc001lhr.2_3'UTR	NM_000274	NP_000265			ornithine aminotransferase precursor						cellular amino acid biosynthetic process|visual perception	mitochondrial matrix	ornithine-oxo-acid transaminase activity|protein binding|pyridoxal phosphate binding				0		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)|Pyridoxal Phosphate(DB00114)													---	---	---	---
OAT	4942	broad.mit.edu	37	10	126091634	126091634	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126091634delA	uc001lhp.2	-						OAT_uc001lhq.2_Intron|OAT_uc001lhr.2_Intron	NM_000274	NP_000265			ornithine aminotransferase precursor						cellular amino acid biosynthetic process|visual perception	mitochondrial matrix	ornithine-oxo-acid transaminase activity|protein binding|pyridoxal phosphate binding				0		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	126599282	126599283	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126599282_126599283delTT								FAM175B (74044 upstream) : ZRANB1 (29689 downstream)																																			---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126720624	126720624	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126720624delA	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320			C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	128072645	128072645	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128072645delA	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465			ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)														---	---	---	---
C10orf90	118611	broad.mit.edu	37	10	128200842	128200845	+	Intron	DEL	AGAA	-	-	rs144322459		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128200842_128200845delAGAA	uc001ljq.2	-						C10orf90_uc010qum.1_Intron|C10orf90_uc009yao.2_Intron|C10orf90_uc001ljs.1_Intron	NM_001004298	NP_001004298			hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	130997645	130997645	+	IGR	DEL	T	-	-	rs115137736	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130997645delT								None (None upstream) : MGMT (267809 downstream)																																			---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131333661	131333661	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131333661delA	uc001lkh.2	+							NM_002412	NP_002403			O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	10	131896017	131896018	+	Intron	INS	-	T	T	rs142306547	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131896017_131896018insT	uc010qus.1	-											Homo sapiens cDNA FLJ36799 fis, clone ADRGL2007357.																														---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133961636	133961637	+	Intron	INS	-	TGAACA	TGAACA	rs141683861	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133961636_133961637insTGAACA	uc001lkx.3	+						JAKMIP3_uc009yba.1_Intron	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	379842	379842	+	Intron	DEL	C	-	-	rs72431160		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:379842delC	uc001lpb.2	+							NM_178537	NP_848632			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
CEND1	51286	broad.mit.edu	37	11	788246	788247	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:788246_788247insC	uc001lrh.1	-	2	509_510	c.330_331insG	c.(328-333)GGGCCTfs	p.G110fs		NM_016564	NP_057648	Q8N111	CEND_HUMAN	cell cycle exit and neuronal differentiation 1	110_111	Cytoplasmic (Potential).					integral to membrane					0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	1400421	1400421	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1400421delT								TOLLIP (69582 upstream) : BRSK2 (10708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1668636	1668637	+	IGR	INS	-	TTTC	TTTC	rs137887865	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1668636_1668637insTTTC								KRTAP5-5 (16479 upstream) : FAM99A (18192 downstream)																																			---	---	---	---
CTSD	1509	broad.mit.edu	37	11	1780829	1780830	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1780829_1780830insG	uc001luc.1	-	3	401_402	c.268_269insC	c.(268-270)CAGfs	p.Q90fs	CTSD_uc009yda.1_RNA	NM_001909	NP_001900	P07339	CATD_HUMAN	cathepsin D preproprotein	90					cell death|proteolysis	extracellular space|lysosome|melanosome	aspartic-type endopeptidase activity				0		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	2243323	2243323	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2243323delA								TH (50288 upstream) : ASCL2 (46406 downstream)																																			---	---	---	---
MRGPRE	116534	broad.mit.edu	37	11	3252847	3252847	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3252847delG	uc001lxq.3	-							NM_001039165	NP_001034254			MAS-related GPR, member E							integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(1)|ovary(1)	2		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	3686385	3686385	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3686385delT								ART1 (739 upstream) : CHRNA10 (433 downstream)																																			---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3727549	3727549	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3727549delT	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyg.2_Intron	NM_016320	NP_057404			nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	11	4253243	4253244	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4253243_4253244insA								RRM1 (29484 upstream) : OR52B4 (135339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	5043076	5043076	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5043076delA								OR51L1 (21918 upstream) : OR52J3 (24680 downstream)																																			---	---	---	---
HBE1	3046	broad.mit.edu	37	11	5345593	5345594	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5345593_5345594insT	uc001mam.1	-						HBG2_uc001mak.1_Intron|OR51B2_uc001mao.1_5'Flank	NM_005330	NP_005321			epsilon globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)												OREG0003719	type=REGULATORY REGION|Gene=OR51B2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
Unknown	0	broad.mit.edu	37	11	6810886	6810889	+	IGR	DEL	AAAC	-	-	rs112998792		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6810886_6810889delAAAC								OR2AG1 (3667 upstream) : OR6A2 (4867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	7130174	7130175	+	IGR	INS	-	TG	TG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7130174_7130175insTG								RBMXL2 (17795 upstream) : MIR302E (125822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	7916073	7916074	+	Intron	INS	-	ACAC	ACAC	rs11041646	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7916073_7916074insACAC	uc001mfs.1	-											Homo sapiens cDNA FLJ34536 fis, clone HLUNG2008384.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7970081	7970081	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7970081delT								OR10A3 (9014 upstream) : NLRP10 (11075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	8306087	8306090	+	IGR	DEL	TGTA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8306087_8306090delTGTA								LMO1 (15905 upstream) : STK33 (107328 downstream)																																			---	---	---	---
TRIM66	9866	broad.mit.edu	37	11	8635431	8635431	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8635431delA	uc010rbo.1	-	20						NM_014818	NP_055633			tripartite motif-containing 66							aggresome|nucleus	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	9386986	9386986	+	IGR	DEL	A	-	-	rs111642575		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9386986delA								TMEM41B (50690 upstream) : IPO7 (19183 downstream)																																			---	---	---	---
IPO7	10527	broad.mit.edu	37	11	9429768	9429769	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9429768_9429769delAA	uc001mho.2	+							NM_006391	NP_006382			importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)														---	---	---	---
IPO7	10527	broad.mit.edu	37	11	9461281	9461282	+	Intron	INS	-	CGG	CGG	rs150798037	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9461281_9461282insCGG	uc001mho.2	+							NM_006391	NP_006382			importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	9652524	9652524	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9652524delA								WEE1 (41213 upstream) : SWAP70 (33104 downstream)																																			---	---	---	---
SBF2	81846	broad.mit.edu	37	11	9820945	9820945	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9820945delC	uc001mib.2	-						uc001mhz.1_Intron|SBF2_uc001mid.2_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	9930866	9930866	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9930866delT	uc001mib.2	-						SBF2_uc001mif.3_Intron|uc001mig.2_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10002137	10002138	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10002137_10002138delTT	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
AMPD3	272	broad.mit.edu	37	11	10527053	10527053	+	Intron	DEL	C	-	-	rs5789638		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10527053delC	uc001mio.1	+						AMPD3_uc010rbz.1_Intron|AMPD3_uc001min.1_Intron|AMPD3_uc009yfw.1_Intron|AMPD3_uc009yfz.2_Intron|AMPD3_uc001mip.1_Intron|AMPD3_uc009yfy.2_Intron	NM_001025389	NP_001020560			adenosine monophosphate deaminase 3 isoform 1B						AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)														---	---	---	---
CTR9	9646	broad.mit.edu	37	11	10778838	10778838	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10778838delA	uc001mja.2	+							NM_014633	NP_055448			SH2 domain binding protein 1						histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	10935387	10935404	+	IGR	DEL	TGTGTGTGTGTGTGTGTG	-	-	rs10566658		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10935387_10935404delTGTGTGTGTGTGTGTGTG								ZBED5 (55767 upstream) : GALNTL4 (357017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11158570	11158570	+	IGR	DEL	A	-	-	rs10574607		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11158570delA								ZBED5 (278950 upstream) : GALNTL4 (133851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11668063	11668076	+	IGR	DEL	ACACACACACACAC	-	-	rs149498297		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11668063_11668076delACACACACACACAC								GALNTL4 (24502 upstream) : USP47 (194894 downstream)																																			---	---	---	---
USP47	55031	broad.mit.edu	37	11	11919865	11919865	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11919865delT	uc001mjq.1	+						USP47_uc001mjr.2_Intron|USP47_uc001mjs.2_Intron	NM_017944	NP_060414			ubiquitin specific protease 47						base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11958114	11958115	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11958114_11958115delTT	uc001mjq.1	+						USP47_uc001mjr.2_Intron|USP47_uc001mjs.2_Intron|USP47_uc001mjt.1_5'Flank	NM_017944	NP_060414			ubiquitin specific protease 47						base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	12672601	12672601	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12672601delA								PARVA (121191 upstream) : TEAD1 (23368 downstream)																																			---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12899207	12899207	+	Intron	DEL	A	-	-	rs112123980		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12899207delA	uc001mkj.3	+						TEAD1_uc001mkk.3_5'Flank|TEAD1_uc009ygl.2_5'Flank	NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	13548250	13548250	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13548250delT								PTH (30683 upstream) : FAR1 (141956 downstream)																																			---	---	---	---
FAR1	84188	broad.mit.edu	37	11	13749086	13749086	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13749086delT	uc001mld.2	+							NM_032228	NP_115604			fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
COPB1	1315	broad.mit.edu	37	11	14498309	14498314	+	Intron	DEL	TTTTTT	-	-	rs11337817		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14498309_14498314delTTTTTT	uc001mli.2	-						COPB1_uc001mlg.2_Intron|COPB1_uc001mlh.2_Intron	NM_016451	NP_057535			coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PSMA1	5682	broad.mit.edu	37	11	14533292	14533292	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14533292delA	uc001mlk.2	-						PSMA1_uc001mll.2_Intron|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Intron	NM_002786	NP_002777			proteasome alpha 1 subunit isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15352668	15352668	+	IGR	DEL	G	-	-	rs66487957		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15352668delG								INSC (83916 upstream) : SOX6 (635328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15524356	15524361	+	IGR	DEL	GCGCGC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15524356_15524361delGCGCGC								INSC (255604 upstream) : SOX6 (463635 downstream)																																			---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16197617	16197620	+	Intron	DEL	GGAT	-	-	rs71826187		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16197617_16197620delGGAT	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																		---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18312907	18312907	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18312907delT	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608			Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21091674	21091675	+	Intron	DEL	TT	-	-	rs71871525		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21091674_21091675delTT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	21971474	21971474	+	IGR	DEL	G	-	-	rs35977528		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21971474delG								NELL1 (374247 upstream) : ANO5 (243248 downstream)																																			---	---	---	---
GAS2	2620	broad.mit.edu	37	11	22702254	22702254	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22702254delT	uc009yie.2	+						GAS2_uc001mqm.2_Intron|GAS2_uc001mqn.2_Intron|GAS2_uc001mqo.2_Intron	NM_001143830	NP_001137302			growth arrest-specific 2						cell cycle arrest|cellular component disassembly involved in apoptosis|regulation of cell shape	actin filament|cytosol|membrane				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	23130206	23130207	+	IGR	INS	-	AC	AC	rs3050460		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23130206_23130207insAC								SVIP (278824 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23824631	23824632	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23824631_23824632delGT								SVIP (973249 upstream) : LUZP2 (693924 downstream)																																			---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	25098153	25098160	+	Intron	DEL	GAAGGAAT	-	-	rs112420548	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25098153_25098160delGAAGGAAT	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909			leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	26930178	26930180	+	IGR	DEL	AAA	-	-	rs78262253		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26930178_26930180delAAA								SLC5A12 (185204 upstream) : FIBIN (85448 downstream)																																			---	---	---	---
BDNF	627	broad.mit.edu	37	11	27699083	27699083	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27699083delA	uc009yje.2	-						BDNFOS_uc001mrm.2_RNA|BDNFOS_uc009yij.2_RNA|BDNFOS_uc009yik.2_RNA|BDNFOS_uc009yil.2_RNA|BDNFOS_uc001mrp.2_RNA|BDNFOS_uc009yim.2_RNA|BDNFOS_uc009yin.2_RNA|BDNFOS_uc009yio.2_RNA|BDNFOS_uc009yip.2_RNA|BDNFOS_uc001mrn.2_RNA|BDNFOS_uc009yiq.2_RNA|BDNFOS_uc001mro.2_RNA|BDNFOS_uc009yir.2_Intron|BDNFOS_uc009yis.2_Intron|BDNFOS_uc009yit.2_Intron|BDNFOS_uc009yiu.2_Intron|BDNFOS_uc009yiv.2_Intron|BDNFOS_uc009yiw.2_Intron|BDNFOS_uc009yix.2_Intron|BDNFOS_uc009yiy.2_Intron|BDNFOS_uc009yiz.2_Intron|BDNFOS_uc001mrq.3_Intron|BDNFOS_uc001mrr.3_Intron|BDNFOS_uc009yja.2_Intron|BDNFOS_uc009yjb.2_Intron|BDNF_uc010rdv.1_Intron|BDNF_uc001mrt.2_Intron|BDNF_uc010rdw.1_Intron|BDNF_uc009yjd.2_Intron|BDNF_uc001mru.2_Intron|BDNF_uc010rdx.1_Intron|BDNF_uc010rdy.1_Intron|BDNF_uc009yjg.2_Intron|BDNF_uc009yjf.2_Intron|BDNF_uc001mrv.2_Intron|BDNF_uc001mrw.3_Intron|BDNF_uc001mrx.2_Intron|BDNF_uc001mry.3_Intron|BDNF_uc001mrz.3_Intron|BDNF_uc001msa.2_Intron	NM_001143810	NP_001137282			brain-derived neurotrophic factor isoform e							extracellular region	growth factor activity				0																		---	---	---	---
MPPED2	744	broad.mit.edu	37	11	30439019	30439019	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30439019delA	uc001msr.2	-						MPPED2_uc001msq.3_Intron|MPPED2_uc009yji.2_Intron	NM_001584	NP_001575			metallophosphoesterase domain containing 2						nervous system development		hydrolase activity|metal ion binding			skin(1)	1																		---	---	---	---
DNAJC24	120526	broad.mit.edu	37	11	31447959	31447959	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31447959delA	uc001msx.2	+						DNAJC24_uc009yjm.2_Intron	NM_181706	NP_859057			zinc finger, CSL domain containing 3						protein folding		heat shock protein binding|metal ion binding|unfolded protein binding			breast(2)	2																		---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31898086	31898087	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31898086_31898087delTG	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32354659	32354659	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32354659delT								RCN1 (227388 upstream) : WT1 (54666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	32391892	32391899	+	IGR	DEL	GAAAGAAA	-	-	rs71967746	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32391892_32391899delGAAAGAAA								RCN1 (264621 upstream) : WT1 (17426 downstream)																																			---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32635951	32635951	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32635951delT	uc001mtv.2	-	16	1957	c.1913delA	c.(1912-1914)AATfs	p.N638fs		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	638										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
PRRG4	79056	broad.mit.edu	37	11	32875385	32875385	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32875385delA	uc001mtx.2	+	6						NM_024081	NP_076986			proline rich Gla (G-carboxyglutamic acid) 4							extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	33210726	33210728	+	Intron	DEL	TTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33210726_33210728delTTG	uc001muk.2	+											Homo sapiens hypothetical protein LOC338739, mRNA (cDNA clone IMAGE:5172825), partial cds.																														---	---	---	---
EHF	26298	broad.mit.edu	37	11	34664615	34664616	+	Intron	INS	-	TG	TG	rs74543059		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34664615_34664616insTG	uc001mvr.1	+						EHF_uc009yke.1_Intron|EHF_uc009ykf.1_Intron	NM_012153	NP_036285			ets homologous factor						cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)															---	---	---	---
EHF	26298	broad.mit.edu	37	11	34678486	34678486	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34678486delC	uc001mvr.1	+	7	687	c.576delC	c.(574-576)GACfs	p.D192fs	EHF_uc009yke.1_Frame_Shift_Del_p.D169fs|EHF_uc009ykf.1_Frame_Shift_Del_p.D195fs	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	ets homologous factor	192					cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)															---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35465742	35465742	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35465742delT	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	35672159	35672159	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35672159delA								FJX1 (29740 upstream) : TRIM44 (12194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38310620	38310620	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38310620delT								None (None upstream) : None (None downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40135879	40135879	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40135879delT	uc001mxa.1	-	2					LRRC4C_uc001mxc.1_3'UTR|LRRC4C_uc001mxd.1_3'UTR|LRRC4C_uc001mxb.1_3'UTR	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	41676595	41676596	+	IGR	DEL	TC	-	-	rs142061392		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41676595_41676596delTC								LRRC4C (195272 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42382868	42382870	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42382868_42382870delTTT								LRRC4C (901545 upstream) : API5 (950635 downstream)																																			---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43393861	43393861	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43393861delT	uc001mxi.2	+						TTC17_uc001mxh.2_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43401008	43401009	+	Intron	INS	-	TG	TG	rs150337177	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43401008_43401009insTG	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43471884	43471884	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43471884delA	uc001mxi.2	+						TTC17_uc010rfj.1_Intron|TTC17_uc001mxl.2_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	44278843	44278844	+	IGR	INS	-	AC	AC	rs139620149	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44278843_44278844insAC								EXT2 (11864 upstream) : ALX4 (7315 downstream)																																			---	---	---	---
KIAA0652	9776	broad.mit.edu	37	11	46666873	46666873	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666873delT	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145			autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)														---	---	---	---
LRP4	4038	broad.mit.edu	37	11	46920561	46920561	+	Frame_Shift_Del	DEL	G	-	-	rs147353838	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46920561delG	uc001ndn.3	-	6	716	c.570delC	c.(568-570)CCCfs	p.P190fs	LRP4_uc009ylh.1_Frame_Shift_Del_p.P141fs	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	190	Extracellular (Potential).|LDL-receptor class A 5.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)														---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	46971728	46971728	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46971728delT	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018			hypothetical protein LOC79096 isoform 3												0																		---	---	---	---
ARFGAP2	84364	broad.mit.edu	37	11	47189507	47189509	+	In_Frame_Del	DEL	CTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47189507_47189509delCTC	uc001ndt.2	-	12	1171_1173	c.1156_1158delGAG	c.(1156-1158)GAGdel	p.E386del	ARFGAP2_uc010rha.1_In_Frame_Del_p.E117del|ARFGAP2_uc010rhb.1_In_Frame_Del_p.E358del|ARFGAP2_uc001ndu.2_In_Frame_Del_p.E250del|ARFGAP2_uc010rhc.1_In_Frame_Del_p.E117del	NM_032389	NP_115765	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating	386	Required for interaction with coatomer.				protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	47221804	47221804	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47221804delA								PACSIN3 (13846 upstream) : DDB2 (14689 downstream)																																			---	---	---	---
MTCH2	23788	broad.mit.edu	37	11	47657242	47657242	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47657242delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157			mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
FNBP4	23360	broad.mit.edu	37	11	47772241	47772241	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47772241delA	uc009ylv.2	-						FNBP4_uc001ngj.2_Intron|FNBP4_uc001ngl.2_Intron	NM_015308	NP_056123			formin binding protein 4											ovary(1)	1																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48079933	48079933	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48079933delT	uc001ngp.3	+						PTPRJ_uc001ngo.3_Intron	NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48849535	48849536	+	IGR	INS	-	CA	CA	rs147911541		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48849535_48849536insCA								OR4A47 (338263 upstream) : FOLH1 (318652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50725172	50725172	+	IGR	DEL	G	-	-	rs148715787		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50725172delG								LOC646813 (345369 upstream) : OR4A5 (686276 downstream)																																			---	---	---	---
OR5J2	282775	broad.mit.edu	37	11	55944055	55944055	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944055delT	uc010rjb.1	+							NM_001005492	NP_001005492			olfactory receptor, family 5, subfamily J,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)																	---	---	---	---
OR9Q1	219956	broad.mit.edu	37	11	57802311	57802312	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57802311_57802312delTT	uc001nmj.2	+							NM_001005212	NP_001005212			olfactory receptor, family 9, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)																---	---	---	---
STX3	6809	broad.mit.edu	37	11	59552803	59552803	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59552803delT	uc001nog.2	+						STX3_uc010rkx.1_Intron|STX3_uc010rky.1_Intron|STX3_uc009ymt.1_5'Flank	NM_004177	NP_004168			syntaxin 3						cellular response to oxidative stress|intracellular protein transport|neuron projection development|neurotransmitter transport	apical plasma membrane|azurophil granule|cell-cell junction|growth cone|integral to membrane|plasma membrane enriched fraction|SNARE complex|specific granule	arachidonic acid binding|SNAP receptor activity			ovary(2)	2																		---	---	---	---
MRPL16	54948	broad.mit.edu	37	11	59574982	59574983	+	Intron	DEL	AA	-	-	rs113228199		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59574982_59574983delAA	uc001noh.2	-							NM_017840	NP_060310			mitochondrial ribosomal protein L16 precursor								rRNA binding			central_nervous_system(1)	1																		---	---	---	---
MS4A3	932	broad.mit.edu	37	11	59834686	59834686	+	Intron	DEL	T	-	-	rs146138976		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59834686delT	uc001nom.2	+						MS4A3_uc001non.2_Intron|MS4A3_uc001noo.2_Intron	NM_006138	NP_006129			membrane-spanning 4-domains, subfamily A, member							endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)|skin(1)	3		all_epithelial(135;0.245)																---	---	---	---
C11orf64	283197	broad.mit.edu	37	11	60451865	60451866	+	Intron	DEL	TT	-	-	rs75606841	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60451865_60451866delTT	uc001npt.2	+						C11orf64_uc001npu.2_Intron	NR_026946				Homo sapiens cDNA FLJ25394 fis, clone TST02552.												0																		---	---	---	---
PRPF19	27339	broad.mit.edu	37	11	60666410	60666410	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60666410delA	uc001nqf.2	-							NM_014502	NP_055317			PRP19/PSO4 pre-mRNA processing factor 19						DNA repair|protein polyubiquitination|spliceosome assembly	catalytic step 2 spliceosome|nuclear speck|spindle|ubiquitin ligase complex	DNA binding|identical protein binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1																OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	11	60835852	60835853	+	IGR	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60835852_60835853delTC								CD6 (48006 upstream) : CD5 (34077 downstream)																																			---	---	---	---
CPSF7	79869	broad.mit.edu	37	11	61183087	61183087	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61183087delA	uc001nrq.2	-						CPSF7_uc001nro.2_Intron|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron	NM_001136040	NP_001129512			pre-mRNA cleavage factor I, 59 kDa subunit						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	61742992	61742992	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61742992delT								FTH1 (7860 upstream) : INCENP (148453 downstream)																																			---	---	---	---
INCENP	3619	broad.mit.edu	37	11	61917392	61917392	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61917392delA	uc001nsw.1	+						INCENP_uc001nsx.1_Intron|INCENP_uc001nsy.1_Intron	NM_001040694	NP_001035784			inner centromere protein antigens 135/155kDa						chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1																		---	---	---	---
NXF1	10482	broad.mit.edu	37	11	62561638	62561639	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62561638_62561639delAA	uc001nvf.1	-						TMEM223_uc001nve.2_5'Flank|NXF1_uc001nvg.1_Intron	NM_006362	NP_006353			nuclear RNA export factor 1 isoform 1						gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3																		---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62637846	62637847	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62637846_62637847insT	uc001nwd.2	+						SLC3A2_uc001nwb.2_Intron|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron	NM_002394	NP_002385			solute carrier family 3, member 2 isoform c						blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0																		---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63465605	63465606	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63465605_63465606delTT	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831			reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
OTUB1	55611	broad.mit.edu	37	11	63765136	63765136	+	3'UTR	DEL	C	-	-	rs35556442		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63765136delC	uc001nyf.1	+	7					OTUB1_uc001nyg.1_3'UTR|OTUB1_uc010rmz.1_3'UTR|OTUB1_uc010rna.1_3'UTR|OTUB1_uc009ypa.2_3'UTR|OTUB1_uc009ypb.1_3'UTR	NM_017670	NP_060140			otubain 1						protein K48-linked deubiquitination	cytoplasm	NEDD8-specific protease activity|omega peptidase activity|ubiquitin binding|ubiquitin-specific protease activity			breast(1)	1																		---	---	---	---
RASGRP2	10235	broad.mit.edu	37	11	64507638	64507638	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64507638delG	uc009ypu.2	-						RASGRP2_uc001oat.2_Frame_Shift_Del_p.P25fs|RASGRP2_uc001oau.2_Intron|RASGRP2_uc009ypv.2_Intron|RASGRP2_uc009ypw.2_Intron	NM_001098671	NP_001092141			RAS guanyl releasing protein 2						platelet activation|Ras protein signal transduction|regulation of cell growth|regulation of small GTPase mediated signal transduction	cell junction|cytosol|ruffle membrane|synapse|synaptosome	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity				0																		---	---	---	---
C11orf85	283129	broad.mit.edu	37	11	64711340	64711340	+	Intron	DEL	C	-	-	rs117873321	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64711340delC	uc001ocb.1	-						C11orf85_uc001occ.1_Intron|C11orf85_uc001ocd.1_Intron	NM_001037225	NP_001032302			hypothetical protein LOC283129												0																		---	---	---	---
CAPN1	823	broad.mit.edu	37	11	64954882	64954882	+	Intron	DEL	C	-	-	rs3832790		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64954882delC	uc009yqd.1	+						CAPN1_uc001odf.1_Intron|CAPN1_uc001odg.1_Intron|CAPN1_uc010roa.1_Intron	NM_005186	NP_005177			calpain 1, large subunit						positive regulation of cell proliferation|proteolysis	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)														---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65272639	65272639	+	RNA	DEL	T	-	-	rs71868390		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65272639delT	uc010roh.1	+	1		c.7407delT			uc001ody.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
LTBP3	4054	broad.mit.edu	37	11	65308845	65308845	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65308845delC	uc001oej.2	-						LTBP3_uc001oef.2_Intron|LTBP3_uc001oeg.2_Intron|LTBP3_uc001oeh.2_Intron|LTBP3_uc010roi.1_Intron|LTBP3_uc001oei.2_Intron|LTBP3_uc010roj.1_Intron|LTBP3_uc010rok.1_Intron	NM_001130144	NP_001123616			latent transforming growth factor beta binding							extracellular region	calcium ion binding|growth factor binding			central_nervous_system(2)|lung(1)	3																OREG0021080	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	11	65463840	65463840	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65463840delA								RELA (33397 upstream) : KAT5 (15649 downstream)																																			---	---	---	---
PACS1	55690	broad.mit.edu	37	11	65857743	65857747	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65857743_65857747delTTTTT	uc001oha.1	+						PACS1_uc001ogz.1_Intron	NM_018026	NP_060496			phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6																		---	---	---	---
SLC29A2	3177	broad.mit.edu	37	11	66136770	66136770	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66136770delG	uc001oht.2	-						SLC29A2_uc001ohs.2_Intron|SLC29A2_uc010rpb.1_Intron|SLC29A2_uc009yrf.2_Intron|SLC29A2_uc001ohu.2_Intron|SLC29A2_uc001ohv.2_Intron|uc001ohw.1_RNA	NM_001532	NP_001523			solute carrier family 29 (nucleoside						cell proliferation|nucleobase, nucleoside and nucleotide metabolic process	basolateral plasma membrane|integral to plasma membrane|nuclear membrane|nucleolus	nucleoside transmembrane transporter activity			ovary(1)	1																		---	---	---	---
PC	5091	broad.mit.edu	37	11	66663553	66663554	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66663553_66663554insT	uc001ojn.1	-						PC_uc001ojo.1_Intron|PC_uc001ojp.1_Intron	NM_022172	NP_071504			pyruvate carboxylase precursor						gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)													---	---	---	---
PPP1CA	5499	broad.mit.edu	37	11	67165933	67165933	+	3'UTR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67165933delC	uc001okw.1	-	7					PPP1CA_uc009yro.1_3'UTR|PPP1CA_uc001okt.1_3'UTR|PPP1CA_uc001oku.1_3'UTR|PPP1CA_uc001okv.1_3'UTR|PPP1CA_uc001okx.1_3'UTR|PPP1CA_uc001oky.2_3'UTR	NM_002708	NP_002699			protein phosphatase 1, catalytic subunit, alpha						cell cycle|cell division|glycogen metabolic process|protein dephosphorylation|triglyceride catabolic process	cytosol|MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein phosphatase type 1 regulator activity|protein serine/threonine phosphatase activity			breast(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)															---	---	---	---
TPCN2	219931	broad.mit.edu	37	11	68844705	68844737	+	Intron	DEL	CCTGCCCTCCTGCCACGTCCCTCCACCTGCCCT	-	-	rs67482528	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68844705_68844737delCCTGCCCTCCTGCCACGTCCCTCCACCTGCCCT	uc001oos.2	+						TPCN2_uc009ysk.1_Intron|TPCN2_uc001oor.2_Intron|TPCN2_uc010rqg.1_Intron|TPCN2_uc001oot.2_Intron	NM_139075	NP_620714			two pore segment channel 2						cellular calcium ion homeostasis|smooth muscle contraction	endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated calcium channel activity				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	72256896	72256896	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72256896delT								CLPB (111212 upstream) : PDE2A (30290 downstream)																																			---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72421218	72421218	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72421218delG	uc001osu.2	-						ARAP1_uc001osv.2_Intron|ARAP1_uc001osr.2_Intron|ARAP1_uc001oss.2_Intron|ARAP1_uc009yth.2_Intron|ARAP1_uc010rre.1_Intron	NM_001040118	NP_001035207			ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
P4HA3	283208	broad.mit.edu	37	11	74000181	74000182	+	Intron	DEL	AA	-	-	rs35776286		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74000181_74000182delAA	uc001ouz.2	-						P4HA3_uc001ouy.3_Intron|P4HA3_uc010rrj.1_Intron	NM_182904	NP_878907			prolyl 4-hydroxylase, alpha III subunit							endoplasmic reticulum lumen	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			skin(1)	1	Breast(11;2.31e-05)																	---	---	---	---
PGM2L1	283209	broad.mit.edu	37	11	74053486	74053486	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74053486delA	uc001ovb.1	-							NM_173582	NP_775853			phosphoglucomutase 2-like 1						glucose 1-phosphate metabolic process	cytosol	glucose-1,6-bisphosphate synthase activity|phosphoglucomutase activity			ovary(1)	1	Breast(11;3.32e-06)																	---	---	---	---
POLD3	10714	broad.mit.edu	37	11	74310715	74310715	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74310715delT	uc001ovf.1	+						POLD3_uc009yua.1_Intron	NM_006591	NP_006582			DNA-directed DNA polymerase delta 3						base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|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	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding			kidney(2)|ovary(1)	3	Breast(11;3.21e-06)																	---	---	---	---
SPCS2	9789	broad.mit.edu	37	11	74683118	74683118	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74683118delT	uc001ovu.2	+							NM_014752	NP_055567			signal peptidase complex subunit 2 homolog						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	integral to membrane|microsome|signal peptidase complex	peptidase activity			breast(1)	1																		---	---	---	---
ARRB1	408	broad.mit.edu	37	11	75055917	75055917	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75055917delT	uc001owe.1	-						ARRB1_uc001owf.1_Intron	NM_004041	NP_004032			arrestin beta 1 isoform A						G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2																		---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75171349	75171349	+	Intron	DEL	T	-	-	rs72230728		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75171349delT	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron|GDPD5_uc009yue.1_5'Flank	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																		---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75716387	75716387	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75716387delA	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron|UVRAG_uc009yuh.1_Intron	NM_003369	NP_003360			UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77436580	77436580	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77436580delA	uc001oyn.2	-							NM_016578	NP_057662			remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78506025	78506025	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78506025delG	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
PRCP	5547	broad.mit.edu	37	11	82560041	82560041	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82560041delA	uc001ozs.2	-						PRCP_uc001ozr.2_Intron	NM_005040	NP_005031			prolylcarboxypeptidase isoform 1 preproprotein						blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	83078959	83078959	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83078959delA	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																														---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84750749	84750749	+	Intron	DEL	A	-	-	rs35111618		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84750749delA	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84881981	84881983	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84881981_84881983delAAA	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85415768	85415768	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85415768delT	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc001pav.2_Intron|SYTL2_uc010rte.1_Intron|SYTL2_uc001pax.2_Intron|SYTL2_uc001paz.2_Intron|SYTL2_uc001pba.2_Intron|SYTL2_uc001pay.2_Intron|SYTL2_uc001paw.2_Intron|SYTL2_uc009yvj.2_Intron|SYTL2_uc001pbd.2_Intron|SYTL2_uc001pbb.2_Intron|SYTL2_uc001pbc.2_Intron|SYTL2_uc010rtf.1_Intron	NM_001162951	NP_001156423			synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	85946315	85946315	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85946315delA								PICALM (165415 upstream) : EED (9500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87125719	87125719	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87125719delA								TMEM135 (91151 upstream) : RAB38 (720712 downstream)																																			---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88798568	88798570	+	Intron	DEL	TTT	-	-	rs113626208		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88798568_88798570delTTT	uc009yvn.1	-						GRM5_uc009yvm.2_5'Flank					SubName: Full=Putative uncharacterized protein GRM5;						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	89493618	89493620	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89493618_89493620delAAA								TRIM77 (42580 upstream) : TRIM49 (37204 downstream)																																			---	---	---	---
NAALAD2	10003	broad.mit.edu	37	11	89925063	89925064	+	3'UTR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89925063_89925064delTT	uc001pdf.3	+	19					NAALAD2_uc009yvx.2_3'UTR|NAALAD2_uc009yvy.2_3'UTR	NM_005467	NP_005458			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	90242166	90242167	+	IGR	INS	-	AC	AC	rs138091718	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90242166_90242167insAC								CHORDC1 (285634 upstream) : MIR1261 (360122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90507869	90507869	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90507869delG								CHORDC1 (551337 upstream) : MIR1261 (94420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91033387	91033387	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91033387delT								MIR1261 (431017 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92837709	92837709	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92837709delA								MTNR1B (121761 upstream) : SLC36A4 (43143 downstream)																																			---	---	---	---
MED17	9440	broad.mit.edu	37	11	93521280	93521280	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93521280delA	uc001pem.3	+	2	639	c.364delA	c.(364-366)AAAfs	p.K122fs	MED17_uc001pel.2_Frame_Shift_Del_p.K122fs	NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	122					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93602132	93602132	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93602132delG								C11orf90 (18464 upstream) : HEPHL1 (152246 downstream)																																			---	---	---	---
MRE11A	4361	broad.mit.edu	37	11	94219326	94219326	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94219326delA	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582			meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)											Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				---	---	---	---
Unknown	0	broad.mit.edu	37	11	98094083	98094083	+	IGR	DEL	T	-	-	rs79787315		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98094083delT								None (None upstream) : CNTN5 (797788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98354559	98354559	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98354559delT								None (None upstream) : CNTN5 (537312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98364644	98364644	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98364644delA								None (None upstream) : CNTN5 (527227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98582250	98582251	+	IGR	INS	-	AC	AC	rs151224666	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98582250_98582251insAC								None (None upstream) : CNTN5 (309620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	100870260	100870261	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100870260_100870261delAG								TMEM133 (5595 upstream) : PGR (30094 downstream)																																			---	---	---	---
C11orf70	85016	broad.mit.edu	37	11	101920861	101920861	+	Intron	DEL	A	-	-	rs80127406		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101920861delA	uc001pgp.2	+						C11orf70_uc001pgo.2_Intron|C11orf70_uc001pgq.2_Intron	NM_032930	NP_116319			hypothetical protein LOC85016											skin(1)	1	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102107745	102107747	+	IGR	DEL	GAA	-	-	rs7950422	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102107745_102107747delGAA								YAP1 (3591 upstream) : BIRC3 (80447 downstream)																																			---	---	---	---
BIRC2	329	broad.mit.edu	37	11	102248668	102248668	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102248668delT	uc001pgy.2	+						BIRC2_uc010ruq.1_Intron|BIRC2_uc010rur.1_Intron	NM_001166	NP_001157			baculoviral IAP repeat-containing protein 2						cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102354822	102354823	+	IGR	INS	-	C	C	rs138871263	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102354822_102354823insC								TMEM123 (31047 upstream) : MMP7 (36417 downstream)																																			---	---	---	---
MMP20	9313	broad.mit.edu	37	11	102491248	102491249	+	Intron	INS	-	A	A	rs146468833	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102491248_102491249insA	uc001phc.2	-							NM_004771	NP_004762			matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102717980	102717980	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102717980delA								MMP3 (3638 upstream) : MMP12 (15485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	102764234	102764234	+	IGR	DEL	A	-	-	rs74452189		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102764234delA								MMP12 (18522 upstream) : MMP13 (49491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	102867565	102867566	+	IGR	DEL	TG	-	-	rs140642233		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102867565_102867566delTG								MMP13 (41103 upstream) : DCUN1D5 (65256 downstream)																																			---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102977858	102977859	+	5'Flank	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102977858_102977859delAA	uc001pho.2	+						DYNC2H1_uc001phn.1_5'Flank|DYNC2H1_uc009yxe.1_5'Flank	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	103645620	103645621	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103645620_103645621insG								DYNC2H1 (295029 upstream) : PDGFD (132294 downstream)																																			---	---	---	---
CASP4	837	broad.mit.edu	37	11	104839464	104839464	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104839464delA	uc001pid.1	-						CASP4_uc009yxg.1_5'Flank|CASP4_uc010rux.1_5'Flank|CASP4_uc010ruy.1_5'Flank	NM_001225	NP_001216			caspase 4 isoform alpha precursor						apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)														---	---	---	---
KBTBD3	143879	broad.mit.edu	37	11	105929470	105929470	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105929470delT	uc001pja.2	-						KBTBD3_uc001pjb.2_Intron|KBTBD3_uc009yxm.2_Intron	NM_198439	NP_940841			BTB and kelch domain containing 3											ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)														---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106824380	106824380	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106824380delT	uc001pjg.1	-						GUCY1A2_uc010rvo.1_Intron|GUCY1A2_uc009yxn.1_Intron	NM_000855	NP_000846			guanylate cyclase 1, soluble, alpha 2						intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107085890	107085891	+	IGR	DEL	TT	-	-	rs72465616		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107085890_107085891delTT								GUCY1A2 (196719 upstream) : CWF19L2 (111183 downstream)																																			---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107207442	107207442	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107207442delA	uc010rvp.1	-						CWF19L2_uc001pjh.3_Intron|CWF19L2_uc009yxo.2_Intron	NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107300936	107300937	+	Intron	DEL	GA	-	-	rs675081	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107300936_107300937delGA	uc010rvp.1	-						CWF19L2_uc001pjh.3_Intron|CWF19L2_uc009yxo.2_Intron	NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107322157	107322157	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107322157delT	uc010rvp.1	-							NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107889401	107889401	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107889401delA	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107904513	107904513	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107904513delT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107923647	107923650	+	Intron	DEL	TAGA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107923647_107923650delTAGA	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
ARHGAP20	57569	broad.mit.edu	37	11	110501197	110501197	+	Intron	DEL	T	-	-	rs35229947		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110501197delT	uc001pkz.1	-						ARHGAP20_uc001pky.1_Intron|ARHGAP20_uc009yyb.1_Intron|ARHGAP20_uc001pla.1_Intron	NM_020809	NP_065860			Rho GTPase activating protein 20						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)														---	---	---	---
BTG4	54766	broad.mit.edu	37	11	111343807	111343808	+	Intron	DEL	AA	-	-	rs149225761		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111343807_111343808delAA	uc001plj.2	-							NM_017589	NP_060059			B-cell translocation gene 4						cell cycle arrest|negative regulation of cell proliferation|neuron differentiation						0		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)														---	---	---	---
BCO2	83875	broad.mit.edu	37	11	112079681	112079681	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112079681delA	uc001pnf.2	+						BCO2_uc001pne.1_Intron|BCO2_uc001png.2_Intron|BCO2_uc001pnh.2_Intron|BCO2_uc010rwt.1_Intron|BCO2_uc009yyn.2_Intron|BCO2_uc001pni.2_Intron	NM_031938	NP_114144			beta-carotene dioxygenase 2 isoform a						carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
C11orf34	349633	broad.mit.edu	37	11	112124913	112124914	+	Intron	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs144110459	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112124913_112124914insGTGTGTGTGT	uc009yyp.2	-						PTS_uc009yyo.2_Intron	NM_001145024	NP_001138496			hypothetical protein LOC349633 precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	112378054	112378055	+	IGR	DEL	AA	-	-	rs5794799		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112378054_112378055delAA								PTS (237377 upstream) : NCAM1 (453940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112739184	112739185	+	IGR	INS	-	CTT	CTT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112739184_112739185insCTT								PTS (598507 upstream) : NCAM1 (92810 downstream)																																			---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113079391	113079392	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113079391_113079392delTC	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
ANKK1	255239	broad.mit.edu	37	11	113266716	113266716	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113266716delC	uc001pny.2	+							NM_178510	NP_848605			ankyrin repeat and kinase domain containing 1								ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	113432606	113432607	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113432606_113432607delGA								DRD2 (86193 upstream) : TMPRSS5 (125662 downstream)																																			---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113608928	113608928	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113608928delA	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715			centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114122492	114122492	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114122492delG								ZBTB16 (1098 upstream) : NNMT (6061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115007521	115007521	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115007521delC								FAM55B (429869 upstream) : CADM1 (32432 downstream)																																			---	---	---	---
ZNF259	8882	broad.mit.edu	37	11	116650281	116650281	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116650281delT	uc001ppp.2	-						ZNF259_uc009yzd.2_Intron|ZNF259_uc001ppq.2_Intron	NM_003904	NP_003895			zinc finger protein 259						cell proliferation|signal transduction	cytoplasm|nucleolus					0	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)														---	---	---	---
APOA1	335	broad.mit.edu	37	11	116710167	116710168	+	5'Flank	INS	-	AT	AT	rs147742678		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116710167_116710168insAT	uc001ppu.1	-						APOA1_uc001ppv.1_5'Flank	NM_000039	NP_000030			apolipoprotein A-I preproprotein						Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|cholesterol import|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|negative regulation of cytokine secretion involved in immune response|negative regulation of interleukin-1 beta secretion|negative regulation of very-low-density lipoprotein particle remodeling|phosphatidylcholine biosynthetic process|phospholipid efflux|platelet activation|platelet degranulation|positive regulation of cholesterol esterification|positive regulation of hydrolase activity|protein stabilization|reverse cholesterol transport	endocytic vesicle|endoplasmic reticulum lumen|plasma membrane|spherical high-density lipoprotein particle|stored secretory granule|very-low-density lipoprotein particle	apolipoprotein A-I receptor binding|beta-amyloid binding|cholesterol binding|cholesterol transporter activity|enzyme binding|high-density lipoprotein particle receptor binding|identical protein binding|phosphatidylcholine-sterol O-acyltransferase activator activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.59e-05)|all cancers(92;0.000162)|OV - Ovarian serous cystadenocarcinoma(223;0.148)														---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116921003	116921004	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116921003_116921004delCA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117125346	117125346	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117125346delT	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226			ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)														---	---	---	---
BACE1	23621	broad.mit.edu	37	11	117163911	117163911	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117163911delA	uc001pqz.2	-						BACE1_uc001pqw.2_Intron|BACE1_uc001pqx.2_Intron|BACE1_uc001pqy.2_Intron|BACE1_uc010rxg.1_Intron|BACE1_uc010rxh.1_Intron|BACE1_uc009yzo.1_5'Flank	NM_012104	NP_036236			beta-site APP-cleaving enzyme 1 isoform A						beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	117904236	117904238	+	Intron	DEL	TTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117904236_117904238delTTG	uc001prx.1	-						uc001pry.1_Intron|uc001prz.1_Intron|uc009yzs.1_Intron|uc001psa.1_Intron					Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit26-03-15-R.																														---	---	---	---
CD3E	916	broad.mit.edu	37	11	118177978	118177978	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118177978delT	uc001psq.3	+						CD3E_uc009yzz.1_Intron|CD3E_uc010rya.1_Intron	NM_000733	NP_000724			CD3E antigen, epsilon polypeptide precursor						G-protein coupled receptor protein signaling pathway|signal complex assembly|T cell costimulation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	external side of plasma membrane|integral to plasma membrane	protein heterodimerization activity|protein kinase binding|receptor signaling complex scaffold activity|receptor signaling protein activity|SH3 domain binding|T cell receptor binding|transmembrane receptor activity			ovary(2)	2	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	118294262	118294262	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118294262delT								ATP5L (13701 upstream) : MLL (12943 downstream)																																			---	---	---	---
TMEM25	84866	broad.mit.edu	37	11	118417202	118417202	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118417202delA	uc001ptl.2	+	9					TMEM25_uc001ptm.2_3'UTR|TMEM25_uc001ptn.2_3'UTR|IFT46_uc001pto.1_Intron|IFT46_uc001ptp.1_Intron|IFT46_uc009zaf.1_Intron	NM_001144037	NP_001137509			transmembrane protein 25 isoform 4							extracellular region|integral to membrane|plasma membrane					0	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)														---	---	---	---
CBL	867	broad.mit.edu	37	11	119153049	119153051	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119153049_119153051delAAA	uc001pwe.2	+							NM_005188	NP_005179			Cas-Br-M (murine) ecotropic retroviral						epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)										CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	11	119477821	119477822	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119477821_119477822delTT								THY1 (183575 upstream) : PVRL1 (30986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	119753427	119753427	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119753427delG								PVRL1 (153992 upstream) : TRIM29 (228568 downstream)																																			---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120131870	120131873	+	Intron	DEL	TGTG	-	-	rs147950740		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120131870_120131873delTGTG	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron|uc001pxd.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120350637	120350637	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120350637delT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120352470	120352473	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120352470_120352473delTTTT	uc001pxl.1	+						ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120732466	120732466	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120732466delT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
CRTAM	56253	broad.mit.edu	37	11	122708171	122708172	+	5'Flank	INS	-	GGAT	GGAT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122708171_122708172insGGAT	uc001pyj.2	+							NM_019604	NP_062550			class-I MHC-restricted T cell associated						cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	122861891	122861892	+	IGR	INS	-	A	A	rs76192257	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122861891_122861892insA								BSX (9512 upstream) : LOC341056 (26382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123921663	123921664	+	IGR	INS	-	TGTG	TGTG	rs145133770	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123921663_123921664insTGTG								OR10G7 (11955 upstream) : VWA5A (64447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124040310	124040310	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124040310delA								VWA5A (22694 upstream) : OR8G2 (55088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124464186	124464186	+	IGR	DEL	T	-	-	rs72287239		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124464186delT								OR8A1 (23242 upstream) : PANX3 (17267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	125026922	125026923	+	IGR	DEL	CA	-	-	rs72463653		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125026922_125026923delCA								TMEM218 (45447 upstream) : PKNOX2 (7636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	125810321	125810321	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125810321delC								DDX25 (17318 upstream) : CDON (16394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	126049208	126049208	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126049208delA								CDON (116021 upstream) : RPUSD4 (22782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128482343	128482343	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128482343delC								ETS1 (24890 upstream) : FLI1 (74087 downstream)																																			---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	129006020	129006020	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129006020delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron	NM_001142685	NP_001136157			Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	129216193	129216193	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129216193delA								ARHGAP32 (154100 upstream) : BARX2 (29688 downstream)																																			---	---	---	---
NTM	50863	broad.mit.edu	37	11	131486669	131486670	+	Intron	DEL	GG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131486669_131486670delGG	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	132261827	132261827	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132261827delA								NTM (55112 upstream) : OPCML (23050 downstream)																																			---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132479880	132479881	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132479880_132479881delCA	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	133269296	133269296	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133269296delA	uc001qgu.2	-							NM_001012393	NP_001012393			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
SPATA19	219938	broad.mit.edu	37	11	133712619	133712619	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133712619delT	uc001qgv.1	-							NM_174927	NP_777587			spermatogenesis associated 19 precursor						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrial outer membrane					0	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)														---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133801455	133801456	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133801455_133801456insG	uc001qgx.3	-	10	1491_1492	c.1260_1261insC	c.(1258-1263)CCCTATfs	p.P420fs	IGSF9B_uc001qgy.1_Frame_Shift_Ins_p.P262fs	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	420_421	Extracellular (Potential).|Ig-like 5.					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)														---	---	---	---
JAM3	83700	broad.mit.edu	37	11	133973585	133973585	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133973585delA	uc001qhb.1	+						JAM3_uc009zcz.1_Intron	NM_032801	NP_116190			junctional adhesion molecule 3 precursor						angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)														---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134078848	134078848	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134078848delA	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron	NM_015261	NP_056076			non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134152066	134152066	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134152066delA	uc009zdf.2	+						GLB1L3_uc010scs.1_Intron|GLB1L3_uc010sct.1_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	70151	70151	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70151delA								None (None upstream) : LOC100288778 (4121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	169815	169815	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:169815delA								FAM138D (20403 upstream) : IQSEC3 (6388 downstream)																																			---	---	---	---
IQSEC3	440073	broad.mit.edu	37	12	192236	192236	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:192236delT	uc001qhu.1	+						IQSEC3_uc001qht.1_Intron	NM_015232	NP_056047			IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)														---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	430051	430051	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:430051delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	442585	442585	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:442585delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1492796	1492797	+	Intron	INS	-	CA	CA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1492796_1492797insCA	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2580850	2580850	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2580850delT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	3707731	3707739	+	IGR	DEL	CTGTATGGT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3707731_3707739delCTGTATGGT								PRMT8 (4595 upstream) : EFCAB4B (8579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4056527	4056527	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4056527delT								PARP11 (73919 upstream) : CCND2 (326375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4082515	4082515	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4082515delA								PARP11 (99907 upstream) : CCND2 (300387 downstream)																																			---	---	---	---
NDUFA9	4704	broad.mit.edu	37	12	4791632	4791632	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4791632delA	uc001qnc.2	+						NDUFA9_uc010ses.1_Intron	NM_005002	NP_004993			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|sodium ion transport	mitochondrial matrix|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5699380	5699380	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5699380delT	uc001qnm.2	-							NM_020373	NP_065106			anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5893327	5893327	+	Intron	DEL	T	-	-	rs36019270		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5893327delT	uc001qnm.2	-							NM_020373	NP_065106			anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	6280782	6280784	+	IGR	DEL	GAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6280782_6280784delGAG								VWF (46946 upstream) : CD9 (28089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6363064	6363064	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6363064delA								CD9 (15637 upstream) : PLEKHG6 (56538 downstream)																																			---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6687517	6687519	+	Intron	DEL	AAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6687517_6687519delAAG	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron|uc001qpq.1_5'Flank	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
LEPREL2	10536	broad.mit.edu	37	12	6938962	6938962	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6938962delG	uc001qra.1	+						LEPREL2_uc001qqz.1_Intron|LEPREL2_uc001qrb.1_5'UTR|GPR162_uc001qqy.1_Intron	NM_014262	NP_055077			leprecan-like 2 precursor						negative regulation of cell proliferation	endoplasmic reticulum	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity				0					L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)											OREG0021637	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C1R	715	broad.mit.edu	37	12	7241343	7241343	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7241343delG	uc010sfy.1	-						C1R_uc010sfz.1_Intron|C1R_uc010sga.1_Intron	NM_001733	NP_001724			complement component 1, r subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
C1R	715	broad.mit.edu	37	12	7241600	7241601	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7241600_7241601delTT	uc010sfy.1	-						C1R_uc010sfz.1_Intron|C1R_uc010sga.1_Intron	NM_001733	NP_001724			complement component 1, r subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
APOBEC1	339	broad.mit.edu	37	12	7808737	7808737	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7808737delT	uc001qtb.2	-						APOBEC1_uc001qtc.2_Intron|APOBEC1_uc010sgf.1_Intron	NM_001644	NP_001635			apolipoprotein B mRNA editing enzyme						cytidine to uridine editing|DNA demethylation|lipid metabolic process|mRNA modification|mRNA processing|negative regulation of methylation-dependent chromatin silencing	nucleoplasm	cytidine deaminase activity|RNA binding|zinc ion binding				0																		---	---	---	---
CLEC4C	170482	broad.mit.edu	37	12	7893444	7893444	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7893444delT	uc001qtg.1	-						CLEC4C_uc001qth.1_Intron|CLEC4C_uc001qti.1_Intron	NM_130441	NP_569708			C-type lectin domain family 4, member C isoform						innate immune response	integral to membrane	sugar binding			ovary(2)|skin(1)	3				Kidney(36;0.0915)														---	---	---	---
CLEC4C	170482	broad.mit.edu	37	12	7898810	7898810	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7898810delA	uc001qtg.1	-						CLEC4C_uc001qth.1_Intron|CLEC4C_uc001qti.1_Intron	NM_130441	NP_569708			C-type lectin domain family 4, member C isoform						innate immune response	integral to membrane	sugar binding			ovary(2)|skin(1)	3				Kidney(36;0.0915)														---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	8032551	8032552	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8032551_8032552insA	uc010sgh.1	-						uc001qtp.1_Intron	NM_153449	NP_703150			glucose transporter 14						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)														---	---	---	---
LOC389634	389634	broad.mit.edu	37	12	8533980	8533980	+	Intron	DEL	T	-	-	rs138058195		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8533980delT	uc001quk.3	-							NR_024420				Homo sapiens cDNA FLJ90405 fis, clone NT2RP2006099.												0																		---	---	---	---
CLEC6A	93978	broad.mit.edu	37	12	8618054	8618054	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8618054delT	uc001qum.1	+							NM_001007033	NP_001007034			dectin-2						defense response to fungus|innate immune response|positive regulation of cytokine secretion|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	sugar binding			breast(1)	1	Lung SC(5;0.184)																	---	---	---	---
CLEC4D	338339	broad.mit.edu	37	12	8666271	8666272	+	5'UTR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8666271_8666272delAA	uc001qun.2	+	1						NM_080387	NP_525126			C-type lectin domain family 4, member D						innate immune response	integral to membrane	sugar binding				0	Lung SC(5;0.184)																	---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8870029	8870029	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8870029delT	uc001quu.2	+						RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_Intron|RIMKLB_uc010sgl.1_Intron|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	9417057	9417057	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9417057delT								MIR1244 (24910 upstream) : LOC642846 (19196 downstream)																																			---	---	---	---
CLEC1B	51266	broad.mit.edu	37	12	10151969	10151969	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10151969delT	uc001qwu.2	-						CLEC1B_uc009zhd.2_5'Flank	NM_016509	NP_057593			C-type lectin domain family 1, member B isoform						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	protein binding|sugar binding|transmembrane receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	10180268	10180269	+	IGR	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10180268_10180269delTC								CLEC12B (8869 upstream) : CLEC9A (3007 downstream)																																			---	---	---	---
CLEC9A	283420	broad.mit.edu	37	12	10205421	10205424	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10205421_10205424delTTTT	uc001qxa.2	+							NM_207345	NP_997228			C-type lectin domain family 9, member A						positive regulation of cytokine secretion|receptor-mediated endocytosis	cell surface|integral to membrane	receptor activity|sugar binding			ovary(1)	1																		---	---	---	---
CREBL2	1389	broad.mit.edu	37	12	12765448	12765449	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12765448_12765449delCT	uc001rap.1	+							NM_001310	NP_001301			cAMP responsive element binding protein-like 2						cell cycle|signal transduction	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Prostate(47;0.0684)		BRCA - Breast invasive adenocarcinoma(232;0.0503)														---	---	---	---
HEBP1	50865	broad.mit.edu	37	12	13139909	13139910	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13139909_13139910delTG	uc001rbd.2	-						HEBP1_uc001rbf.2_3'UTR	NM_015987	NP_057071			heme binding protein 1						circadian rhythm	extracellular region				breast(1)	1		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)														---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13764619	13764619	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13764619delA	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
RERG	85004	broad.mit.edu	37	12	15313116	15313116	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15313116delT	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307			RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15406179	15406180	+	IGR	INS	-	TG	TG	rs149803083	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15406179_15406180insTG								RERG (31875 upstream) : PTPRO (69307 downstream)																																			---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15699475	15699475	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15699475delT	uc001rcv.1	+						PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcx.1_5'UTR|PTPRO_uc001rcy.1_5'UTR|PTPRO_uc001rcz.1_5'UTR|PTPRO_uc001rda.1_5'UTR	NM_030667	NP_109592			receptor-type protein tyrosine phosphatase O							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)																---	---	---	---
EPS8	2059	broad.mit.edu	37	12	15835909	15835909	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15835909delA	uc009zif.2	-						EPS8_uc001rdb.2_Intron|EPS8_uc009zig.2_Intron	NM_004447	NP_004438			epidermal growth factor receptor pathway						cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	16192482	16192482	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16192482delT								DERA (2168 upstream) : MGST1 (307594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16988793	16988793	+	IGR	DEL	A	-	-	rs66837084		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16988793delA								LMO3 (226035 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18218145	18218145	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18218145delT								None (None upstream) : RERGL (15659 downstream)																																			---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18599351	18599352	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18599351_18599352delCT	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	19196024	19196025	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19196024_19196025insA								CAPZA3 (303903 upstream) : PLEKHA5 (86623 downstream)																																			---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19406761	19406761	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19406761delA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	19552186	19552187	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19552186_19552187delTT								PLEKHA5 (22855 upstream) : AEBP2 (40421 downstream)																																			---	---	---	---
AEBP2	121536	broad.mit.edu	37	12	19664967	19664967	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19664967delT	uc001ref.2	+						AEBP2_uc001ree.2_Intron|AEBP2_uc001reg.1_Intron	NM_001114176	NP_001107648			AE binding protein 2 isoform b						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	20096042	20096042	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20096042delA								AEBP2 (420869 upstream) : PDE3A (426155 downstream)																																			---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21208314	21208324	+	Intron	DEL	GTGAAATGAGG	-	-	rs72246350		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21208314_21208324delGTGAAATGAGG	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron					SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	21848830	21848831	+	IGR	INS	-	TA	TA	rs71053337		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21848830_21848831insTA								LDHB (38054 upstream) : KCNJ8 (69059 downstream)																																			---	---	---	---
KIAA0528	9847	broad.mit.edu	37	12	22625136	22625137	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22625136_22625137delAA	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron	NM_014802	NP_055617			hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	25201155	25201155	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25201155delT								C12orf77 (50782 upstream) : LRMP (4086 downstream)																																			---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26782678	26782679	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26782678_26782679delTC	uc001rhg.2	-							NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ARNTL2	56938	broad.mit.edu	37	12	27567949	27567950	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27567949_27567950delAA	uc001rht.1	+						ARNTL2_uc001rhw.2_Intron|ARNTL2_uc010sjp.1_Intron|ARNTL2_uc001rhu.1_Intron|ARNTL2_uc009zji.1_Intron|ARNTL2_uc001rhv.1_Intron|uc001rhx.2_Intron	NM_020183	NP_064568			aryl hydrocarbon receptor nuclear						circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)																	---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27841020	27841020	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27841020delA	uc001ric.1	+						PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron|PPFIBP1_uc001rif.1_Intron	NM_003622	NP_003613			PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)																	---	---	---	---
MRPS35	60488	broad.mit.edu	37	12	27860733	27860733	+	5'Flank	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27860733delC	uc001rih.2	+						MRPS35_uc001rii.2_5'Flank	NM_021821	NP_068593			mitochondrial ribosomal protein S35 precursor						DNA damage response, detection of DNA damage	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28754877	28754878	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28754877_28754878insA								CCDC91 (51779 upstream) : FAR2 (547354 downstream)																																			---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29748946	29748947	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29748946_29748947delTT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057			transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	30246805	30246806	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30246805_30246806insG								TMTC1 (309113 upstream) : IPO8 (535117 downstream)																																			---	---	---	---
FAM60A	58516	broad.mit.edu	37	12	31435557	31435557	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31435557delA	uc010sjz.1	-	6					FAM60A_uc001rkd.2_3'UTR|FAM60A_uc010ska.1_3'UTR|FAM60A_uc001rke.2_3'UTR|FAM60A_uc010skb.1_RNA|FAM60A_uc001rkc.2_3'UTR	NM_021238	NP_067061			family with sequence similarity 60, member A												0	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31585222	31585222	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31585222delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31630952	31630952	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630952delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31686822	31686824	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31686822_31686824delTTT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc001rkj.2_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
BICD1	636	broad.mit.edu	37	12	32284584	32284584	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32284584delA	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
BICD1	636	broad.mit.edu	37	12	32292807	32292807	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32292807delA	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
BICD1	636	broad.mit.edu	37	12	32520461	32520461	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32520461delA	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	34244366	34244366	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34244366delT								ALG10 (63132 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38528994	38528994	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38528994delA								None (None upstream) : ALG10B (181563 downstream)																																			---	---	---	---
CPNE8	144402	broad.mit.edu	37	12	39087296	39087296	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39087296delT	uc001rls.1	-						CPNE8_uc001rlr.1_Intron	NM_153634	NP_705898			copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	40799882	40799882	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40799882delT								LRRK2 (36798 upstream) : CNTN1 (286476 downstream)																																			---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41407336	41407336	+	Intron	DEL	A	-	-	rs34197329		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41407336delA	uc001rmm.1	+						CNTN1_uc001rmn.1_Intron	NM_001843	NP_001834			contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41408228	41408228	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41408228delT	uc001rmm.1	+						CNTN1_uc001rmn.1_Intron	NM_001843	NP_001834			contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41846251	41846252	+	Intron	INS	-	AG	AG	rs5007225		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41846251_41846252insAG	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron	NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41923031	41923032	+	Intron	INS	-	TG	TG	rs141128777	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41923031_41923032insTG	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron|PDZRN4_uc001rmr.2_Intron	NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46287391	46287391	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46287391delT	uc001ros.1	+						ARID2_uc001ror.2_Intron|ARID2_uc009zkg.1_Intron|ARID2_uc009zkh.1_Intron|ARID2_uc001rou.1_Intron	NM_152641	NP_689854			AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	46393336	46393337	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46393336_46393337insG								SFRS2IP (7433 upstream) : SLC38A1 (183506 downstream)																																			---	---	---	---
SLC38A4	55089	broad.mit.edu	37	12	47197582	47197582	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47197582delA	uc001rpi.2	-						SLC38A4_uc001rpj.2_Intron|SLC38A4_uc009zkl.2_Intron	NM_018018	NP_060488			solute carrier family 38, member 4						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)																	---	---	---	---
PFKM	5213	broad.mit.edu	37	12	48539184	48539185	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48539184_48539185delTT	uc001rrc.2	+						PFKM_uc001rra.1_Intron|PFKM_uc001rrb.1_Intron|PFKM_uc001rrd.2_Intron|PFKM_uc001rre.1_Intron|PFKM_uc001rrg.1_Intron	NM_000289	NP_000280			phosphofructokinase, muscle						fructose 6-phosphate metabolic process|glycolysis|muscle cell homeostasis	6-phosphofructokinase complex|apical plasma membrane	6-phosphofructokinase activity|ATP binding|identical protein binding|kinase binding|metal ion binding|protein C-terminus binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4																		---	---	---	---
LALBA	3906	broad.mit.edu	37	12	48963167	48963167	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48963167delA	uc001rrt.2	-							NM_002289	NP_002280			lactalbumin, alpha- precursor						cell-cell signaling|defense response to bacterium|induction of apoptosis|lactose biosynthetic process|signal transduction	extracellular space	calcium ion binding|lactose synthase activity				0																		---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49095046	49095047	+	Intron	INS	-	CAC	CAC	rs149152239	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49095046_49095047insCAC	uc001rse.1	-						CCNT1_uc009zkz.1_Intron	NM_001240	NP_001231			cyclin T1						cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding			ovary(3)|lung(1)|breast(1)|skin(1)	6																		---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49421242	49421242	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49421242delT	uc001rta.3	-							NM_003482	NP_003473			myeloid/lymphoid or mixed-lineage leukemia 2						chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49431873	49431874	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49431873_49431874insC	uc001rta.3	-	34	9265_9266	c.9265_9266insG	c.(9265-9267)GTGfs	p.V3089fs		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	3089					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
FMNL3	91010	broad.mit.edu	37	12	50041888	50041888	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50041888delA	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron|FMNL3_uc001rut.1_Intron|FMNL3_uc001ruu.1_Intron	NM_175736	NP_783863			formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4																		---	---	---	---
FMNL3	91010	broad.mit.edu	37	12	50058862	50058863	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50058862_50058863delTC	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron	NM_175736	NP_783863			formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4																		---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50742999	50742999	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50742999delT	uc001rwl.2	-						FAM186A_uc010smt.1_Intron	NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50834163	50834163	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50834163delA	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc009zlr.1_Intron|LARP4_uc001rwt.1_5'Flank|LARP4_uc001rwm.2_Intron|LARP4_uc001rwn.2_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	51034721	51034721	+	Intron	DEL	C	-	-	rs2731436	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51034721delC	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron|DIP2B_uc009zls.1_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
LETMD1	25875	broad.mit.edu	37	12	51453270	51453273	+	3'UTR	DEL	AACA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51453270_51453273delAACA	uc001rxm.2	+	9					LETMD1_uc001rxl.2_3'UTR|LETMD1_uc009zlv.2_RNA|LETMD1_uc001rxs.2_3'UTR|LETMD1_uc009zlw.2_3'UTR|LETMD1_uc001rxn.2_3'UTR|LETMD1_uc001rxo.2_RNA|LETMD1_uc001rxp.2_3'UTR|LETMD1_uc001rxq.2_3'UTR|LETMD1_uc001rxr.2_RNA|LETMD1_uc001rxt.2_3'UTR	NM_015416	NP_056231			LETM1 domain containing 1 isoform 1							integral to membrane|mitochondrial outer membrane	protein binding			central_nervous_system(2)	2																		---	---	---	---
KRT79	338785	broad.mit.edu	37	12	53223675	53223676	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53223675_53223676delAA	uc001sbb.2	-						KRT79_uc001sba.2_Intron	NM_175834	NP_787028			keratin 6L							keratin filament	structural molecule activity			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54885753	54885753	+	IGR	DEL	C	-	-	rs111497993		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54885753delC								GTSF1 (18367 upstream) : NCKAP1L (5742 downstream)																																			---	---	---	---
PDE1B	5153	broad.mit.edu	37	12	54943791	54943791	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54943791delG	uc001sgd.1	+						PDE1B_uc010soz.1_Intron|PDE1B_uc010spa.1_5'Flank	NM_000924	NP_000915			phosphodiesterase 1B isoform 1						activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
ITGA7	3679	broad.mit.edu	37	12	56092301	56092301	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56092301delC	uc001shh.2	-	7	1290	c.1070delG	c.(1069-1071)GGTfs	p.G357fs	ITGA7_uc001shg.2_Frame_Shift_Del_p.G353fs|ITGA7_uc010sps.1_Frame_Shift_Del_p.G260fs|ITGA7_uc009znw.2_5'Flank|ITGA7_uc009znx.2_Frame_Shift_Del_p.G240fs	NM_001144996	NP_001138468	Q13683	ITA7_HUMAN	integrin alpha 7 isoform 1 precursor	397	FG-GAP 5.|Extracellular (Potential).				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																		---	---	---	---
STAT2	6773	broad.mit.edu	37	12	56736218	56736218	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56736218delA	uc001slc.2	-	24					STAT2_uc001slb.2_3'UTR|STAT2_uc001sld.2_3'UTR	NM_005419	NP_005410			signal transducer and activator of transcription						interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3																		---	---	---	---
APOF	319	broad.mit.edu	37	12	56757171	56757171	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56757171delA	uc001sle.1	-							NM_001638	NP_001629			apolipoprotein F precursor						cholesterol metabolic process	high-density lipoprotein particle|low-density lipoprotein particle	cholesterol binding|lipid transporter activity|receptor binding				0																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	57000641	57000641	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57000641delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477			bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	57311065	57311067	+	IGR	DEL	TTT	-	-	rs63224260		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57311065_57311067delTTT								HSD17B6 (129491 upstream) : SDR9C7 (6552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	58055592	58055592	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58055592delT								B4GALNT1 (28607 upstream) : OS9 (32294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61195744	61195744	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61195744delA								None (None upstream) : FAM19A2 (906299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61721133	61721133	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61721133delA								None (None upstream) : FAM19A2 (380910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61727443	61727443	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61727443delA								None (None upstream) : FAM19A2 (374600 downstream)																																			---	---	---	---
MON2	23041	broad.mit.edu	37	12	62937379	62937379	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62937379delT	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron	NM_015026	NP_055841			MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)														---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63314404	63314404	+	Intron	DEL	A	-	-	rs35298534		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63314404delA	uc001srk.3	-							NM_020700	NP_065751			protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)														---	---	---	---
AVPR1A	552	broad.mit.edu	37	12	63541343	63541343	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63541343delA	uc001sro.1	-	2	3027	c.1053delT	c.(1051-1053)TTTfs	p.F351fs		NM_000706	NP_000697	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	351	Helical; Name=7; (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)													---	---	---	---
DPY19L2	283417	broad.mit.edu	37	12	63964390	63964390	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63964390delT	uc001srp.1	-						DPY19L2_uc010sso.1_Intron	NM_173812	NP_776173			dpy-19-like 2						multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	64078781	64078782	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64078781_64078782insG								DPY19L2 (16427 upstream) : TMEM5 (94855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	64099009	64099011	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64099009_64099011delAAA								DPY19L2 (36655 upstream) : TMEM5 (74626 downstream)																																			---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64701937	64701937	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64701937delA	uc001ssa.3	-						uc001srx.2_Intron	NM_001099676	NP_001093146			hypothetical protein LOC115749												0			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)														---	---	---	---
TBK1	29110	broad.mit.edu	37	12	64886512	64886512	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64886512delT	uc001ssc.1	+							NM_013254	NP_037386			TANK-binding kinase 1						I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1)	5				GBM - Glioblastoma multiforme(28;0.0386)														---	---	---	---
TBK1	29110	broad.mit.edu	37	12	64890524	64890524	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64890524delT	uc001ssc.1	+							NM_013254	NP_037386			TANK-binding kinase 1						I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1)	5				GBM - Glioblastoma multiforme(28;0.0386)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65254251	65254251	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65254251delT	uc001ssh.1	+						uc010sss.1_Intron|uc010sst.1_Intron|uc001ssi.1_Intron					RecName: Full=TBC1 domain family member 30;																														---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65765354	65765355	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65765354_65765355delTG	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346			methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	67052705	67052705	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67052705delA	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973			glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67706721	67706721	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67706721delT	uc001stn.2	+	15					CAND1_uc001sto.2_3'UTR	NM_018448	NP_060918			TIP120 protein						cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	68139245	68139246	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68139245_68139246insT								DYRK2 (82802 upstream) : IFNG (409304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68267249	68267249	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68267249delT								DYRK2 (210806 upstream) : IFNG (281301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68944571	68944571	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68944571delG								MDM1 (218410 upstream) : RAP1B (60081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68985329	68985329	+	IGR	DEL	A	-	-	rs35253148		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68985329delA								MDM1 (259168 upstream) : RAP1B (19323 downstream)																																			---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69048132	69048132	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69048132delG	uc001sub.2	+						RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Intron|RAP1B_uc010stf.1_Intron|RAP1B_uc010stg.1_Intron|RAP1B_uc010sth.1_Intron|RAP1B_uc010sti.1_Intron	NM_001089704	NP_001083173			SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;						blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)														---	---	---	---
CNOT2	4848	broad.mit.edu	37	12	70739865	70739865	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70739865delT	uc001svv.2	+						CNOT2_uc009zro.2_Intron|CNOT2_uc009zrp.2_Intron|CNOT2_uc009zrq.2_Intron	NM_014515	NP_055330			CCR4-NOT transcription complex, subunit 2						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71523013	71523014	+	Intron	DEL	TT	-	-	rs112700480		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71523013_71523014delTT	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
RAB21	23011	broad.mit.edu	37	12	72163724	72163726	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72163724_72163726delTTT	uc001swt.2	+							NM_014999	NP_055814			RAB21, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	cleavage furrow|cytoplasmic vesicle membrane|early endosome membrane|endoplasmic reticulum membrane|Golgi membrane	GDP binding|GTP binding|GTPase activity|protein binding				0																		---	---	---	---
TBC1D15	64786	broad.mit.edu	37	12	72286901	72286903	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72286901_72286903delTTT	uc001swu.2	+						TBC1D15_uc009zrv.2_Intron|TBC1D15_uc010stt.1_Intron|TBC1D15_uc001swv.2_Intron|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608			TBC1 domain family, member 15 isoform 1								protein binding|Rab GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	73916640	73916641	+	IGR	DEL	AA	-	-	rs78906812		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73916640_73916641delAA								TRHDE (857219 upstream) : None (None downstream)																																			---	---	---	---
KCNC2	3747	broad.mit.edu	37	12	75522435	75522435	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75522435delA	uc001sxg.1	-						KCNC2_uc009zry.2_Intron|KCNC2_uc001sxe.2_Intron|KCNC2_uc001sxf.2_Intron|KCNC2_uc010stw.1_Intron	NM_139137	NP_631875			Shaw-related voltage-gated potassium channel						energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6																		---	---	---	---
ZDHHC17	23390	broad.mit.edu	37	12	77209614	77209615	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77209614_77209615delTT	uc001syk.1	+						ZDHHC17_uc001syi.1_Intron|ZDHHC17_uc001syj.2_Intron	NM_015336	NP_056151			huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	77302314	77302314	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77302314delA								CSRP2 (29515 upstream) : E2F7 (112713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78200782	78200782	+	IGR	DEL	T	-	-	rs78464851		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78200782delT								E2F7 (741422 upstream) : NAV3 (24287 downstream)																																			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78592505	78592505	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78592505delG	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
PPP1R12A	4659	broad.mit.edu	37	12	80223884	80223884	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80223884delA	uc001syz.2	-						PPP1R12A_uc010suc.1_Intron|PPP1R12A_uc001sza.2_Intron|PPP1R12A_uc010sud.1_Intron|PPP1R12A_uc001szb.2_Intron|PPP1R12A_uc001szc.2_Intron	NM_002480	NP_002471			protein phosphatase 1, regulatory (inhibitor)							contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80434132	80434132	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80434132delT								PPP1R12A (104897 upstream) : PTPRQ (403994 downstream)																																			---	---	---	---
MYF6	4618	broad.mit.edu	37	12	81102231	81102231	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81102231delC	uc001szf.1	+							NM_002469	NP_002460			myogenic factor 6						muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	82399878	82399893	+	IGR	DEL	AAGGAAGGAAGGAAGG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82399878_82399893delAAGGAAGGAAGGAAGG								PPFIA2 (246769 upstream) : CCDC59 (346197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	82662308	82662308	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82662308delA								PPFIA2 (509199 upstream) : CCDC59 (83782 downstream)																																			---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83163091	83163091	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83163091delA	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801			transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85554294	85554294	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85554294delT	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85566730	85566730	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85566730delA	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	85748973	85748973	+	IGR	DEL	C	-	-	rs1913132	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85748973delC								ALX1 (53414 upstream) : RASSF9 (449358 downstream)																																			---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	86443083	86443084	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86443083_86443084delTG	uc001tai.3	-						MGAT4C_uc001tal.3_Intron|MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron|MGAT4C_uc010sum.1_Intron|MGAT4C_uc001tah.3_Intron	NM_013244	NP_037376			alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3																		---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	87180359	87180359	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87180359delT	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376			alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	87605070	87605070	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87605070delA								MGAT4C (372389 upstream) : C12orf50 (768746 downstream)																																			---	---	---	---
C12orf29	91298	broad.mit.edu	37	12	88427049	88427049	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88427049delA	uc001tao.2	+						C12orf29_uc001tap.2_5'Flank|C12orf29_uc009zsk.2_5'Flank	NM_001009894	NP_001009894			hypothetical protein LOC91298												0																		---	---	---	---
C12orf29	91298	broad.mit.edu	37	12	88441883	88441883	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88441883delA	uc001tao.2	+						C12orf29_uc001tap.2_Intron|C12orf29_uc009zsk.2_Intron	NM_001009894	NP_001009894			hypothetical protein LOC91298												0																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88448067	88448067	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88448067delT	uc001tar.2	-						CEP290_uc001taq.2_Intron|uc001tas.2_5'Flank	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	89723850	89723850	+	IGR	DEL	T	-	-	rs68168920		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89723850delT								KITLG (749612 upstream) : DUSP6 (17989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89758726	89758726	+	IGR	DEL	A	-	-	rs74508465		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89758726delA								DUSP6 (12430 upstream) : POC1B (54775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90345461	90345461	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90345461delA								LOC338758 (239733 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90900971	90900972	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90900971_90900972insA								LOC338758 (795243 upstream) : C12orf12 (445021 downstream)																																			---	---	---	---
DCN	1634	broad.mit.edu	37	12	91547101	91547102	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91547101_91547102insT	uc001tbs.2	-						DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Intron|DCN_uc001tbu.2_Intron	NM_133503	NP_598010			decorin isoform a preproprotein						organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	92337956	92337956	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92337956delT								DCN (761150 upstream) : BTG1 (40910 downstream)																																			---	---	---	---
BTG1	694	broad.mit.edu	37	12	92456624	92456624	+	Intron	DEL	A	-	-	rs63436360		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92456624delA	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron					Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)						T	MYC	BCLL								---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94707888	94707889	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94707888_94707889insT	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94834291	94834291	+	Intron	DEL	A	-	-	rs112658393		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94834291delA	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron|CCDC41_uc001tdf.2_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95123687	95123694	+	IGR	DEL	GTGTGTGA	-	-	rs68016874		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95123687_95123694delGTGTGTGA								TMCC3 (79363 upstream) : MIR492 (104480 downstream)																																			---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95453642	95453642	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95453642delT	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
CCDC38	120935	broad.mit.edu	37	12	96284755	96284755	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96284755delA	uc001tek.1	-							NM_182496	NP_872302			coiled-coil domain containing 38											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	96857454	96857455	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96857454_96857455insT								CDK17 (63231 upstream) : C12orf63 (184298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98623781	98623781	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98623781delA								RMST (664988 upstream) : LOC100128191 (282972 downstream)																																			---	---	---	---
SLC25A3	5250	broad.mit.edu	37	12	98985037	98985037	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98985037delT	uc001tfo.2	+						SLC25A3_uc001tfm.2_5'Flank|SLC25A3_uc001tfn.2_5'Flank|SLC25A3_uc001tfp.2_5'Flank|SLC25A3_uc001tfq.2_5'Flank|SLC25A3_uc001tfr.2_5'Flank|SLC25A3_uc001tfs.2_5'Flank|SLC25A3_uc009ztn.2_5'Flank|SLC25A3_uc001tft.2_5'Flank	NM_005888	NP_005879			solute carrier family 25 member 3 isoform a						generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99639945	99639945	+	Intron	DEL	T	-	-	rs35408837		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99639945delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99691684	99691684	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99691684delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100480150	100480151	+	Intron	INS	-	G	G	rs57522109		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100480150_100480151insG	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron|UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
NR1H4	9971	broad.mit.edu	37	12	100887051	100887051	+	5'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100887051delT	uc001thq.1	+	4					NR1H4_uc001thp.1_5'UTR|NR1H4_uc010svj.1_RNA|NR1H4_uc001thr.1_5'UTR|NR1H4_uc010svk.1_5'UTR	NM_005123	NP_005114			nuclear receptor subfamily 1, group H, member 4						bile acid metabolic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	100961963	100961963	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100961963delT								NR1H4 (4320 upstream) : GAS2L3 (5526 downstream)																																			---	---	---	---
SLC5A8	160728	broad.mit.edu	37	12	101587313	101587313	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101587313delT	uc001thz.3	-							NM_145913	NP_666018			solute carrier family 5 (iodide transporter),						apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0																		---	---	---	---
SLC5A8	160728	broad.mit.edu	37	12	101598351	101598352	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101598351_101598352delAA	uc001thz.3	-							NM_145913	NP_666018			solute carrier family 5 (iodide transporter),						apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102468961	102468961	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102468961delT	uc001tjc.2	-							NM_024057	NP_076962			nucleoporin 37kDa						carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
IGF1	3479	broad.mit.edu	37	12	102811350	102811350	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102811350delT	uc001tjm.2	-						IGF1_uc001tjn.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111283	NP_001104753			insulin-like growth factor 1 isoform 1						anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	103346094	103346094	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103346094delT								PAH (34713 upstream) : ASCL1 (5358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103358931	103358931	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103358931delG								ASCL1 (4644 upstream) : C12orf42 (272439 downstream)																																			---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104083273	104083273	+	Intron	DEL	A	-	-	rs11315983		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104083273delA	uc001tjw.2	+							NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
NT5DC3	51559	broad.mit.edu	37	12	104171942	104171943	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104171942_104171943delTT	uc010swe.1	-						NT5DC3_uc010swd.1_5'Flank	NM_001031701	NP_001026871			5'-nucleotidase domain containing 3								hydrolase activity|metal ion binding			ovary(2)|skin(1)	3																		---	---	---	---
NT5DC3	51559	broad.mit.edu	37	12	104223664	104223665	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104223664_104223665delAA	uc010swe.1	-							NM_001031701	NP_001026871			5'-nucleotidase domain containing 3								hydrolase activity|metal ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	106272996	106272997	+	IGR	INS	-	A	A	rs140607172	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106272996_106272997insA								C12orf75 (507701 upstream) : NUAK1 (184128 downstream)																																			---	---	---	---
CRY1	1407	broad.mit.edu	37	12	107399041	107399042	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107399041_107399042insG	uc001tmi.3	-							NM_004075	NP_004066			cryptochrome 1 (photolyase-like)						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	109175300	109175300	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109175300delT								CORO1C (50005 upstream) : SSH1 (1167 downstream)																																			---	---	---	---
SSH1	54434	broad.mit.edu	37	12	109211983	109211984	+	Intron	INS	-	A	A	rs75291911	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109211983_109211984insA	uc001tnm.2	-						SSH1_uc010sxg.1_Intron|SSH1_uc001tnn.3_Intron|SSH1_uc001tno.1_5'Flank	NM_018984	NP_061857			slingshot 1 isoform 1						actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110134701	110134703	+	IGR	DEL	TTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110134701_110134703delTTG								MVK (99631 upstream) : C12orf34 (17487 downstream)																																			---	---	---	---
ANKRD13A	88455	broad.mit.edu	37	12	110469163	110469163	+	Intron	DEL	T	-	-	rs112846454		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110469163delT	uc001tpx.2	+						ANKRD13A_uc010sxw.1_Intron|ANKRD13A_uc001tpy.2_Intron|ANKRD13A_uc001tpz.2_Intron|ANKRD13A_uc001tqa.2_Intron	NM_033121	NP_149112			ankyrin repeat domain 13												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110517862	110517863	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110517862_110517863delGA								C12orf76 (6423 upstream) : IFT81 (44277 downstream)																																			---	---	---	---
C12orf24	29902	broad.mit.edu	37	12	110911025	110911025	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110911025delT	uc001tqu.3	+						C12orf24_uc010sxz.1_Intron|C12orf24_uc009zvo.2_Intron|C12orf24_uc001tqt.2_Intron|C12orf24_uc001tqv.3_Intron	NM_013300	NP_037432			hypothetical protein LOC29902												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111244250	111244253	+	IGR	DEL	TTTT	-	-	rs141945006		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111244250_111244253delTTTT								PPP1CC (63493 upstream) : CCDC63 (40558 downstream)																																			---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111537985	111537986	+	Intron	INS	-	TGTG	TGTG	rs144834847	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111537985_111537986insTGTG	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082			cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
SH2B3	10019	broad.mit.edu	37	12	111841491	111841493	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111841491_111841493delTTT	uc001tse.2	+							NM_005475	NP_005466			SH2B adaptor protein 3						blood coagulation	cytosol	signal transducer activity			ovary(1)	1																		---	---	---	---
SH2B3	10019	broad.mit.edu	37	12	111855899	111855899	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111855899delC	uc001tse.2	+						SH2B3_uc010syf.1_5'Flank|SH2B3_uc001tsf.2_5'Flank	NM_005475	NP_005466			SH2B adaptor protein 3						blood coagulation	cytosol	signal transducer activity			ovary(1)	1																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111998561	111998561	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111998561delA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsm.1_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	112076318	112076318	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112076318delA								ATXN2 (38838 upstream) : BRAP (3633 downstream)																																			---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112103882	112103882	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112103882delC	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759			BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
RPL6	6128	broad.mit.edu	37	12	112846670	112846670	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112846670delT	uc001ttu.2	-						RPL6_uc001ttv.2_Intron|RPL6_uc009zwd.1_Intron	NM_001024662	NP_001019833			ribosomal protein L6						endocrine pancreas development|regulation of transcription, DNA-dependent|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	DNA binding|RNA binding|structural constituent of ribosome			large_intestine(1)	1																		---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113132487	113132490	+	Intron	DEL	ACAG	-	-	rs138563635		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113132487_113132490delACAG	uc010syl.1	+							NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113265486	113265486	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113265486delT	uc010syl.1	+						RPH3A_uc001ttz.2_Intron|RPH3A_uc001tty.2_Intron|RPH3A_uc009zwe.1_Intron|RPH3A_uc010sym.1_Intron	NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	113579030	113579030	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113579030delT								RASAL1 (5001 upstream) : CCDC42B (8633 downstream)																																			---	---	---	---
IQCD	115811	broad.mit.edu	37	12	113637528	113637528	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113637528delT	uc001tuu.2	-							NM_138451	NP_612460			IQ motif containing D											ovary(1)	1																		---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115110242	115110242	+	Intron	DEL	T	-	-	rs112710097		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115110242delT	uc001tvt.1	-						TBX3_uc001tvu.1_Intron	NM_016569	NP_057653			T-box 3 protein isoform 2						anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	115252074	115252074	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115252074delT								TBX3 (130105 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115318075	115318077	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115318075_115318077delTTT								TBX3 (196106 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115812340	115812341	+	IGR	INS	-	AGG	AGG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115812340_115812341insAGG								TBX3 (690371 upstream) : MED13L (584042 downstream)																																			---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116675100	116675101	+	Intron	INS	-	A	A	rs144743515	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116675100_116675101insA	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	117033635	117033638	+	IGR	DEL	TGGA	-	-	rs34663247		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117033635_117033638delTGGA								MAP1LC3B2 (19210 upstream) : C12orf49 (119958 downstream)																																			---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117236031	117236031	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117236031delA	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron	NM_001109903	NP_001103373			transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117289549	117289549	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117289549delA	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron|RNFT2_uc001twd.2_RNA	NM_001109903	NP_001103373			transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117612801	117612801	+	Intron	DEL	A	-	-	rs138433024		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117612801delA	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron	NM_033624	NP_296373			F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)														---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117765883	117765884	+	Intron	INS	-	CT	CT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117765883_117765884insCT	uc001twm.1	-							NM_000620	NP_000611			nitric oxide synthase 1, neuronal						multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	118412165	118412165	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118412165delA								KSR2 (6137 upstream) : RFC5 (42343 downstream)																																			---	---	---	---
SRRM4	84530	broad.mit.edu	37	12	119419618	119419618	+	5'UTR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119419618delC	uc001txa.1	+	1						NM_194286	NP_919262			KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2																		---	---	---	---
SRRM4	84530	broad.mit.edu	37	12	119592030	119592030	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119592030delC	uc001txa.1	+							NM_194286	NP_919262			KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2																		---	---	---	---
TMEM233	387890	broad.mit.edu	37	12	120035275	120035276	+	Intron	DEL	AA	-	-	rs35408506		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120035275_120035276delAA	uc010szd.1	+						uc001txf.2_5'Flank	NM_001136534	NP_001130006			hypothetical protein LOC387890						response to biotic stimulus	integral to membrane					0																		---	---	---	---
TMEM233	387890	broad.mit.edu	37	12	120064278	120064279	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120064278_120064279delAA	uc010szd.1	+							NM_001136534	NP_001130006			hypothetical protein LOC387890						response to biotic stimulus	integral to membrane					0																		---	---	---	---
CIT	11113	broad.mit.edu	37	12	120146289	120146289	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120146289delT	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105			citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	120720659	120720659	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120720659delA								NME2P1 (27 upstream) : SIRT4 (19504 downstream)																																			---	---	---	---
MSI1	4440	broad.mit.edu	37	12	120801065	120801065	+	Intron	DEL	C	-	-	rs34243955		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120801065delC	uc001tye.1	-							NM_002442	NP_002433			musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SFRS9	8683	broad.mit.edu	37	12	120903593	120903593	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120903593delA	uc001tyi.2	-						SFRS9_uc009zwy.2_Intron	NM_003769	NP_003760			splicing factor, arginine/serine-rich 9						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121379931	121379931	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121379931delT								SPPL3 (37780 upstream) : C12orf27 (27710 downstream)																																			---	---	---	---
P2RX7	5027	broad.mit.edu	37	12	121581357	121581357	+	Intron	DEL	A	-	-	rs140924868		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121581357delA	uc001tzm.2	+						P2RX7_uc001tzn.2_Intron|P2RX7_uc001tzo.2_Intron|P2RX7_uc001tzp.2_Intron|P2RX7_uc001tzq.2_Intron	NM_002562	NP_002553			purinergic receptor P2X7							integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)|skin(1)	5	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
P2RX4	5025	broad.mit.edu	37	12	121660176	121660177	+	Intron	INS	-	G	G	rs2567995	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121660176_121660177insG	uc001tzr.2	+						P2RX4_uc010szr.1_Intron|P2RX4_uc010szs.1_Intron|P2RX4_uc009zxc.2_Intron|P2RX4_uc001tzs.2_Intron|P2RX4_uc009zxb.2_Intron|P2RX4_uc010szt.1_Intron	NM_002560	NP_002551			purinergic receptor P2X4						endothelial cell activation|negative regulation of cardiac muscle hypertrophy|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|regulation of apoptosis|regulation of blood pressure|regulation of sodium ion transport|relaxation of cardiac muscle|response to ATP|response to fluid shear stress|sensory perception of pain|tissue homeostasis	cell junction|perinuclear region of cytoplasm	cadherin binding|copper ion binding|extracellular ATP-gated cation channel activity|protein homodimerization activity|purinergic nucleotide receptor activity|receptor binding|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	122017788	122017788	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122017788delT	uc001uat.2	-						KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
MLXIP	22877	broad.mit.edu	37	12	122584608	122584608	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122584608delT	uc001ubq.2	+							NM_014938	NP_055753			MLX interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial outer membrane|nucleus	DNA binding			ovary(2)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)														---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122741131	122741131	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122741131delA	uc001ucd.2	-						VPS33A_uc001ucc.2_Intron|VPS33A_uc001uce.2_Intron	NM_022916	NP_075067			vacuolar protein sorting 33A						lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)														---	---	---	---
GPR81	27198	broad.mit.edu	37	12	123204812	123204812	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123204812delA	uc001ucw.1	-							NM_032554				G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123285648	123285648	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123285648delT	uc001udc.2	+						CCDC62_uc010tah.1_Intron|CCDC62_uc001udf.2_Intron|CCDC62_uc001ude.2_Intron	NM_201435	NP_958843			coiled-coil domain containing 62 isoform b							cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	123404205	123404205	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123404205delG								VPS37B (23493 upstream) : ABCB9 (9335 downstream)																																			---	---	---	---
EIF2B1	1967	broad.mit.edu	37	12	124118041	124118041	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124118041delC	uc001ufm.2	-						GTF2H3_uc001ufo.1_5'Flank|GTF2H3_uc010tau.1_5'Flank|EIF2B1_uc001ufn.2_Intron|EIF2B1_uc010tat.1_Intron	NM_001414	NP_001405			eukaryotic translation initiation factor 2B,						cellular response to stimulus|oligodendrocyte development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex|membrane fraction|plasma membrane	protein binding|translation initiation factor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.67e-05)|Epithelial(86;0.000353)|all cancers(50;0.00489)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	124755001	124755001	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124755001delA								ZNF664 (255034 upstream) : FAM101A (18709 downstream)																																			---	---	---	---
AACS	65985	broad.mit.edu	37	12	125564095	125564095	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125564095delT	uc001uhc.2	+						AACS_uc009zyg.2_Intron|AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Intron	NM_023928	NP_076417			acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)														---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125997395	125997395	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125997395delA	uc001uhe.1	+							NM_052907	NP_443139			transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	126521883	126521891	+	IGR	DEL	AACAACAAC	-	-	rs113871958		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126521883_126521891delAACAACAAC								TMEM132B (378294 upstream) : LOC100128554 (405136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126574033	126574034	+	IGR	INS	-	A	A	rs142528228	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126574033_126574034insA								TMEM132B (430444 upstream) : LOC100128554 (352993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128058240	128058247	+	IGR	DEL	TTCTTTCT	-	-	rs72311715		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128058240_128058247delTTCTTTCT								None (None upstream) : TMEM132C (841044 downstream)																																			---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131151339	131151350	+	Intron	DEL	GGAGGGAGGAAG	-	-	rs148423387		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131151339_131151350delGGAGGGAGGAAG	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
STX2	2054	broad.mit.edu	37	12	131292855	131292855	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131292855delT	uc001uio.2	-						STX2_uc001uip.2_Intron|STX2_uc010tbj.1_Intron	NM_194356	NP_919337			syntaxin 2 isoform 2						acrosome reaction|ectoderm development|intracellular protein transport|organ morphogenesis|signal transduction	basolateral plasma membrane|integral to membrane|microsome|soluble fraction	calcium-dependent protein binding|SNAP receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)														---	---	---	---
RAN	5901	broad.mit.edu	37	12	131359373	131359373	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131359373delT	uc001uir.2	+						RAN_uc010tbk.1_Intron|RAN_uc010tbl.1_Intron|RAN_uc001uis.2_Intron	NM_006325	NP_006316			ras-related nuclear protein						androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	131874396	131874397	+	IGR	INS	-	A	A	rs143800184	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131874396_131874397insA								LOC116437 (176921 upstream) : SFRS8 (321238 downstream)																																			---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132237985	132237985	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132237985delG	uc001uja.1	+						SFRS8_uc010tbn.1_Intron|SFRS8_uc001ujb.1_Intron|SFRS8_uc001uiz.1_Intron	NM_004592	NP_004583			splicing factor, arginine/serine-rich 8						mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)														---	---	---	---
CHFR	55743	broad.mit.edu	37	12	133455060	133455062	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133455060_133455062delAAA	uc001ulf.2	-						CHFR_uc001ulc.1_5'Flank|CHFR_uc001ule.2_Intron|CHFR_uc010tbs.1_Intron|CHFR_uc001uld.2_Intron|CHFR_uc010tbt.1_Intron	NM_001161344	NP_001154816			checkpoint with forkhead and ring finger domains						cell division|mitosis|mitotic cell cycle checkpoint|modification-dependent protein catabolic process|protein polyubiquitination	PML body	nucleotide binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)														---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19668675	19668676	+	Intron	DEL	TT	-	-	rs74880887		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19668675_19668676delTT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19670764	19670764	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19670764delG	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	19761247	19761247	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19761247delT								TUBA3C (5311 upstream) : LOC100101938 (75694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	19801216	19801216	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19801216delT								TUBA3C (45280 upstream) : LOC100101938 (35725 downstream)																																			---	---	---	---
LOC100101938	100101938	broad.mit.edu	37	13	19866329	19866329	+	RNA	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19866329delA	uc010tck.1	-	14		c.2833delT				NR_027248				Homo sapiens cDNA clone IMAGE:5265638.												0																		---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20325238	20325238	+	Intron	DEL	C	-	-	rs9508872	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20325238delC	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20972064	20972065	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20972064_20972065delAA								GJB6 (165530 upstream) : CRYL1 (5744 downstream)																																			---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21951540	21951541	+	Intron	DEL	CT	-	-	rs5802108		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21951540_21951541delCT	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron|uc001uoa.1_5'Flank	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
EFHA1	221154	broad.mit.edu	37	13	22140640	22140641	+	Intron	DEL	TT	-	-	rs78330860		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22140640_22140641delTT	uc001uof.2	-							NM_152726	NP_689939			EF-hand domain family, member A1								calcium ion binding				0		all_cancers(29;1.24e-15)|all_epithelial(30;5.4e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000171)|Epithelial(112;0.000398)|OV - Ovarian serous cystadenocarcinoma(117;0.00641)|Lung(94;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22323943	22323944	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22323943_22323944insA								FGF9 (45303 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22417545	22417546	+	IGR	INS	-	A	A	rs149085740	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22417545_22417546insA								FGF9 (138905 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23269986	23269986	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23269986delT								FGF9 (991346 upstream) : SGCG (485074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23508537	23508538	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23508537_23508538delCA								None (None upstream) : SGCG (246522 downstream)																																			---	---	---	---
MIPEP	4285	broad.mit.edu	37	13	24410203	24410204	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24410203_24410204insT	uc001uox.3	-							NM_005932	NP_005923			mitochondrial intermediate peptidase precursor						protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25034266	25034266	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25034266delA	uc001upl.2	-	18	2248	c.2142delT	c.(2140-2142)TTTfs	p.F714fs	PARP4_uc010tdc.1_Frame_Shift_Del_p.F714fs	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	714	VIT.				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)														---	---	---	---
TPTE2P1	646405	broad.mit.edu	37	13	25523589	25523590	+	Intron	DEL	AT	-	-	rs75695712		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25523589_25523590delAT	uc010tdh.1	-						TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	26809636	26809636	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26809636delT								RNF6 (13128 upstream) : CDK8 (19120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27017082	27017083	+	IGR	INS	-	ATGA	ATGA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27017082_27017083insATGA								CDK8 (38513 upstream) : WASF3 (114757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27808434	27808434	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27808434delC								USP12 (62405 upstream) : RPL21 (17258 downstream)																																			---	---	---	---
RPL21	6144	broad.mit.edu	37	13	27830671	27830671	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27830671delA	uc001ura.2	+	6						NM_000982	NP_000973			ribosomal protein L21						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0		Lung SC(185;0.0156)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0287)|OV - Ovarian serous cystadenocarcinoma(117;0.118)|Epithelial(112;0.139)|GBM - Glioblastoma multiforme(144;0.21)														---	---	---	---
ATP5EP2	432369	broad.mit.edu	37	13	28519646	28519646	+	RNA	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28519646delA	uc001uru.2	+	1		c.304delA				NR_002162				Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit pseudogene 2 (ATP5EP2), transcript variant 6, non-coding RNA.											ovary(1)	1																		---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28886057	28886057	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28886057delA	uc001usb.3	-						FLT1_uc010aap.2_Intron|FLT1_uc010aaq.2_Intron|FLT1_uc001usa.3_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	30065779	30065780	+	Intron	INS	-	TG	TG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30065779_30065780insTG	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron	NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
UBL3	5412	broad.mit.edu	37	13	30346153	30346153	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30346153delT	uc001usp.2	-							NM_007106	NP_009037			ubiquitin-like 3 precursor							intracellular|plasma membrane					0		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)														---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31204893	31204893	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31204893delT	uc001utc.2	+						USPL1_uc001utb.2_Intron|USPL1_uc001utd.2_Intron	NM_005800	NP_005791			ubiquitin specific peptidase like 1						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			pancreas(2)|skin(1)	3		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)														---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31728906	31728906	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31728906delA	uc001utj.2	-						HSPH1_uc001utk.2_Intron|HSPH1_uc010aaw.2_Intron|HSPH1_uc001utl.2_Intron|HSPH1_uc010tds.1_Intron|HSPH1_uc010tdt.1_Intron|HSPH1_uc010aax.1_Intron|HSPH1_uc010aay.1_Intron	NM_006644	NP_006635			heat shock 105kD						positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	31740362	31740363	+	IGR	DEL	GT	-	-	rs7987324	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31740362_31740363delGT								HSPH1 (3860 upstream) : B3GALTL (33749 downstream)																																			---	---	---	---
RXFP2	122042	broad.mit.edu	37	13	32313942	32313942	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32313942delA	uc001utt.2	+						RXFP2_uc010aba.2_Intron	NM_130806	NP_570718			relaxin/insulin-like family peptide receptor 2							integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)														---	---	---	---
RXFP2	122042	broad.mit.edu	37	13	32376253	32376253	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32376253delT	uc001utt.2	+						RXFP2_uc010aba.2_Intron	NM_130806	NP_570718			relaxin/insulin-like family peptide receptor 2							integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32698727	32698727	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32698727delT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32770717	32770718	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32770717_32770718delGT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32868490	32868490	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32868490delT	uc001utx.2	+						FRY_uc010tdw.1_Intron|FRY_uc001utz.2_Intron|FRY_uc010tdx.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32950659	32950659	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32950659delA	uc001uub.1	+							NM_000059	NP_000050			breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
N4BP2L2	10443	broad.mit.edu	37	13	33058621	33058621	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33058621delT	uc010abe.1	-						N4BP2L2_uc010abd.1_Intron|N4BP2L2_uc001uuh.2_Intron|N4BP2L2_uc001uuj.2_Intron|N4BP2L2_uc010tdz.1_Intron	NM_033111	NP_149102			phosphonoformate immuno-associated protein 5												0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33338570	33338570	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33338570delA	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33344888	33344888	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33344888delA	uc010abf.2	+	33	4319	c.4161delA	c.(4159-4161)CCAfs	p.P1387fs	PDS5B_uc010abg.2_RNA	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	1387					cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	33380212	33380213	+	IGR	INS	-	AAG	AAG	rs139142523	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33380212_33380213insAAG								PDS5B (28057 upstream) : KL (209988 downstream)																																			---	---	---	---
SOHLH2	54937	broad.mit.edu	37	13	36798440	36798440	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36798440delA	uc010tei.1	-							NM_017826	NP_060296			spermatogenesis and oogenesis specific basic						cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	37068971	37068971	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37068971delA								CCNA1 (51953 upstream) : C13orf36 (179078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37175014	37175015	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37175014_37175015insG								CCNA1 (157996 upstream) : C13orf36 (73034 downstream)																																			---	---	---	---
UFM1	51569	broad.mit.edu	37	13	38921619	38921619	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38921619delT	uc001uwu.2	+						UFM1_uc010abz.2_5'Flank|UFM1_uc010aca.2_5'Flank	NM_016617	NP_057701			ubiquitin-fold modifier 1 precursor						protein ufmylation	cytoplasm|nucleus	protein binding				0		Lung NSC(96;3.18e-06)|Prostate(109;0.00314)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;1.05e-08)|Epithelial(112;1.44e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000855)|BRCA - Breast invasive adenocarcinoma(63;0.00342)|GBM - Glioblastoma multiforme(144;0.0132)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39600600	39600600	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39600600delA	uc001uwy.2	-						C13orf23_uc001uwz.2_Intron	NM_025138	NP_079414			hypothetical protein LOC80209 isoform 1											ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
NHLRC3	387921	broad.mit.edu	37	13	39618052	39618052	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39618052delA	uc001uxc.2	+						NHLRC3_uc001uxb.1_Intron|NHLRC3_uc001uxd.2_Intron|NHLRC3_uc001uxe.2_Intron	NM_001012754	NP_001012772			NHL repeat containing 3 isoform a							extracellular region				skin(1)	1		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)														---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	40947628	40947628	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40947628delA	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	41017342	41017343	+	Intron	DEL	GT	-	-	rs71772859		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41017342_41017343delGT	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	41301948	41301948	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41301948delT								FOXO1 (61214 upstream) : MIR320D-1 (16 downstream)																																			---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41517026	41517026	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41517026delT	uc001uxs.2	-						ELF1_uc010tfc.1_Intron|ELF1_uc010acd.2_Intron	NM_172373	NP_758961			E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
NAA16	79612	broad.mit.edu	37	13	41941505	41941505	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41941505delT	uc001uyf.2	+						NAA16_uc010tfg.1_Intron	NM_024561	NP_078837			NMDA receptor regulated 1-like protein isoform						N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1																		---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42273417	42273417	+	Intron	DEL	A	-	-	rs145657948	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42273417delA	uc001uyj.2	-							NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42748332	42748332	+	Intron	DEL	A	-	-	rs77403765		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42748332delA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44013377	44013377	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44013377delT	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44302778	44302778	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44302778delA	uc001uzc.3	-							NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44355656	44355657	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44355656_44355657delTT	uc001uzc.3	-							NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	45495353	45495353	+	IGR	DEL	T	-	-	rs11321257		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45495353delT								TSC22D1 (344652 upstream) : NUFIP1 (18031 downstream)																																			---	---	---	---
SLC25A30	253512	broad.mit.edu	37	13	45971487	45971487	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45971487delA	uc001vag.2	-						SLC25A30_uc010tfs.1_Intron|SLC25A30_uc001vah.2_Intron|SLC25A30_uc010tft.1_Intron|SLC25A30_uc001vaf.2_3'UTR	NM_001010875	NP_001010875			solute carrier family 25, member 30						mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding			breast(1)	1		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.95e-05)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46704724	46704725	+	Intron	DEL	TT	-	-	rs35095925		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46704724_46704725delTT	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716270	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269_46716270delAA	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
RB1	5925	broad.mit.edu	37	13	48937186	48937186	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48937186delT	uc001vcb.2	+						RB1_uc010act.1_Intron	NM_000321	NP_000312			retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(5)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	13	49484605	49484605	+	IGR	DEL	A	-	-	rs34536291		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49484605delA								CYSLTR2 (201107 upstream) : FNDC3A (65443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	51472065	51472065	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51472065delT								DLEU7 (54180 upstream) : RNASEH2B (11827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	52449459	52449459	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52449459delT								CCDC70 (9088 upstream) : ATP7B (57347 downstream)																																			---	---	---	---
NEK5	341676	broad.mit.edu	37	13	52686568	52686568	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52686568delG	uc001vge.2	-						NEK5_uc001vgf.2_Intron	NM_199289	NP_954983			NIMA-related kinase 5								ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)														---	---	---	---
THSD1P1	374500	broad.mit.edu	37	13	52857402	52857402	+	RNA	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52857402delA	uc001vgm.1	-	3		c.292delT								Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0																		---	---	---	---
THSD1	55901	broad.mit.edu	37	13	52959072	52959072	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52959072delA	uc001vgo.2	-						THSD1_uc001vgp.2_Intron|THSD1_uc010tgz.1_Intron|THSD1_uc010aea.2_Intron	NM_018676	NP_061146			thrombospondin type I domain-containing 1							extracellular region|integral to membrane|intracellular membrane-bounded organelle				ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	54039335	54039335	+	IGR	DEL	T	-	-	rs113918508		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54039335delT								OLFM4 (413149 upstream) : MIR1297 (846772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55644625	55644625	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55644625delA								MIR1297 (758442 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59415240	59415241	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59415240_59415241insT								None (None upstream) : DIAPH3 (824484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65062164	65062164	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65062164delA								OR7E156P (745463 upstream) : None (None downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	66919506	66919506	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66919506delT	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67030964	67030964	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67030964delA	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67205231	67205232	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67205231_67205232insA	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	68850701	68850701	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68850701delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71469473	71469474	+	IGR	DEL	TG	-	-	rs111635037		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71469473_71469474delTG								ATXN8OS (755588 upstream) : DACH1 (542624 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72131053	72131053	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72131053delT	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937			dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	72854805	72854806	+	IGR	INS	-	GATA	GATA	rs141160029	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72854805_72854806insGATA								DACH1 (413475 upstream) : C13orf37 (427689 downstream)																																			---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73348049	73348049	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73348049delA	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
PIBF1	10464	broad.mit.edu	37	13	73547716	73547716	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73547716delT	uc001vjc.2	+						PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337			progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)														---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74274719	74274720	+	Intron	INS	-	A	A	rs7982643	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74274719_74274720insA	uc001vjf.2	-						KLF12_uc010aeq.2_Intron	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75863376	75863376	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75863376delA	uc001vjl.1	-						TBC1D4_uc010tht.1_Intron|TBC1D4_uc010thu.1_Intron|TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	76039052	76039052	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76039052delT	uc001vjl.1	-						TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76377952	76377952	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76377952delT	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_5'Flank|LMO7_uc001vju.1_Intron	NM_015842	NP_056667			LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76565058	76565058	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76565058delT								LMO7 (131054 upstream) : KCTD12 (889246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76682662	76682662	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76682662delT								LMO7 (248658 upstream) : KCTD12 (771642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77410498	77410499	+	IGR	INS	-	AC	AC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77410498_77410499insAC								LMO7 (976494 upstream) : KCTD12 (43805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	78354702	78354702	+	IGR	DEL	T	-	-	rs112319988		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78354702delT								SLAIN1 (16325 upstream) : EDNRB (114914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79782551	79782554	+	IGR	DEL	GAAT	-	-	rs141704308		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79782551_79782554delGAAT								RNF219 (547851 upstream) : RBM26 (111546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80154613	80154613	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80154613delA								NDFIP2 (24408 upstream) : SPRY2 (755501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80881175	80881175	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80881175delA								NDFIP2 (750970 upstream) : SPRY2 (28939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84470032	84470033	+	IGR	DEL	TT	-	-	rs67208765		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84470032_84470033delTT								SLITRK1 (13504 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88738620	88738621	+	IGR	INS	-	AGAG	AGAG	rs143698292	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88738620_88738621insAGAG								SLITRK5 (406752 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91641164	91641164	+	IGR	DEL	G	-	-	rs35339182		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91641164delG								LOC144776 (62313 upstream) : MIR17HG (358910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91699612	91699612	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91699612delA								LOC144776 (120761 upstream) : MIR17HG (300462 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94075834	94075835	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94075834_94075835insT	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94570712	94570712	+	Intron	DEL	A	-	-	rs35508835		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94570712delA	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95673939	95673939	+	Intron	DEL	A	-	-	rs9524765	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95673939delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	97893477	97893477	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97893477delT	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	98694523	98694526	+	IGR	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98694523_98694526delAAAA								IPO5 (17974 upstream) : FARP1 (100290 downstream)																																			---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99601919	99601919	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99601919delA	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron	NM_015296	NP_056111			dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
TM9SF2	9375	broad.mit.edu	37	13	100192902	100192902	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100192902delT	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791			transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)																	---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100312814	100312815	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100312814_100312815delTG	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100600063	100600063	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100600063delT								CLYBL (55240 upstream) : ZIC5 (15212 downstream)																																			---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101073832	101073832	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101073832delT	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
A2LD1	87769	broad.mit.edu	37	13	101215148	101215148	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101215148delA	uc001vor.2	-							NM_033110	NP_149101			AIG2-like domain 1						cellular modified amino acid catabolic process		acyltransferase activity|gamma-glutamylcyclotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	101412297	101412300	+	IGR	DEL	TCTC	-	-	rs11843124		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101412297_101412300delTCTC								TMTC4 (85194 upstream) : NALCN (293830 downstream)																																			---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101952718	101952719	+	Intron	INS	-	TTCC	TTCC	rs560750	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101952718_101952719insTTCC	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
ITGBL1	9358	broad.mit.edu	37	13	102123884	102123899	+	Intron	DEL	TGTGTGTGTGTGTGTG	-	-	rs66938354	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102123884_102123899delTGTGTGTGTGTGTGTG	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782			integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
BIVM	54841	broad.mit.edu	37	13	103472834	103472834	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103472834delA	uc001vps.2	+						BIVM_uc010agc.2_Intron|ERCC5_uc001vpu.1_Intron|BIVM_uc001vpv.2_5'UTR	NM_017693	NP_060163			basic, immunoglobulin-like variable motif							cytoplasm|nucleus					0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	106367011	106367011	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106367011delT	uc001vqf.1	+											Homo sapiens cDNA FLJ25324 fis, clone TST00330.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	106604590	106604591	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106604590_106604591delAC								DAOA (461208 upstream) : EFNB2 (537507 downstream)																																			---	---	---	---
EFNB2	1948	broad.mit.edu	37	13	107166515	107166515	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107166515delT	uc001vqi.2	-							NM_004093	NP_004084			ephrin B2 precursor						cell differentiation|cell-cell signaling|interspecies interaction between organisms|nervous system development	integral to plasma membrane	ephrin receptor binding			ovary(1)	1	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)																	---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109700758	109700758	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109700758delT	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	109865086	109865086	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109865086delT								MYO16 (4731 upstream) : IRS2 (541100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110124271	110124272	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110124271_110124272delAA								MYO16 (263916 upstream) : IRS2 (281914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110628256	110628256	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110628256delT								IRS2 (189342 upstream) : COL4A1 (173055 downstream)																																			---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110861640	110861640	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110861640delT	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836			alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
RAB20	55647	broad.mit.edu	37	13	111178541	111178542	+	Intron	INS	-	ACTA	ACTA	rs149917215	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111178541_111178542insACTA	uc001vqy.2	-							NM_017817	NP_060287			RAB20, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	all_cancers(4;1.54e-11)|all_epithelial(4;1.22e-06)|all_lung(23;1e-05)|Lung NSC(43;0.000453)|Colorectal(4;0.00323)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.197)															---	---	---	---
CARS2	79587	broad.mit.edu	37	13	111339867	111339867	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111339867delA	uc001vrd.2	-						CARS2_uc010tjm.1_Intron	NM_024537	NP_078813			cysteinyl-tRNA synthetase 2, mitochondrial						cysteinyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|cysteine-tRNA ligase activity|metal ion binding				0	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)													---	---	---	---
ING1	3621	broad.mit.edu	37	13	111367770	111367771	+	5'UTR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111367770_111367771insC	uc001vri.2	+	1					CARS2_uc010tjm.1_5'Flank|uc001vre.2_5'Flank|ING1_uc001vrf.2_Intron|ING1_uc001vrg.2_Intron|ING1_uc001vrh.2_Intron	NM_005537	NP_005528			inhibitor of growth family, member 1 isoform D						cell cycle|negative regulation of cell growth|negative regulation of cell proliferation	nucleus	zinc ion binding			ovary(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111953300	111953302	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111953300_111953302delTTT	uc010tjo.1	+						ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron	NM_003899	NP_003890			PAK-interacting exchange factor beta isoform a						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	113012287	113012288	+	IGR	DEL	GT	-	-	rs113454636		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113012287_113012288delGT								SOX1 (286267 upstream) : C13orf28 (18381 downstream)																																			---	---	---	---
TMCO3	55002	broad.mit.edu	37	13	114193570	114193570	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114193570delT	uc001vtu.3	+							NM_017905	NP_060375			transmembrane and coiled-coil domains 3							integral to membrane	solute:hydrogen antiporter activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	114519182	114519183	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114519182_114519183insG								FAM70B (4287 upstream) : GAS6 (4341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19010254	19010255	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19010254_19010255insG								None (None upstream) : OR11H12 (367339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19044801	19044802	+	IGR	INS	-	AA	AA	rs144525371		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19044801_19044802insAA								None (None upstream) : OR11H12 (332792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19086379	19086379	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19086379delG								None (None upstream) : OR11H12 (291215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19516108	19516108	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19516108delT								OR11H12 (137536 upstream) : POTEG (37257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19900199	19900200	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19900199_19900200insA	uc001vvq.1	-						uc001vvr.1_Intron|uc010ahe.1_Intron|uc001vvs.1_Intron|uc001vvt.2_Intron					Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	20171045	20171045	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20171045delG								P704P (150773 upstream) : OR4Q3 (44542 downstream)																																			---	---	---	---
OR4K1	79544	broad.mit.edu	37	14	20402835	20402835	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20402835delT	uc001vwj.1	+							NM_001004063	NP_001004063			olfactory receptor, family 4, subfamily K,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)														---	---	---	---
PARP2	10038	broad.mit.edu	37	14	20818654	20818654	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20818654delT	uc001vxc.2	+						PARP2_uc001vxd.2_Intron|PARP2_uc001vxb.1_Intron	NM_005484	NP_005475			poly (ADP-ribose) polymerase family, member 2						protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity			ovary(1)|pancreas(1)	2	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)									Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20845375	20845376	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20845375_20845376delAA	uc001vxe.2	-						TEP1_uc010ahk.2_Intron|TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron|TEP1_uc010tlh.1_Intron	NM_007110	NP_009041			telomerase-associated protein 1						telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22056115	22056116	+	IGR	INS	-	AA	AA	rs146872764	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22056115_22056116insAA								OR10G3 (17240 upstream) : OR10G2 (45951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22564928	22564929	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22564928_22564929insA	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22892202	22892202	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22892202delA	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron|uc001wdv.3_Intron|uc001wdt.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
PSMB5	5693	broad.mit.edu	37	14	23502434	23502434	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23502434delA	uc001wii.2	-						PSMB5_uc001wij.2_Intron|PSMB5_uc010tni.1_Intron	NM_002797	NP_002788			proteasome beta 5 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus	protein binding|threonine-type endopeptidase activity			ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	25558321	25558321	+	IGR	DEL	T	-	-	rs7159074	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25558321delT								STXBP6 (39150 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	27643243	27643243	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27643243delG								NOVA1 (576283 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28071290	28071290	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28071290delT	uc010amc.1	-											Homo sapiens cDNA clone IMAGE:40107853.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	29578360	29578361	+	IGR	INS	-	GAAA	GAAA	rs11849529		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29578360_29578361insGAAA								C14orf23 (314361 upstream) : PRKD1 (467328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30709286	30709287	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30709286_30709287delAG								PRKD1 (312387 upstream) : G2E3 (319042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30801074	30801075	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30801074_30801075delTT								PRKD1 (404175 upstream) : G2E3 (227254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	32019217	32019217	+	IGR	DEL	T	-	-	rs112510915		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32019217delT								HEATR5A (92537 upstream) : NUBPL (11374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	32524100	32524100	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32524100delA								NUBPL (193683 upstream) : C14orf128 (20526 downstream)																																			---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	32858612	32858613	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32858612_32858613insT	uc001wrq.2	+						AKAP6_uc010aml.2_Intron	NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33678630	33678630	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33678630delT	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35072492	35072492	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35072492delA	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419			sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)														---	---	---	---
MIPOL1	145282	broad.mit.edu	37	14	38016070	38016070	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38016070delT	uc001wuc.2	+						MIPOL1_uc001wud.2_Intron|MIPOL1_uc010ams.2_Intron|MIPOL1_uc001wue.2_Intron|MIPOL1_uc010amt.2_Intron	NM_138731	NP_620059			mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38214202	38214203	+	Intron	INS	-	AC	AC	rs147986899	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38214202_38214203insAC	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38311287	38311287	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38311287delT	uc001wug.2	+						uc001wuh.2_Intron|uc001wui.2_Intron|uc001wuj.2_Intron					Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
SEC23A	10484	broad.mit.edu	37	14	39517656	39517659	+	Intron	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39517656_39517659delAAAA	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron	NM_006364	NP_006355			SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)														---	---	---	---
SIP1	8487	broad.mit.edu	37	14	39601151	39601151	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39601151delT	uc001wuq.2	+						SIP1_uc001wur.2_Intron|SIP1_uc001wus.2_Intron|SIP1_uc010amx.2_Intron	NM_003616	NP_003607			SMN-interacting protein 1 isoform alpha						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)														---	---	---	---
FBXO33	254170	broad.mit.edu	37	14	39886741	39886741	+	Intron	DEL	T	-	-	rs71842989		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39886741delT	uc001wvk.2	-							NM_203301	NP_976046			F-box protein 33												0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)														---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45398007	45398007	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45398007delT	uc001wvq.2	-	5					KLHL28_uc001wvr.2_3'UTR	NM_017658	NP_060128			BTB (POZ) domain containing 5											ovary(1)	1																		---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47830745	47830746	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47830745_47830746insT	uc001wwj.3	-						MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970			MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	49668672	49668674	+	IGR	DEL	TTC	-	-	rs74310280	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49668672_49668674delTTC								None (None upstream) : SDCCAG1 (364353 downstream)																																			---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50050223	50050223	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50050223delA	uc010anj.1	-						RPS29_uc001wwl.2_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
CDKL1	8814	broad.mit.edu	37	14	50818086	50818086	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50818086delA	uc010anu.1	-						CDKL1_uc001wxz.2_Intron	NM_004196	NP_004187			cyclin-dependent kinase-like 1							cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50941877	50941877	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50941877delA	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50953353	50953353	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50953353delA	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	51764060	51764060	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51764060delA								TMX1 (39690 upstream) : FRMD6 (191795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51907404	51907405	+	IGR	INS	-	AG	AG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51907404_51907405insAG								TMX1 (183034 upstream) : FRMD6 (48450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	52617464	52617464	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52617464delG								NID2 (81518 upstream) : PTGDR (116967 downstream)																																			---	---	---	---
FERMT2	10979	broad.mit.edu	37	14	53326539	53326540	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53326539_53326540delTT	uc001xad.2	-						FERMT2_uc001xac.2_Intron|FERMT2_uc001xae.2_Intron|FERMT2_uc001xaf.2_Intron	NM_006832	NP_006823			fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53681195	53681196	+	IGR	INS	-	G	G	rs137919131	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53681195_53681196insG								DDHD1 (61149 upstream) : BMP4 (735261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54210334	54210334	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54210334delT								DDHD1 (590288 upstream) : BMP4 (206123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54361815	54361818	+	IGR	DEL	CTTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54361815_54361818delCTTC								DDHD1 (741769 upstream) : BMP4 (54639 downstream)																																			---	---	---	---
CNIH	10175	broad.mit.edu	37	14	54894605	54894605	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54894605delA	uc001xat.1	-						CNIH_uc001xav.1_Intron	NM_005776	NP_005767			cornichon-like						immune response|intracellular signal transduction|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane					0				GBM - Glioblastoma multiforme(112;0.00341)														---	---	---	---
FBXO34	55030	broad.mit.edu	37	14	55880258	55880258	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55880258delT	uc001xbv.2	+						KIAA0831_uc001xbx.1_5'Flank	NM_152231				F-box only protein 34											ovary(2)|lung(2)|skin(1)	5																		---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56150851	56150851	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56150851delA	uc001xcb.2	+	46					KTN1_uc001xce.2_3'UTR|KTN1_uc001xcc.2_3'UTR|KTN1_uc001xcd.2_3'UTR|KTN1_uc010trb.1_3'UTR|KTN1_uc010aoq.2_3'UTR|KTN1_uc010trc.1_3'UTR|KTN1_uc001xcg.2_3'UTR	NM_182926	NP_891556			kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7								T	RET	papillary thryoid								---	---	---	---
Unknown	0	broad.mit.edu	37	14	59216860	59216861	+	IGR	INS	-	CTGC	CTGC	rs139495048	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59216860_59216861insCTGC								DACT1 (101824 upstream) : DAAM1 (438538 downstream)																																			---	---	---	---
DAAM1	23002	broad.mit.edu	37	14	59724097	59724097	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59724097delA	uc001xdz.1	+						DAAM1_uc001xea.1_Intron|DAAM1_uc001xeb.1_Intron|DAAM1_uc001xdy.2_Intron	NM_014992	NP_055807			dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)														---	---	---	---
DAAM1	23002	broad.mit.edu	37	14	59835592	59835592	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59835592delT	uc001xdz.1	+	26					DAAM1_uc001xea.1_3'UTR|DAAM1_uc001xec.1_RNA	NM_014992	NP_055807			dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)														---	---	---	---
C14orf149	112849	broad.mit.edu	37	14	59945631	59945632	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59945631_59945632insA	uc001xee.1	-						C14orf149_uc010trx.1_3'UTR	NM_144581	NP_653182			proline racemase-like								proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	61047875	61047875	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61047875delT								SIX6 (69352 upstream) : SIX1 (63543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	62298445	62298445	+	IGR	DEL	T	-	-	rs77981820		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62298445delT								SNAPC1 (35300 upstream) : SYT16 (155358 downstream)																																			---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63842468	63842468	+	3'UTR	DEL	T	-	-	rs34338079		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63842468delT	uc001xgd.1	-	14					PPP2R5E_uc010tsf.1_3'UTR|PPP2R5E_uc010tsg.1_3'UTR|PPP2R5E_uc001xge.2_3'UTR|PPP2R5E_uc010tsh.1_3'UTR	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64444522	64444522	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64444522delT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron	NM_015180	NP_055995			spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	64849796	64849796	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64849796delA								ESR2 (44528 upstream) : MTHFD1 (4963 downstream)																																			---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66166980	66166981	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66166980_66166981insA	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron|FUT8_uc001xis.2_Intron	NM_178155	NP_835368			fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	66447578	66447578	+	IGR	DEL	T	-	-	rs78000217	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66447578delT								FUT8 (237617 upstream) : C14orf53 (505531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66847167	66847168	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66847167_66847168delCA								FUT8 (637206 upstream) : C14orf53 (105941 downstream)																																			---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67240454	67240454	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67240454delT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67490462	67490462	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67490462delA	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
ATP6V1D	51382	broad.mit.edu	37	14	67809927	67809927	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67809927delT	uc001xjf.2	-						ATP6V1D_uc001xje.2_Intron	NM_015994	NP_057078			H(+)-transporting two-sector ATPase						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting two-sector ATPase complex, catalytic domain|vacuolar proton-transporting V-type ATPase complex	protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)|lung(1)	2				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)														---	---	---	---
EIF2S1	1965	broad.mit.edu	37	14	67831425	67831425	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67831425delT	uc001xjg.2	+							NM_004094	NP_004085			eukaryotic translation initiation factor 2,							cytosol|eukaryotic translation initiation factor 2 complex|polysome|stress granule	protein binding|ribosome binding|translation initiation factor activity			ovary(1)	1				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)														---	---	---	---
KIAA0247	9766	broad.mit.edu	37	14	70122358	70122359	+	Intron	DEL	AA	-	-	rs75751166		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70122358_70122359delAA	uc001xlk.2	+						KIAA0247_uc010aqz.2_Intron	NM_014734	NP_055549			hypothetical protein LOC9766 precursor							integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70283160	70283161	+	IGR	INS	-	C	C	rs147540074	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70283160_70283161insC								SLC10A1 (19154 upstream) : SMOC1 (62982 downstream)																																			---	---	---	---
SLC8A3	6547	broad.mit.edu	37	14	70546954	70546954	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70546954delT	uc001xly.2	-						SLC8A3_uc001xlu.2_5'Flank|SLC8A3_uc001xlv.2_5'Flank|SLC8A3_uc001xlw.2_Intron|SLC8A3_uc001xlx.2_Intron|SLC8A3_uc001xlz.2_Intron|SLC8A3_uc010ara.2_Intron|SLC8A3_uc001xma.2_5'Flank	NM_183002	NP_892114			solute carrier family 8 (sodium/calcium						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)														---	---	---	---
TTC9	23508	broad.mit.edu	37	14	71114076	71114076	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71114076delG	uc001xmi.2	+							NM_015351	NP_056166			tetratricopeptide repeat domain 9								binding				0				all cancers(60;0.00545)|BRCA - Breast invasive adenocarcinoma(234;0.00747)|OV - Ovarian serous cystadenocarcinoma(108;0.0538)														---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71267150	71267150	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71267150delA	uc001xmm.2	-						MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71493712	71493712	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71493712delA	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71502647	71502647	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71502647delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	71967030	71967030	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71967030delC	uc001xmr.1	+											Homo sapiens high-risk human papilloma viruses E6 oncoproteins targeted protein E6TP1 alpha mRNA, complete cds.						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72054805	72054805	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72054805delA	uc001xms.2	+	2	564	c.216delA	c.(214-216)CCAfs	p.P72fs	SIPA1L1_uc001xmt.2_Frame_Shift_Del_p.P72fs|SIPA1L1_uc001xmu.2_Frame_Shift_Del_p.P72fs|SIPA1L1_uc001xmv.2_Frame_Shift_Del_p.P72fs	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	72					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
DCAF4	26094	broad.mit.edu	37	14	73414036	73414036	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73414036delA	uc001xng.2	+						DCAF4_uc001xnj.2_Intron|DCAF4_uc010ttr.1_Intron|DCAF4_uc001xnh.2_Intron|DCAF4_uc010tts.1_Intron|DCAF4_uc010ttt.1_Intron|DCAF4_uc001xni.2_Intron|DCAF4_uc001xnk.2_Intron	NM_015604	NP_056419			DDB1 and CUL4 associated factor 4 isoform 1							CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73578581	73578581	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73578581delA	uc001xno.2	+						RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73578681	73578681	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73578681delT	uc001xno.2	+						RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
HEATR4	399671	broad.mit.edu	37	14	73993133	73993134	+	Intron	INS	-	GT	GT			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73993133_73993134insGT	uc010tub.1	-						HEATR4_uc010tua.1_Intron	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)														---	---	---	---
ACOT6	641372	broad.mit.edu	37	14	74081792	74081793	+	5'Flank	INS	-	A	A	rs141164878		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74081792_74081793insA	uc001xop.2	+							NM_001037162	NP_001032239			acyl-CoA thioesterase 6							cytosol	carboxylesterase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00331)														---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74125865	74125867	+	Intron	DEL	TTT	-	-	rs36115036		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74125865_74125867delTTT	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615			axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)														---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74153808	74153808	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74153808delA	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615			axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)														---	---	---	---
ZNF410	57862	broad.mit.edu	37	14	74364949	74364949	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74364949delA	uc001xoz.1	+	5	746	c.564delA	c.(562-564)GCAfs	p.A188fs	ZNF410_uc001xoy.1_RNA|ZNF410_uc010ary.1_RNA|ZNF410_uc010tuf.1_RNA|ZNF410_uc010tug.1_5'UTR|ZNF410_uc010tuh.1_Frame_Shift_Del_p.A115fs|ZNF410_uc010tui.1_RNA|ZNF410_uc010arz.1_Frame_Shift_Del_p.A205fs|ZNF410_uc001xpa.1_Frame_Shift_Del_p.Q2fs|ZNF410_uc001xpb.1_Frame_Shift_Del_p.A188fs|ZNF410_uc001xpc.1_Frame_Shift_Del_p.A135fs|ZNF410_uc010tuj.1_Frame_Shift_Del_p.Q2fs	NM_021188	NP_067011	Q86VK4	ZN410_HUMAN	zinc finger protein 410	188					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00369)														---	---	---	---
ENTPD5	957	broad.mit.edu	37	14	74441598	74441598	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74441598delC	uc010tuo.1	-						ENTPD5_uc001xpi.2_Intron	NM_001249	NP_001240			ectonucleoside triphosphate diphosphohydrolase 5						'de novo' posttranslational protein folding|ATP metabolic process|cell growth|cell proliferation|glycolysis|protein N-linked glycosylation|regulation of phosphatidylinositol 3-kinase cascade	endoplasmic reticulum lumen	guanosine-diphosphatase activity|uridine-diphosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00394)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74746551	74746551	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74746551delT								VSX2 (17117 upstream) : ABCD4 (5429 downstream)																																			---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75171747	75171748	+	Intron	DEL	TT	-	-	rs71943049		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75171747_75171748delTT	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron|KIAA0317_uc001xqc.2_Intron|KIAA0317_uc001xqd.1_Intron	NM_001039479	NP_001034568			hypothetical protein LOC9870						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77106505	77106505	+	IGR	DEL	G	-	-	rs850741	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77106505delG								ESRRB (138327 upstream) : VASH1 (121730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77170470	77170471	+	IGR	INS	-	T	T	rs140908043	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77170470_77170471insT								ESRRB (202292 upstream) : VASH1 (57764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77595947	77595947	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77595947delC								KIAA1737 (12318 upstream) : ZDHHC22 (1667 downstream)																																			---	---	---	---
POMT2	29954	broad.mit.edu	37	14	77767163	77767163	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77767163delA	uc001xti.2	-						POMT2_uc001xth.1_5'UTR|POMT2_uc010asr.2_Intron	NM_013382	NP_037514			protein-O-mannosyltransferase 2						protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81005054	81005054	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81005054delT	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81302906	81302906	+	Intron	DEL	T	-	-	rs111834655		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81302906delT	uc001xux.2	-						C14orf145_uc010asz.1_5'Flank|C14orf145_uc001xuz.2_Intron|C14orf145_uc001xuy.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81422338	81422339	+	Intron	INS	-	TG	TG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81422338_81422339insTG	uc001xvd.1	+						C14orf145_uc001xva.1_Intron|TSHR_uc001xvb.1_Intron|TSHR_uc001xvc.2_Intron|TSHR_uc010tvs.1_Intron	NM_000369	NP_000360			thyroid stimulating hormone receptor isoform 1						cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						---	---	---	---
GTF2A1	2957	broad.mit.edu	37	14	81654965	81654966	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81654965_81654966insA	uc001xvf.1	-						GTF2A1_uc010atb.1_Intron|GTF2A1_uc001xvg.1_Intron	NM_015859	NP_056943			TFIIA alpha, p55 isoform 1						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|transcription factor TFIIA complex	DNA binding|protein binding|protein heterodimerization activity|TBP-class protein binding|transcription coactivator activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0287)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	83780221	83780221	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83780221delT								None (None upstream) : None (None downstream)																																			---	---	---	---
FLRT2	23768	broad.mit.edu	37	14	86073285	86073285	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86073285delT	uc001xvr.2	+						FLRT2_uc010atd.2_Intron	NM_013231	NP_037363			fibronectin leucine rich transmembrane protein 2						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)														---	---	---	---
FLRT2	23768	broad.mit.edu	37	14	86090075	86090075	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86090075delA	uc001xvr.2	+	2					FLRT2_uc010atd.2_3'UTR	NM_013231	NP_037363			fibronectin leucine rich transmembrane protein 2						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	86342075	86342075	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86342075delA								FLRT2 (247806 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90822304	90822305	+	IGR	INS	-	AGTC	AGTC	rs138102588	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90822304_90822305insAGTC								C14orf102 (24025 upstream) : CALM1 (41068 downstream)																																			---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91170936	91170936	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91170936delA	uc001xyp.2	-							NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92491769	92491769	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92491769delA	uc001xzy.2	-							NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
BTBD7	55727	broad.mit.edu	37	14	93709547	93709548	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93709547_93709548delTT	uc001ybo.2	-						BTBD7_uc010aur.2_Intron|BTBD7_uc010two.1_Intron|BTBD7_uc001ybp.2_Intron	NM_001002860	NP_001002860			BTB (POZ) domain containing 7 isoform 1											pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)														---	---	---	---
PRIMA1	145270	broad.mit.edu	37	14	94223546	94223549	+	Intron	DEL	AAGG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94223546_94223549delAAGG	uc001ybw.1	-						PRIMA1_uc001ybx.1_Intron	NM_178013	NP_821092			proline rich membrane anchor 1 precursor						neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)|skin(1)	2		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	95117650	95117651	+	IGR	INS	-	AG	AG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95117650_95117651insAG								SERPINA13 (4320 upstream) : GSC (116910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98449910	98449910	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98449910delA								C14orf64 (5449 upstream) : C14orf177 (728040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98586954	98586955	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98586954_98586955delTT								C14orf64 (142493 upstream) : C14orf177 (590995 downstream)																																			---	---	---	---
EML1	2009	broad.mit.edu	37	14	100376546	100376547	+	Intron	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100376546_100376547delAT	uc001ygs.2	+						EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425			echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)																---	---	---	---
MIR544	664613	broad.mit.edu	37	14	101515057	101515057	+	RNA	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101515057delT	hsa-mir-544|MI0003515	+			c.63delT			MIR655_hsa-mir-655|MI0003677_5'Flank																	0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	102116598	102116599	+	IGR	INS	-	G	G	rs142761235	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102116598_102116599insG								DIO3 (86809 upstream) : C14orf72 (80175 downstream)																																			---	---	---	---
WDR20	91833	broad.mit.edu	37	14	102653747	102653747	+	Intron	DEL	G	-	-	rs67079462		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102653747delG	uc001ykz.2	+						WDR20_uc001yky.1_Intron|WDR20_uc001yla.2_Intron|WDR20_uc001ylb.2_Intron|WDR20_uc010txu.1_Intron|WDR20_uc001ylc.2_Intron|WDR20_uc001yld.2_Intron|WDR20_uc001yle.2_Intron|WDR20_uc001ylf.2_Intron	NM_144574	NP_653175			WD repeat domain 20 isoform 2												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	102999637	102999637	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102999637delA								ANKRD9 (23509 upstream) : RCOR1 (59596 downstream)																																			---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103180720	103180720	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103180720delT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
CDC42BPB	9578	broad.mit.edu	37	14	103441860	103441860	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103441860delA	uc001ymi.1	-							NM_006035	NP_006026			CDC42-binding protein kinase beta						actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)														---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105412200	105412200	+	Frame_Shift_Del	DEL	G	-	-	rs55752740		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105412200delG	uc010axc.1	-	7	9708	c.9588delC	c.(9586-9588)CCCfs	p.P3196fs	AHNAK2_uc001ypx.2_Frame_Shift_Del_p.P3096fs	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3196						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106015709	106015710	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106015709_106015710delAA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106131549	106131550	+	Intron	DEL	TT	-	-	rs139899819		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106131549_106131550delTT	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
KIAA0125	9834	broad.mit.edu	37	14	106368654	106368654	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106368654delG	uc001ysq.2	+						ADAM6_uc010tyt.1_Intron|KIAA0125_uc001ysr.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20144683	20144683	+	IGR	DEL	C	-	-	rs143228371		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20144683delC								None (None upstream) : GOLGA6L6 (592411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20164415	20164415	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20164415delA								None (None upstream) : GOLGA6L6 (572679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20394609	20394610	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20394609_20394610insA								None (None upstream) : GOLGA6L6 (342484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20488228	20488229	+	Splice_Site	INS	-	TGAA	TGAA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20488228_20488229insTGAA	uc001ytf.1	+	1		c.231_splice	c.e1+1							full-length cDNA clone CS0DI026YN18 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20509327	20509343	+	IGR	DEL	TGGCCCTGGCCCTGTCT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20509327_20509343delTGGCCCTGGCCCTGTCT								None (None upstream) : GOLGA6L6 (227751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20556972	20556973	+	IGR	INS	-	C	C	rs55977129		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20556972_20556973insC								None (None upstream) : GOLGA6L6 (180121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20607082	20607082	+	Intron	DEL	A	-	-	rs28755877		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20607082delA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	21910501	21910501	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21910501delT								NF1P1 (775876 upstream) : LOC646214 (22013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21923491	21923493	+	IGR	DEL	AGA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21923491_21923493delAGA								NF1P1 (788866 upstream) : LOC646214 (9021 downstream)																																			---	---	---	---
POTEB	339010	broad.mit.edu	37	15	22070888	22070889	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22070888_22070889insT	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238			protein expressed in prostate, ovary, testis,												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	22492135	22492136	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22492135_22492136insC								OR4N3P (77750 upstream) : MIR1268 (21093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22527913	22527913	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22527913delT								MIR1268 (14633 upstream) : GOLGA8DP (174372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22567982	22567982	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22567982delA								MIR1268 (54702 upstream) : GOLGA8DP (134303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22812763	22812763	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22812763delT								GOLGA6L1 (66761 upstream) : TUBGCP5 (20632 downstream)																																			---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22843168	22843168	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22843168delC	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
NIPA2	81614	broad.mit.edu	37	15	23005669	23005670	+	3'UTR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23005669_23005670insT	uc001yux.2	-	8					NIPA2_uc001yuy.2_3'UTR|NIPA2_uc001yuz.2_3'UTR|NIPA2_uc001yva.2_3'UTR|NIPA2_uc001yvb.2_3'UTR|NIPA2_uc010ayb.2_3'UTR	NM_030922	NP_112184			non imprinted in Prader-Willi/Angelman syndrome							early endosome|integral to membrane|plasma membrane				haematopoietic_and_lymphoid_tissue(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	23685826	23685828	+	IGR	DEL	TCT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23685826_23685828delTCT								GOLGA8E (237403 upstream) : MKRN3 (124626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23805776	23805776	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23805776delT								GOLGA8E (357353 upstream) : MKRN3 (4678 downstream)																																			---	---	---	---
PWRN1	791114	broad.mit.edu	37	15	24811788	24811788	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24811788delT	uc001ywm.2	+						PWRN1_uc001ywn.2_Intron					Homo sapiens cDNA FLJ25418 fis, clone TST03512.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	25025721	25025722	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25025721_25025722delTT								C15orf2 (97129 upstream) : SNRPN (43072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	25283798	25283798	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25283798delA								PAR-SN (17300 upstream) : SNORD109B (3323 downstream)																																			---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25600932	25600933	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25600932_25600933delTT	uc001zaq.2	-						uc001zae.2_Intron|UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453			ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	25759125	25759126	+	IGR	INS	-	TG	TG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25759125_25759126insTG								UBE3A (74997 upstream) : ATP10A (164736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26220209	26220210	+	IGR	INS	-	ATCC	ATCC	rs150816390	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26220209_26220210insATCC								ATP10A (109892 upstream) : GABRB3 (568485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26299642	26299643	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26299642_26299643delAG								ATP10A (189325 upstream) : GABRB3 (489052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26654871	26654871	+	IGR	DEL	A	-	-	rs113031284		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26654871delA								ATP10A (544554 upstream) : GABRB3 (133824 downstream)																																			---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27523204	27523204	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27523204delT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28195176	28195176	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28195176delA	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				---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28235602	28235602	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28235602delA	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				---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28499435	28499435	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28499435delA	uc001zbj.2	-							NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	28751705	28751706	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28751705_28751706delTT								GOLGA8G (114534 upstream) : WHAMML2 (231023 downstream)																																			---	---	---	---
APBA2	321	broad.mit.edu	37	15	29350716	29350716	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29350716delA	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron	NM_005503	NP_005494			amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29590078	29590078	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29590078delA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30049558	30049559	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30049558_30049559insT	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248			tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	30314203	30314203	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30314203delA								TJP1 (199497 upstream) : FAM7A3 (81732 downstream)																																			---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31359898	31359898	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31359898delT	uc001zfm.2	-						TRPM1_uc010azy.2_Intron|TRPM1_uc001zfl.2_Intron|uc010ubm.1_5'Flank|MIR211_hsa-mir-211|MI0000287_5'Flank|uc010ubn.1_5'Flank	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
ARHGAP11A	9824	broad.mit.edu	37	15	32927960	32927960	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32927960delT	uc001zgy.1	+						ARHGAP11A_uc010ubw.1_Intron|ARHGAP11A_uc001zgw.2_Intron|ARHGAP11A_uc001zgx.2_Intron|ARHGAP11A_uc010ubx.1_Intron	NM_014783	NP_055598			Rho GTPase activating protein 11A isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	33533212	33533212	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33533212delT								FMN1 (173127 upstream) : RYR3 (69965 downstream)																																			---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34117948	34117948	+	Intron	DEL	C	-	-	rs59294324		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34117948delC	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
AVEN	57099	broad.mit.edu	37	15	34239737	34239737	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34239737delA	uc001zhj.2	-							NM_020371	NP_065104			cell death regulator aven						anti-apoptosis|apoptosis	endomembrane system|intracellular|membrane|membrane fraction	protein binding			kidney(1)	1		all_lung(180;1.78e-08)		all cancers(64;1.66e-15)|GBM - Glioblastoma multiforme(113;1.42e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0359)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	34781959	34781960	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34781959_34781960insG								GOLGA8A (99958 upstream) : GOLGA8B (35525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35423887	35423887	+	IGR	DEL	A	-	-	rs79341832		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35423887delA								ZNF770 (143433 upstream) : LOC723972 (105640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36040312	36040312	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36040312delG	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	36164649	36164649	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36164649delA								ATPBD4 (326245 upstream) : C15orf41 (707163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36696291	36696291	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36696291delA								ATPBD4 (857887 upstream) : C15orf41 (175521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38382361	38382362	+	IGR	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38382361_38382362delTC								TMCO5A (122436 upstream) : SPRED1 (162690 downstream)																																			---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38792549	38792549	+	Intron	DEL	G	-	-	rs12904148	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38792549delG	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38895776	38895776	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38895776delA								RASGRP1 (38769 upstream) : C15orf53 (93023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39083130	39083130	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39083130delC								C15orf53 (90891 upstream) : C15orf54 (459755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39396569	39396569	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39396569delA								C15orf53 (404330 upstream) : C15orf54 (146316 downstream)																																			---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40099171	40099171	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40099171delA	uc001zkj.1	-						GPR176_uc010uck.1_Intron	NM_007223	NP_009154			G protein-coupled receptor 176						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)														---	---	---	---
DNAJC17	55192	broad.mit.edu	37	15	41060071	41060071	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41060071delA	uc001zms.1	-	11					C15orf62_uc010bby.2_5'Flank	NM_018163	NP_060633			DnaJ (Hsp40) homolog, subfamily C, member 17						protein folding		heat shock protein binding|nucleotide binding|RNA binding|unfolded protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	41180111	41180111	+	IGR	DEL	A	-	-	rs111240197		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41180111delA								RHOV (13624 upstream) : VPS18 (6517 downstream)																																			---	---	---	---
EXD1	161829	broad.mit.edu	37	15	41508830	41508830	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41508830delA	uc001znk.2	-						EXD1_uc010ucv.1_Intron	NM_152596	NP_689809			exonuclease 3'-5' domain containing 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding			ovary(1)	1																		---	---	---	---
TMEM62	80021	broad.mit.edu	37	15	43475845	43475845	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43475845delT	uc001zqr.2	+						TMEM62_uc010bda.2_Intron|TMEM62_uc001zqt.2_Intron|CCNDBP1_uc001zqu.2_5'Flank|CCNDBP1_uc001zqv.2_5'Flank|CCNDBP1_uc010bdc.2_5'Flank|CCNDBP1_uc010bdb.2_5'Flank|CCNDBP1_uc010udl.1_5'Flank|CCNDBP1_uc001zqw.2_5'Flank|CCNDBP1_uc001zqx.2_5'Flank|CCNDBP1_uc010bdd.2_5'Flank|CCNDBP1_uc001zqy.2_5'Flank	NM_024956	NP_079232			transmembrane protein 62							integral to membrane				ovary(1)|breast(1)	2		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)														---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44067474	44067474	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44067474delA	uc001zsw.1	-						ELL3_uc001zsv.1_Intron|ELL3_uc001zsx.1_Intron|uc001zsy.2_5'Flank	NM_025165	NP_079441			elongation factor RNA polymerase II-like 3						positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
FRMD5	84978	broad.mit.edu	37	15	44356786	44356787	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44356786_44356787insA	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281			FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	46475132	46475132	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46475132delT								SQRDL (491654 upstream) : None (None downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	48057375	48057375	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48057375delT	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvx.1_3'UTR|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871			semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
MYEF2	50804	broad.mit.edu	37	15	48444345	48444345	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48444345delT	uc001zwi.3	-						MYEF2_uc001zwg.3_5'Flank|MYEF2_uc001zwh.3_5'UTR|MYEF2_uc001zwj.3_Intron	NM_016132	NP_057216			myelin expression factor 2						transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
GALK2	2585	broad.mit.edu	37	15	49488016	49488016	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49488016delT	uc001zxj.1	+						GALK2_uc001zxi.1_Intron|GALK2_uc010ufb.1_Intron|GALK2_uc001zxk.2_Intron|GALK2_uc010ufc.1_Intron	NM_002044	NP_002035			galactokinase 2 isoform 1						galactose metabolic process	cytoplasm	ATP binding|galactokinase activity|N-acetylgalactosamine kinase activity			breast(1)	1		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)														---	---	---	---
C15orf33	196951	broad.mit.edu	37	15	49786781	49786781	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49786781delT	uc001zxl.2	-						C15orf33_uc001zxm.2_Intron	NM_152647	NP_689860			hypothetical protein LOC196951											ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)														---	---	---	---
C15orf33	196951	broad.mit.edu	37	15	49854745	49854745	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49854745delA	uc001zxl.2	-						C15orf33_uc001zxm.2_Intron	NM_152647	NP_689860			hypothetical protein LOC196951											ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)														---	---	---	---
CYP19A1	1588	broad.mit.edu	37	15	51510860	51510860	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51510860delA	uc001zyz.3	-						CYP19A1_uc001zza.3_Intron|CYP19A1_uc001zzb.2_Intron|CYP19A1_uc001zzc.1_5'Flank	NM_031226	NP_112503			cytochrome P450, family 19						estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)													---	---	---	---
CYP19A1	1588	broad.mit.edu	37	15	51595751	51595751	+	Intron	DEL	T	-	-	rs72175503		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51595751delT	uc001zyz.3	-						CYP19A1_uc001zza.3_Intron|CYP19A1_uc001zzb.2_Intron|CYP19A1_uc010bey.1_Intron|CYP19A1_uc001zze.1_Intron|uc010ufw.1_5'Flank|uc002aau.1_5'Flank|uc002aav.1_5'Flank|uc002aaw.2_5'Flank|uc002aax.2_5'Flank|uc010ufx.1_5'Flank	NM_031226	NP_112503			cytochrome P450, family 19						estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)													---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51772718	51772718	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51772718delA	uc002abf.2	-						DMXL2_uc002abd.2_Intron|DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron	NM_015263	NP_056078			Dmx-like 2							cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
TMOD2	29767	broad.mit.edu	37	15	52073168	52073169	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52073168_52073169insT	uc002abk.2	+						TMOD2_uc002abl.3_Intron|TMOD2_uc010bfb.2_Intron	NM_014548	NP_055363			neuronal tropomodulin isoform a						nervous system development	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(2)	2				all cancers(107;0.00435)														---	---	---	---
MYO5C	55930	broad.mit.edu	37	15	52513603	52513603	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52513603delT	uc010bff.2	-						MYO5C_uc010uga.1_Intron	NM_018728	NP_061198			myosin VC							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53604534	53604534	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53604534delT								ONECUT1 (522325 upstream) : WDR72 (201404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53725234	53725234	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53725234delA								ONECUT1 (643025 upstream) : WDR72 (80704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	54173334	54173335	+	IGR	DEL	TG	-	-	rs35342295		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54173334_54173335delTG								WDR72 (121475 upstream) : UNC13C (131766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55343830	55343830	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55343830delT								UNC13C (423025 upstream) : RSL24D1 (129691 downstream)																																			---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55723120	55723120	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55723120delT	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55726958	55726958	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55726958delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56531476	56531476	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56531476delT	uc010bfn.2	-							NM_022841	NP_073752			regulatory factor X domain containing 2						regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	56969746	56969746	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56969746delA	uc002adu.2	-						ZNF280D_uc002adv.2_Intron|ZNF280D_uc010bfq.2_Intron|ZNF280D_uc002adw.1_Intron|ZNF280D_uc010bfr.1_Intron|ZNF280D_uc010bfp.2_Intron	NM_017661	NP_060131			suppressor of hairy wing homolog 4 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)														---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57836003	57836003	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57836003delC	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255			cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58271837	58271837	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58271837delA	uc002aex.2	-						ALDH1A2_uc002aey.2_Intron|ALDH1A2_uc010ugv.1_Intron|ALDH1A2_uc010ugw.1_Intron|ALDH1A2_uc002aew.2_Intron	NM_003888	NP_003879			aldehyde dehydrogenase 1A2 isoform 1						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
GTF2A2	2958	broad.mit.edu	37	15	59948786	59948786	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59948786delA	uc002agg.2	-							NM_004492	NP_004483			general transcription factor IIA, 2, 12kDa						interspecies interaction between organisms|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex	protein heterodimerization activity|protein homodimerization activity|TBP-class protein binding|transcription coactivator activity			central_nervous_system(2)	2																		---	---	---	---
BNIP2	663	broad.mit.edu	37	15	59961571	59961571	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59961571delA	uc010uhc.1	-						BNIP2_uc002agi.3_5'Flank|BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321			BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1																		---	---	---	---
NARG2	79664	broad.mit.edu	37	15	60716481	60716482	+	Intron	INS	-	A	A	rs139152945	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60716481_60716482insA	uc002agp.2	-						NARG2_uc002ago.2_Intron	NM_024611	NP_078887			NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2																		---	---	---	---
NARG2	79664	broad.mit.edu	37	15	60745782	60745782	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60745782delA	uc002agp.2	-						NARG2_uc002ago.2_Intron|NARG2_uc002agq.3_Intron|NARG2_uc010bgk.2_Frame_Shift_Del_p.F382fs	NM_024611	NP_078887			NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61334579	61334580	+	Intron	INS	-	AC	AC	rs141791344	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61334579_61334580insAC	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62154635	62154635	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62154635delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62173853	62173854	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62173853_62173854insA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62284088	62284089	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62284088_62284089delTT	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	63014438	63014438	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63014438delT	uc002alb.3	+							NM_015059	NP_055874			talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
CA12	771	broad.mit.edu	37	15	63620537	63620538	+	Intron	DEL	CT	-	-	rs113264382		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63620537_63620538delCT	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209			carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)													---	---	---	---
SPG21	51324	broad.mit.edu	37	15	65266813	65266813	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65266813delA	uc002aod.2	-						SPG21_uc002aoe.2_Intron|SPG21_uc010bhb.2_Intron|SPG21_uc010bhc.2_Intron	NM_001127889	NP_001121361			spastic paraplegia 21 isoform a						cell death	cytosol|endosome membrane|trans-Golgi network transport vesicle	CD4 receptor binding				0																		---	---	---	---
MTFMT	123263	broad.mit.edu	37	15	65295301	65295304	+	3'UTR	DEL	AAAA	-	-	rs140680377		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65295301_65295304delAAAA	uc002aof.3	-	9						NM_139242	NP_640335			mitochondrial methionyl-tRNA formyltransferase							mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)													---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66368542	66368549	+	Intron	DEL	GGATGGAT	-	-	rs72045221		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66368542_66368549delGGATGGAT	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	66670994	66670994	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66670994delA								TIPIN (21940 upstream) : MAP2K1 (8217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	66925896	66925897	+	Intron	INS	-	C	C	rs141920516	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66925896_66925897insC	uc002aqe.2	+											Homo sapiens cDNA FLJ38816 fis, clone LIVER2007568.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	67252044	67252047	+	IGR	DEL	TGTG	-	-	rs72016504		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67252044_67252047delTGTG								SMAD6 (177709 upstream) : SMAD3 (106148 downstream)																																			---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67421440	67421440	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67421440delC	uc002aqj.2	+						SMAD3_uc010ujr.1_Intron	NM_005902	NP_005893			mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	68251939	68251939	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68251939delA								LBXCOR1 (125765 upstream) : PIAS1 (94633 downstream)																																			---	---	---	---
CLN6	54982	broad.mit.edu	37	15	68544175	68544178	+	Intron	DEL	AATT	-	-	rs34789893		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68544175_68544178delAATT	uc010ujz.1	-							NM_017882	NP_060352			CLN6 protein						cell death|cholesterol metabolic process|ganglioside metabolic process|glycosaminoglycan metabolic process|lysosomal lumen acidification|positive regulation of proteolysis|protein catabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	protein homodimerization activity				0																		---	---	---	---
ANP32A	8125	broad.mit.edu	37	15	69072347	69072348	+	3'UTR	DEL	GG	-	-	rs3214818		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69072347_69072348delGG	uc002arl.2	-	7						NM_006305	NP_006296			acidic (leucine-rich) nuclear phosphoprotein 32						intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
NOX5	79400	broad.mit.edu	37	15	69301738	69301738	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69301738delT	uc002arp.1	+						NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002aro.2_Intron	NM_024505	NP_078781			NADPH oxidase, EF-hand calcium binding domain 5						angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2																		---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69715488	69715488	+	Intron	DEL	C	-	-	rs7180624	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69715488delC	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron|KIF23_uc010bih.1_Intron	NM_138555	NP_612565			kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69727950	69727950	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69727950delT	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron|KIF23_uc010bih.1_Intron	NM_138555	NP_612565			kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69729100	69729101	+	Intron	DEL	TT	-	-	rs72161188		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69729100_69729101delTT	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron	NM_138555	NP_612565			kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	69989665	69989666	+	IGR	DEL	AG	-	-	rs111329880		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69989665_69989666delAG								LOC145837 (125886 upstream) : C15orf50 (137907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70817473	70817473	+	IGR	DEL	T	-	-	rs35599353		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70817473delT								TLE3 (427217 upstream) : UACA (129422 downstream)																																			---	---	---	---
LRRC49	54839	broad.mit.edu	37	15	71179211	71179211	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71179211delA	uc002asu.2	+						THAP10_uc002asv.2_Intron	NM_017691	NP_060161			leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1																		---	---	---	---
LRRC49	54839	broad.mit.edu	37	15	71341735	71341735	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71341735delT	uc002asw.2	+						LRRC49_uc002asu.2_Intron|LRRC49_uc002asx.2_Intron|LRRC49_uc010ukf.1_Intron|LRRC49_uc002asy.2_Intron|LRRC49_uc002asz.2_Intron	NM_017691	NP_060161			leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	73034502	73034503	+	IGR	INS	-	G	G	rs147920536	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73034502_73034503insG								BBS4 (3686 upstream) : ADPGK (9207 downstream)																																			---	---	---	---
LOXL1	4016	broad.mit.edu	37	15	74235166	74235166	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74235166delC	uc002awc.1	+							NM_005576	NP_005567			lysyl oxidase-like 1 preproprotein						protein deamination	extracellular space	copper ion binding				0																		---	---	---	---
CCDC33	80125	broad.mit.edu	37	15	74597291	74597291	+	Intron	DEL	T	-	-	rs5813756		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74597291delT	uc002axo.2	+						CCDC33_uc002axp.2_Intron	NM_025055	NP_079331			coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5																		---	---	---	---
SEMA7A	8482	broad.mit.edu	37	15	74724444	74724444	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74724444delG	uc002axv.2	-						SEMA7A_uc010ulk.1_Intron|SEMA7A_uc010ull.1_Intron	NM_003612	NP_003603			semaphorin 7A isoform 1 preproprotein						axon guidance|immune response|inflammatory response|integrin-mediated signaling pathway|positive regulation of axon extension|positive regulation of ERK1 and ERK2 cascade|positive regulation of macrophage cytokine production|regulation of inflammatory response	anchored to membrane|external side of plasma membrane	receptor activity			breast(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	74783278	74783278	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74783278delT								UBL7 (29749 upstream) : ARID3B (50270 downstream)																																			---	---	---	---
EDC3	80153	broad.mit.edu	37	15	74947009	74947010	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74947009_74947010delTT	uc002ayn.2	-						EDC3_uc002ayo.2_Intron|EDC3_uc002aym.2_Intron	NM_001142443	NP_001135915			enhancer of mRNA decapping 3						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75066269	75066269	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75066269delT								CYP1A2 (17328 upstream) : CSK (8156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	75283680	75283680	+	IGR	DEL	T	-	-	rs113795651		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75283680delT								RPP25 (33905 upstream) : SCAMP5 (4221 downstream)																																			---	---	---	---
SCAMP5	192683	broad.mit.edu	37	15	75311041	75311041	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75311041delT	uc002azk.1	+						SCAMP5_uc002azl.1_Intron|SCAMP5_uc002azm.1_Intron|SCAMP5_uc002azn.1_Intron|SCAMP5_uc010uly.1_Intron	NM_138967	NP_620417			secretory carrier membrane protein 5						exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75354195	75354195	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75354195delT								PPCDC (11129 upstream) : C15orf39 (137038 downstream)																																			---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75695887	75695887	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75695887delT	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292			transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5																		---	---	---	---
SNUPN	10073	broad.mit.edu	37	15	75891517	75891517	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75891517delA	uc002ban.2	-						SNUPN_uc002bao.2_Intron|SNUPN_uc002bap.2_Intron|SNUPN_uc002baq.2_Intron|SNUPN_uc002bar.2_Intron|SNUPN_uc002bas.2_Intron	NM_005701	NP_005692			snurportin 1						ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	76079339	76079339	+	5'Flank	DEL	A	-	-	rs77222978		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76079339delA	uc002bbb.1	-						uc002bbc.1_5'Flank					DQ577530																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	76104581	76104581	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76104581delC								DNM1P35 (72079 upstream) : UBE2Q2 (31041 downstream)																																			---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76866353	76866353	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76866353delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78157341	78157341	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78157341delT								LINGO1 (168866 upstream) : LOC645752 (49218 downstream)																																			---	---	---	---
CRABP1	1381	broad.mit.edu	37	15	78639336	78639338	+	Intron	DEL	TTT	-	-	rs68194317		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78639336_78639338delTTT	uc002bdp.2	+							NM_004378	NP_004369			cellular retinoic acid binding protein 1						multicellular organismal development|signal transduction	cytoplasm	retinal binding|retinol binding|transporter activity				0					Alitretinoin(DB00523)|Etretinate(DB00926)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	78686232	78686233	+	IGR	INS	-	AAGA	AAGA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78686232_78686233insAAGA								CRABP1 (45660 upstream) : IREB2 (44285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	78710308	78710309	+	IGR	DEL	AA	-	-	rs76752108		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78710308_78710309delAA								CRABP1 (69736 upstream) : IREB2 (20209 downstream)																																			---	---	---	---
MORF4L1	10933	broad.mit.edu	37	15	79176546	79176546	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79176546delA	uc002bel.2	+						MORF4L1_uc010bli.1_Intron|MORF4L1_uc010blj.1_Intron|MORF4L1_uc002bem.2_Intron|MORF4L1_uc010une.1_Intron	NM_206839	NP_996670			MORF-related gene 15 isoform 2						double-strand break repair via homologous recombination|histone deacetylation|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Sin3 complex	protein N-terminus binding				0																		---	---	---	---
TMED3	23423	broad.mit.edu	37	15	79653323	79653328	+	Intron	DEL	TACAAC	-	-	rs140270856		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79653323_79653328delTACAAC	uc010unj.1	+							NM_007364	NP_031390			transmembrane emp24 domain containing 3						protein transport	ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
MESDC1	59274	broad.mit.edu	37	15	81296130	81296130	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81296130delT	uc002bfz.2	+	1						NM_022566	NP_072088			mesoderm development candidate 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	82134058	82134058	+	IGR	DEL	A	-	-	rs80042069		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82134058delA								TMC3 (467640 upstream) : MEX3B (200070 downstream)																																			---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83437347	83437350	+	Intron	DEL	TGAA	-	-	rs71971612		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83437347_83437350delTGAA	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123			fibronectin type III and SPRY domain containing											central_nervous_system(1)	1																		---	---	---	---
HOMER2	9455	broad.mit.edu	37	15	83527539	83527540	+	Intron	INS	-	TC	TC	rs143295864	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83527539_83527540insTC	uc002bjg.2	-						HOMER2_uc002bjh.2_Intron|HOMER2_uc002bjj.2_Intron|HOMER2_uc002bji.2_Intron	NM_199330	NP_955362			homer 2 isoform 2						metabotropic glutamate receptor signaling pathway	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	83641435	83641435	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83641435delA	uc002bjk.1	-											Homo sapiens, clone IMAGE:5164756, mRNA.																														---	---	---	---
TM6SF1	53346	broad.mit.edu	37	15	83805210	83805210	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83805210delT	uc002bjp.2	+						TM6SF1_uc010bmq.2_Intron|TM6SF1_uc002bjq.2_Intron|TM6SF1_uc010bmr.2_Intron|TM6SF1_uc002bjr.2_Intron	NM_023003	NP_075379			transmembrane 6 superfamily member 1 isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	84944245	84944246	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84944245_84944246delTT								LOC388152 (45325 upstream) : GOLGA6L5 (103492 downstream)																																			---	---	---	---
PDE8A	5151	broad.mit.edu	37	15	85582659	85582659	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85582659delA	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron	NM_002605	NP_002596			phosphodiesterase 8A isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85815438	85815439	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85815438_85815439insC								PDE8A (133068 upstream) : AKAP13 (108432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	87964663	87964664	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87964663_87964664delAA								AGBL1 (392380 upstream) : NCRNA00052 (155496 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88423337	88423337	+	Intron	DEL	T	-	-	rs71851481		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88423337delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron	NM_001012338	NP_001012338			neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)					T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			---	---	---	---
Unknown	0	broad.mit.edu	37	15	90785322	90785322	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90785322delT								C15orf58 (11 upstream) : TTLL13 (7442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92285632	92285633	+	IGR	INS	-	A	A	rs137944806	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92285632_92285633insA								SV2B (446984 upstream) : SLCO3A1 (111305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98105939	98105940	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98105939_98105940insG								SPATA8 (777095 upstream) : LOC91948 (179906 downstream)																																			---	---	---	---
ASB7	140460	broad.mit.edu	37	15	101146398	101146398	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101146398delT	uc002bwk.2	+						ASB7_uc002bwj.2_Intron	NM_198243	NP_937886			ankyrin repeat and SOCS box-containing protein 7						intracellular signal transduction					skin(1)	1	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	102287990	102287990	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102287990delT	uc010usj.1	+											RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																														---	---	---	---
MPG	4350	broad.mit.edu	37	16	129406	129406	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:129406delT	uc002cfn.2	+						MPG_uc002cfm.2_Intron|MPG_uc010bqp.2_Intron|MPG_uc002cfo.2_Intron	NM_002434	NP_002425			N-methylpurine-DNA glycosylase isoform a						depurination|DNA dealkylation involved in DNA repair	nucleoplasm	alkylbase DNA N-glycosylase activity|damaged DNA binding|identical protein binding			ovary(1)|skin(1)	2		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)											BER_DNA_glycosylases					---	---	---	---
LUC7L	55692	broad.mit.edu	37	16	240581	240581	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:240581delA	uc002cgc.1	-						LUC7L_uc002cga.1_Intron|LUC7L_uc002cgd.1_Intron|LUC7L_uc002cge.1_Intron|LUC7L_uc002cgb.1_Intron	NM_201412	NP_958815			LUC7-like isoform b								metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)																---	---	---	---
RGS11	8786	broad.mit.edu	37	16	320963	320964	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:320963_320964insT	uc002cgj.1	-						RGS11_uc002cgi.1_Intron|RGS11_uc010bqs.1_Intron|RGS11_uc002cgk.1_Intron	NM_183337	NP_899180			regulator of G-protein signalling 11 isoform 1						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			lung(1)|pancreas(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)																---	---	---	---
DECR2	26063	broad.mit.edu	37	16	454942	454942	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:454942delT	uc002chb.2	+						DECR2_uc002chc.2_Intron|DECR2_uc010bqv.2_Intron|DECR2_uc002chd.2_Intron|DECR2_uc002che.1_5'Flank	NM_020664	NP_065715			2,4-dienoyl CoA reductase 2							peroxisome	2,4-dienoyl-CoA reductase (NADPH) activity|binding				0		Hepatocellular(16;0.00015)																---	---	---	---
NARFL	64428	broad.mit.edu	37	16	786519	786520	+	Intron	DEL	TT	-	-	rs72346687		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:786519_786520delTT	uc002cjr.2	-						NARFL_uc002cjp.2_Intron|NARFL_uc002cjq.2_Intron|NARFL_uc002cjs.2_Intron|NARFL_uc010brc.1_Intron|NARFL_uc010uur.1_Intron	NM_022493	NP_071938			nuclear prelamin A recognition factor-like						iron-sulfur cluster assembly|oxygen homeostasis|regulation of transcription, DNA-dependent|response to hypoxia		4 iron, 4 sulfur cluster binding|metal ion binding				0		Hepatocellular(780;0.0218)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	1075451	1075474	+	IGR	DEL	GGTGTGGAGGGTGCTGAGGTCCCC	-	-	rs72269290	by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1075451_1075474delGGTGTGGAGGGTGCTGAGGTCCCC								SOX8 (38473 upstream) : LOC146336 (38610 downstream)																																			---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1226527	1226527	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1226527delC	uc002cks.2	+						CACNA1H_uc002ckt.2_Intron	NM_021098	NP_066921			calcium channel, voltage-dependent, T type,						aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
SLC9A3R2	9351	broad.mit.edu	37	16	2087453	2087453	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2087453delG	uc002coi.2	+						SLC9A3R2_uc002coj.2_Intron|SLC9A3R2_uc002cok.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																		---	---	---	---
PGP	283871	broad.mit.edu	37	16	2263693	2263693	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2263693delT	uc002cpk.1	-	2					C16orf79_uc002cpi.1_5'Flank|C16orf79_uc010bsh.2_5'Flank|PGP_uc010uvz.1_RNA	NM_001042371	NP_001035830			phosphoglycolate phosphatase						carbohydrate metabolic process		phosphoglycolate phosphatase activity			skin(1)	1																		---	---	---	---
CCNF	899	broad.mit.edu	37	16	2488060	2488060	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2488060delT	uc002cqd.1	+						CCNF_uc002cqe.1_Intron	NM_001761	NP_001752			cyclin F						cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	centriole|nucleus|SCF ubiquitin ligase complex	protein binding			central_nervous_system(1)|kidney(1)	2		Ovarian(90;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	2872870	2872870	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2872870delT								PRSS21 (1154 upstream) : ZG16B (7303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	3039604	3039604	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3039604delG	uc002csr.1	+						uc002css.1_5'Flank					Homo sapiens cDNA FLJ40698 fis, clone THYMU2025557.																														---	---	---	---
IL32	9235	broad.mit.edu	37	16	3116880	3116880	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3116880delG	uc002cto.2	+						IL32_uc002ctk.2_Intron|IL32_uc010uwp.1_Intron|IL32_uc010btb.2_Intron|IL32_uc002ctl.2_Intron|IL32_uc002ctm.2_Intron|IL32_uc002ctn.2_Intron|IL32_uc010btc.1_Intron|IL32_uc002cts.3_Intron|IL32_uc002ctp.2_Intron|IL32_uc010uwq.1_Intron|IL32_uc002ctq.2_Intron|IL32_uc002ctr.2_Intron|IL32_uc002ctt.2_Intron|IL32_uc010uwr.1_Intron|IL32_uc002ctu.2_Intron	NM_004221	NP_004212			interleukin 32 isoform B						cell adhesion|defense response|immune response	extracellular space	cytokine activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	3429787	3429787	+	IGR	DEL	T	-	-	rs76050258		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3429787delT								OR2C1 (22863 upstream) : ZNF434 (2299 downstream)																																			---	---	---	---
ZNF597	146434	broad.mit.edu	37	16	3486434	3486434	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3486434delT	uc002cvd.2	-	4	1449	c.1265delA	c.(1264-1266)AACfs	p.N422fs		NM_152457	NP_689670	Q96LX8	ZN597_HUMAN	zinc finger protein 597	422					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
CLUAP1	23059	broad.mit.edu	37	16	3569691	3569691	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3569691delA	uc002cvk.1	+						CLUAP1_uc002cvj.1_Intron|CLUAP1_uc002cvl.1_Intron|CLUAP1_uc002cvm.1_Intron	NM_015041	NP_055856			clusterin associated protein 1 isoform 1							nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3828862	3828862	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3828862delT	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371			CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
SRL	6345	broad.mit.edu	37	16	4243181	4243182	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4243181_4243182insT	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
SRL	6345	broad.mit.edu	37	16	4282178	4282179	+	Intron	INS	-	A	A	rs139533015		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4282178_4282179insA	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
TFAP4	7023	broad.mit.edu	37	16	4310226	4310226	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4310226delG	uc010uxg.1	-	6	941	c.687delC	c.(685-687)CCCfs	p.P229fs		NM_003223	NP_003214	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer	229	Pro-rich.				DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
HMOX2	3163	broad.mit.edu	37	16	4556075	4556075	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4556075delT	uc010bts.2	+						HMOX2_uc002cwr.3_Intron|HMOX2_uc002cwq.3_Intron|HMOX2_uc002cws.3_Intron|HMOX2_uc010btt.2_Intron|HMOX2_uc002cwt.2_Intron	NM_001127206	NP_001120678			heme oxygenase (decyclizing) 2						cellular iron ion homeostasis|heme catabolic process|heme oxidation|response to hypoxia|transmembrane transport	endoplasmic reticulum membrane|microsome|plasma membrane	electron carrier activity|heme oxygenase (decyclizing) activity|metal ion binding|protein binding				0					NADH(DB00157)											OREG0023582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C16orf71	146562	broad.mit.edu	37	16	4788056	4788056	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4788056delT	uc002cxn.2	+							NM_139170	NP_631909			hypothetical protein LOC146562											central_nervous_system(1)	1																		---	---	---	---
ROGDI	79641	broad.mit.edu	37	16	4852639	4852640	+	5'UTR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4852639_4852640insC	uc002cxv.2	-	1					ROGDI_uc002cxu.2_5'Flank|ROGDI_uc010bua.2_RNA|ROGDI_uc002cxw.2_5'UTR|ROGDI_uc010bub.1_5'Flank|ROGDI_uc010uxu.1_5'UTR	NM_024589	NP_078865			leucine zipper domain protein							intracellular				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5574546	5574547	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5574546_5574547delTT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	5878712	5878712	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5878712delA								FAM86A (730923 upstream) : A2BP1 (190420 downstream)																																			---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6227188	6227193	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6227188_6227193delTTTTTT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6493397	6493397	+	Intron	DEL	C	-	-	rs75065314		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6493397delC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7058678	7058679	+	Intron	INS	-	T	T	rs112141029		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7058678_7058679insT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7215964	7215965	+	Intron	INS	-	AT	AT	rs28556692	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7215964_7215965insAT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7559969	7559970	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7559969_7559970delTT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	8547234	8547234	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8547234delT								A2BP1 (783894 upstream) : TMEM114 (72269 downstream)																																			---	---	---	---
USP7	7874	broad.mit.edu	37	16	8997303	8997303	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8997303delA	uc002czl.2	-						USP7_uc010uyk.1_Intron|USP7_uc002czj.2_Intron|USP7_uc010uyj.1_Intron|USP7_uc002czk.2_Intron|USP7_uc010uyl.1_Intron	NM_003470	NP_003461			ubiquitin specific peptidase 7						interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	9402628	9402629	+	IGR	INS	-	G	G	rs146762815	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9402628_9402629insG								C16orf72 (189083 upstream) : GRIN2A (444638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9738901	9738901	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9738901delA								C16orf72 (525356 upstream) : GRIN2A (108366 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9849713	9849714	+	3'UTR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9849713_9849714delAA	uc002czo.3	-	13					GRIN2A_uc010uym.1_3'UTR	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9953500	9953501	+	Intron	INS	-	AG	AG	rs144711120	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9953500_9953501insAG	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10046318	10046318	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10046318delA	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10092586	10092587	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10092586_10092587delTC	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	10342387	10342387	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10342387delT								GRIN2A (65776 upstream) : ATF7IP2 (137525 downstream)																																			---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11063215	11063217	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11063215_11063217delTTT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11194139	11194139	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11194139delA	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																OREG0023610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12130122	12130122	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12130122delT	uc002dbw.1	+							NM_032167	NP_115543			RUN domain containing 2A											ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12336518	12336518	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12336518delT	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13003134	13003134	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13003134delC	uc010uyy.1	+						SHISA9_uc002dcd.2_3'UTR	NM_001145204	NP_001138676			shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	13951225	13951226	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13951225_13951226delGA								SHISA9 (616953 upstream) : ERCC4 (62788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14122696	14122699	+	IGR	DEL	TTGT	-	-	rs76834234		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14122696_14122699delTTGT								ERCC4 (76491 upstream) : MKL2 (42497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	15053924	15053924	+	IGR	DEL	T	-	-	rs78217806		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15053924delT								NPIP (7994 upstream) : PDXDC1 (14675 downstream)																																			---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15079956	15079956	+	Intron	DEL	A	-	-	rs72009445		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15079956delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15870226	15870226	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15870226delA	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_Intron	NM_002474	NP_002465			smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16151898	16151899	+	Intron	INS	-	T	T	rs75194824	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16151898_16151899insT	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16275221	16275226	+	Intron	DEL	AAAAAG	-	-	rs66783638		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16275221_16275226delAAAAAG	uc002den.3	-						ABCC6_uc010bvo.2_Intron	NM_001171	NP_001162			ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
NOMO3	408050	broad.mit.edu	37	16	16354188	16354188	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16354188delT	uc002deq.2	+						NOMO3_uc002dep.2_Intron|NOMO3_uc010bvp.1_Intron	NM_001004067	NP_001004067			nodal modulator 3 precursor							integral to membrane	carbohydrate binding|carboxypeptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	18131195	18131197	+	IGR	DEL	ATA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18131195_18131197delATA								XYLT1 (566457 upstream) : NOMO2 (379986 downstream)																																			---	---	---	---
NOMO2	283820	broad.mit.edu	37	16	18573941	18573942	+	5'Flank	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18573941_18573942delCA	uc002dfe.2	-						NOMO2_uc002dff.2_5'Flank|NOMO2_uc010bvx.2_5'Flank	NM_001004060	NP_001004060			nodal modulator 2 isoform 1							endoplasmic reticulum membrane|integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			skin(1)	1																		---	---	---	---
ARL6IP1	23204	broad.mit.edu	37	16	18810349	18810349	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18810349delT	uc002dfl.1	-						ARL6IP1_uc010van.1_Intron|ARL6IP1_uc010bvz.1_Intron	NM_015161	NP_055976			ADP-ribosylation factor-like 6 interacting							integral to membrane	protein binding				0																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18883764	18883764	+	Intron	DEL	A	-	-	rs117332168	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18883764delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18895528	18895528	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18895528delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18897136	18897137	+	Intron	DEL	AT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18897136_18897137delAT	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18914313	18914313	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18914313delT	uc002dfm.2	-							NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19627861	19627862	+	Intron	DEL	AA	-	-	rs113166809		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19627861_19627862delAA	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron|C16orf62_uc002dgm.1_Intron	NM_020314	NP_064710			hypothetical protein LOC57020							integral to membrane				ovary(1)	1																		---	---	---	---
ACSM5	54988	broad.mit.edu	37	16	20429352	20429352	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20429352delT	uc002dhe.2	+						ACSM5_uc002dhd.1_Intron	NM_017888	NP_060358			acyl-CoA synthetase medium-chain family member 5						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	21464447	21464447	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21464447delT	uc002diq.3	+						LOC100271836_uc002diu.1_Intron|LOC100271836_uc002diz.1_Intron					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21517590	21517590	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21517590delA	uc002diq.3	+						LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21519524	21519524	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21519524delT	uc002diq.3	+						LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21540222	21540223	+	Intron	DEL	TT	-	-	rs76602208		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21540222_21540223delTT	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
IGSF6	10261	broad.mit.edu	37	16	21652761	21652762	+	3'UTR	INS	-	T	T	rs141804055	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21652761_21652762insT	uc002djg.1	-	6					uc002diq.3_Intron|METTL9_uc002dje.2_Intron|METTL9_uc002djf.2_Intron	NM_005849	NP_005840			immunoglobulin superfamily, member 6 precursor						cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0				GBM - Glioblastoma multiforme(48;0.066)														---	---	---	---
RRN3P1	730092	broad.mit.edu	37	16	21814068	21814068	+	Intron	DEL	A	-	-	rs58942468		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21814068delA	uc010vbl.1	-						uc002diq.3_Intron	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0																		---	---	---	---
RRN3P3	100131998	broad.mit.edu	37	16	22446191	22446191	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22446191delA	uc002dkp.2	-						RRN3P3_uc010vbu.1_Intron|LOC641298_uc010bxf.2_5'Flank	NR_027460				Homo sapiens cDNA FLJ31180 fis, clone KIDNE2000266.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	22662052	22662052	+	IGR	DEL	A	-	-	rs112918197		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22662052delA								LOC653786 (73866 upstream) : HS3ST2 (163808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22715165	22715165	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22715165delT								LOC653786 (126979 upstream) : HS3ST2 (110695 downstream)																																			---	---	---	---
USP31	57478	broad.mit.edu	37	16	23117811	23117811	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23117811delA	uc002dll.2	-							NM_020718	NP_065769			ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)														---	---	---	---
SCNN1G	6340	broad.mit.edu	37	16	23209903	23209903	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23209903delA	uc002dlm.1	+							NM_001039	NP_001030			sodium channel, nonvoltage-gated 1, gamma						excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
PLK1	5347	broad.mit.edu	37	16	23691715	23691715	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23691715delT	uc002dlz.1	+							NM_005030	NP_005021			polo-like kinase 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24127057	24127058	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24127057_24127058insT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
CACNG3	10368	broad.mit.edu	37	16	24277844	24277844	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24277844delA	uc002dmf.2	+							NM_006539	NP_006530			voltage-dependent calcium channel gamma-3						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)														---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24872912	24872915	+	Intron	DEL	AAGG	-	-	rs149777560		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24872912_24872915delAAGG	uc002dmu.2	+						SLC5A11_uc002dms.2_Intron|SLC5A11_uc010vcd.1_Intron|SLC5A11_uc002dmt.2_Intron|SLC5A11_uc010vce.1_Intron|SLC5A11_uc010bxt.2_Intron	NM_052944	NP_443176			solute carrier family 5 (sodium/glucose						apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	25031511	25031512	+	IGR	INS	-	GGAAGGAA	GGAAGGAA	rs7498498	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25031511_25031512insGGAAGGAA								ARHGAP17 (4836 upstream) : LCMT1 (91535 downstream)																																			---	---	---	---
LCMT1	51451	broad.mit.edu	37	16	25183629	25183630	+	Intron	INS	-	A	A	rs76217419		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25183629_25183630insA	uc002dnx.1	+						LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Intron|LCMT1_uc002doa.1_Intron	NM_016309	NP_057393			leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	25201852	25201853	+	IGR	DEL	TT	-	-	rs67953455		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25201852_25201853delTT								LCMT1 (12301 upstream) : AQP8 (26432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25245677	25245677	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25245677delT								AQP8 (5425 upstream) : ZKSCAN2 (1647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25482275	25482276	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25482275_25482276delAA								ZKSCAN2 (213420 upstream) : HS3ST4 (221071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26374123	26374124	+	IGR	INS	-	G	G	rs35533138		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26374123_26374124insG								HS3ST4 (225115 upstream) : C16orf82 (704095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26720900	26720900	+	IGR	DEL	T	-	-	rs112343208	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26720900delT								HS3ST4 (571892 upstream) : C16orf82 (357319 downstream)																																			---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	28009178	28009180	+	Intron	DEL	TTT	-	-	rs146173953		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28009178_28009180delTTT	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	29254231	29254231	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29254231delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29721423	29721423	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29721423delA	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
PRRT2	112476	broad.mit.edu	37	16	29825016	29825016	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29825016delC	uc002due.3	+	2	942	c.641delC	c.(640-642)GCCfs	p.A214fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002duc.1_5'Flank|PRRT2_uc002dud.2_Frame_Shift_Del_p.A214fs|PRRT2_uc002duf.1_Frame_Shift_Del_p.A214fs|C16orf53_uc002dug.3_5'Flank	NM_145239	NP_660282	Q7Z6L0	PRRT2_HUMAN	proline-rich transmembrane protein 2	214	Extracellular (Potential).|Pro-rich.			A -> AP (in Ref. 3; CAD38881).	response to biotic stimulus	integral to membrane					0																		---	---	---	---
SEZ6L2	26470	broad.mit.edu	37	16	29891491	29891491	+	Intron	DEL	T	-	-	rs71373211		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29891491delT	uc002duq.3	-						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Intron|SEZ6L2_uc002dur.3_Intron|SEZ6L2_uc002dus.3_Intron|SEZ6L2_uc010vec.1_Intron|SEZ6L2_uc010ved.1_Intron	NM_201575	NP_963869			seizure related 6 homolog (mouse)-like 2 isoform							endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
TBC1D10B	26000	broad.mit.edu	37	16	30376910	30376911	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30376910_30376911delCT	uc002dxu.2	-	2	979_980	c.961_962delAG	c.(961-963)AGCfs	p.S321fs		NM_015527	NP_056342	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	321						cytoplasm	Rab GTPase activator activity				0			Colorectal(24;0.193)															---	---	---	---
ZNF689	115509	broad.mit.edu	37	16	30622813	30622813	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30622813delT	uc002dyx.2	-						ZNF689_uc010bzy.2_5'Flank	NM_138447	NP_612456			zinc finger protein HIT-39						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)															---	---	---	---
BCL7C	9274	broad.mit.edu	37	16	30901720	30901720	+	Intron	DEL	A	-	-	rs78725622		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30901720delA	uc002dzv.2	-						BCL7C_uc002dzt.1_Intron|uc002dzu.2_Intron	NM_004765	NP_004756			B-cell CLL/lymphoma 7C						apoptosis						0			Colorectal(24;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	16	30929989	30930013	+	IGR	DEL	CTTCTTCTCCTTCTCCTTCTTCTTC	-	-	rs71151428		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30929989_30930013delCTTCTTCTCCTTCTCCTTCTTCTTC								CTF1 (15109 upstream) : NCRNA00095 (627 downstream)																																			---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30978484	30978485	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30978484_30978485insT	uc002ead.1	+							NM_014712	NP_055527			SET domain containing 1A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
MYST1	84148	broad.mit.edu	37	16	31129637	31129637	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31129637delC	uc002eay.2	+						MYST1_uc002eax.2_Intron	NM_032188	NP_115564			MYST histone acetyltransferase 1 isoform 1						histone H4-K16 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex|MSL complex	histone acetyltransferase activity|metal ion binding|methylated histone residue binding|transcription factor binding			ovary(1)	1																		---	---	---	---
ITGAM	3684	broad.mit.edu	37	16	31288524	31288524	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31288524delT	uc002ebq.2	+						ITGAM_uc002ebr.2_Intron|ITGAM_uc010cam.1_Intron	NM_000632	NP_000623			integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1																		---	---	---	---
ITGAD	3681	broad.mit.edu	37	16	31437011	31437011	+	Intron	DEL	T	-	-	rs78166333		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31437011delT	uc002ebv.1	+						ITGAD_uc010cap.1_Intron	NM_005353	NP_005344			integrin, alpha D precursor						cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32485424	32485424	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32485424delA								HERC2P4 (321550 upstream) : TP53TG3B (199417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32522545	32522545	+	IGR	DEL	C	-	-	rs76051919		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32522545delC								HERC2P4 (358671 upstream) : TP53TG3B (162296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32526249	32526250	+	IGR	INS	-	A	A	rs148676631		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32526249_32526250insA								HERC2P4 (362375 upstream) : TP53TG3B (158591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32846023	32846023	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32846023delT								TP53TG3B (157145 upstream) : SLC6A10P (42774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33361840	33361840	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33361840delT								SLC6A10P (465377 upstream) : MIR1826 (603668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33387787	33387787	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33387787delT								SLC6A10P (491324 upstream) : MIR1826 (577721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33396504	33396505	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33396504_33396505delAA								SLC6A10P (500041 upstream) : MIR1826 (569003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33413684	33413685	+	IGR	INS	-	TT	TT	rs138008730		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33413684_33413685insTT								SLC6A10P (517221 upstream) : MIR1826 (551823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33863853	33863853	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33863853delT								SLC6A10P (967390 upstream) : MIR1826 (101655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33946421	33946422	+	IGR	INS	-	A	A	rs112464617		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33946421_33946422insA								None (None upstream) : MIR1826 (19086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33967631	33967631	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33967631delA								MIR1826 (2039 upstream) : UBE2MP1 (436171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34221719	34221720	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34221719_34221720delAC								MIR1826 (256127 upstream) : UBE2MP1 (182082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34575151	34575151	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34575151delT								UBE2MP1 (170389 upstream) : LOC283914 (22636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46448230	46448230	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46448230delA								None (None upstream) : ANKRD26P1 (55019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46457875	46457875	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46457875delG								None (None upstream) : ANKRD26P1 (45374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46876745	46876746	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46876745_46876746delTT								C16orf87 (11671 upstream) : GPT2 (41562 downstream)																																			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47347603	47347603	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47347603delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
SIAH1	6477	broad.mit.edu	37	16	48475362	48475362	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48475362delT	uc002efl.2	-											Homo sapiens SIAH1 mRNA for seven in absentia homolog 1 isoform a, complete cds, clone: FLJ08065AAAN.						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	49510975	49510977	+	IGR	DEL	GAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49510975_49510977delGAG								C16orf78 (77658 upstream) : ZNF423 (13545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49928385	49928386	+	IGR	DEL	AA	-	-	rs67352893		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49928385_49928386delAA								ZNF423 (67467 upstream) : TMEM188 (130803 downstream)																																			---	---	---	---
ADCY7	113	broad.mit.edu	37	16	50325867	50325867	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50325867delG	uc002egd.1	+						ADCY7_uc002egb.1_Intron|ADCY7_uc002egc.1_Intron	NM_001114	NP_001105			adenylate cyclase 7						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	50407424	50407424	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50407424delG								BRD7 (4595 upstream) : NKD1 (174817 downstream)																																			---	---	---	---
SNX20	124460	broad.mit.edu	37	16	50707236	50707236	+	3'UTR	DEL	A	-	-	rs75121949	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50707236delA	uc002egk.2	-	4					SNX20_uc010vgp.1_Intron|SNX20_uc002egi.3_Intron	NM_182854	NP_878274			sorting nexin 20 isoform 1						cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	50721178	50721179	+	IGR	DEL	AA	-	-	rs5816714		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50721178_50721179delAA								SNX20 (5914 upstream) : NOD2 (6335 downstream)																																			---	---	---	---
SALL1	6299	broad.mit.edu	37	16	51171507	51171507	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51171507delG	uc010vgs.1	-						SALL1_uc010vgr.1_Intron|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959			sal-like 1 isoform a						adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	16	52129442	52129442	+	IGR	DEL	G	-	-	rs33333	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52129442delG								SALL1 (944259 upstream) : TOX3 (342476 downstream)																																			---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53326632	53326632	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53326632delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53348724	53348724	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53348724delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
FTO	79068	broad.mit.edu	37	16	53835153	53835153	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53835153delT	uc002ehr.2	+						FTO_uc010vha.1_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54491407	54491408	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54491407_54491408delTT								IRX3 (171029 upstream) : IRX5 (473703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55340705	55340705	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55340705delA								IRX5 (372312 upstream) : IRX6 (17766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55658595	55658595	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55658595delT								LPCAT2 (38014 upstream) : SLC6A2 (31427 downstream)																																			---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57027154	57027154	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57027154delT	uc002ekk.1	+							NM_032206	NP_115582			nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57246811	57246811	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57246811delA	uc002elb.2	+						RSPRY1_uc002elc.2_Intron|RSPRY1_uc002eld.2_Intron	NM_133368	NP_588609			ring finger and SPRY domain containing 1							extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	57401024	57401024	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57401024delT								CCL22 (925 upstream) : CX3CL1 (5390 downstream)																																			---	---	---	---
COQ9	57017	broad.mit.edu	37	16	57494403	57494404	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57494403_57494404delAA	uc002elq.2	+						COQ9_uc002elr.2_Intron|COQ9_uc002els.2_Intron|POLR2C_uc010vhq.1_5'Flank|POLR2C_uc002elt.1_5'Flank	NM_020312	NP_064708			coenzyme Q9 homolog precursor						ubiquinone biosynthetic process	mitochondrion				breast(1)	1																		---	---	---	---
KATNB1	10300	broad.mit.edu	37	16	57776654	57776654	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57776654delT	uc002eml.1	+							NM_005886	NP_005877			katanin p80 subunit B 1						cell division|mitosis|negative regulation of microtubule depolymerization|positive regulation of microtubule depolymerization|protein targeting	katanin complex|microtubule|spindle pole	microtubule binding|protein heterodimerization activity				0		all_neural(199;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	58375022	58375022	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58375022delT								PRSS54 (46071 upstream) : GINS3 (51276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59237184	59237184	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59237184delC								GOT2 (468938 upstream) : None (None downstream)																																			---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61759806	61759807	+	Intron	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61759806_61759807delGT	uc002eog.1	-							NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CDH8	1006	broad.mit.edu	37	16	62036956	62036956	+	Intron	DEL	A	-	-	rs112057283		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62036956delA	uc002eog.1	-							NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	62431164	62431165	+	IGR	INS	-	GAGGGAAGGAAGCAGG	GAGGGAAGGAAGCAGG	rs144312843	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62431164_62431165insGAGGGAAGGAAGCAGG								CDH8 (361128 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64044073	64044074	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64044073_64044074delCA								None (None upstream) : CDH11 (936611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64747160	64747160	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64747160delC								None (None upstream) : CDH11 (233525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64899366	64899366	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64899366delT								None (None upstream) : CDH11 (81319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65654305	65654305	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65654305delT								LOC283867 (44102 upstream) : CDH5 (746220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65939643	65939643	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65939643delT								LOC283867 (329440 upstream) : CDH5 (460882 downstream)																																			---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66852580	66852580	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66852580delA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron|NAE1_uc010cdw.1_Intron	NM_003905	NP_003896			NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	66986285	66986285	+	IGR	DEL	A	-	-	rs75936438		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66986285delA								CES2 (7293 upstream) : CES3 (8853 downstream)																																			---	---	---	---
C16orf70	80262	broad.mit.edu	37	16	67165179	67165179	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67165179delT	uc002erc.2	+						C16orf70_uc002erd.2_Intron|C16orf70_uc002ere.1_Intron	NM_025187	NP_079463			lin-10											ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)														---	---	---	---
NOL3	8996	broad.mit.edu	37	16	67205485	67205486	+	5'Flank	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67205485_67205486insG	uc010vjd.1	+						NOL3_uc010vjc.1_Intron|NOL3_uc002erp.2_5'Flank					RecName: Full=Nucleolar protein 3; AltName: Full=Apoptosis repressor with CARD; AltName: Full=Muscle-enriched cytoplasmic protein;          Short=Myp; AltName: Full=Nucleolar protein of 30 kDa;          Short=Nop30;						anti-apoptosis|apoptosis|mRNA processing|RNA splicing	cytosol|nucleolus	identical protein binding|RNA binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)														---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67354312	67354312	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67354312delT	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)														---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67645310	67645310	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67645310delA	uc002etl.2	+	3	865	c.575delA	c.(574-576)CAAfs	p.Q192fs	CTCF_uc010cek.2_Intron	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	192					chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67849710	67849710	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67849710delT	uc002euj.2	+						TSNAXIP1_uc010cep.2_Intron|TSNAXIP1_uc010vjz.1_Intron|TSNAXIP1_uc002euf.3_Intron|TSNAXIP1_uc010vka.1_Intron|TSNAXIP1_uc010vkb.1_Intron|TSNAXIP1_uc002eug.3_Intron|TSNAXIP1_uc002euh.3_Intron|TSNAXIP1_uc002eui.3_Intron	NM_018430	NP_060900			translin-associated factor X interacting protein						cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)														---	---	---	---
SMPD3	55512	broad.mit.edu	37	16	68404695	68404695	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68404695delC	uc002ewa.2	-						SMPD3_uc010cfe.2_Intron|SMPD3_uc010vlh.1_Intron	NM_018667	NP_061137			neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)													---	---	---	---
SMPD3	55512	broad.mit.edu	37	16	68461656	68461656	+	Intron	DEL	G	-	-	rs67002357		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68461656delG	uc002ewa.2	-							NM_018667	NP_061137			neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)													---	---	---	---
ZFP90	146198	broad.mit.edu	37	16	68567085	68567085	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68567085delT	uc002ewb.2	+											Homo sapiens mRNA for KIAA1954 protein.						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)														---	---	---	---
CDH1	999	broad.mit.edu	37	16	68867504	68867505	+	3'UTR	INS	-	A	A	rs1138534		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68867504_68867505insA	uc002ewg.1	+	16					CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_3'UTR	NM_004360	NP_004351			cadherin 1, type 1 preproprotein						adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response	actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm	cell adhesion molecule binding|gamma-catenin binding			breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1)	243		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)				Mis|N|F|S		lobular breast|gastric	gastric			Hereditary_Diffuse_Gastric_Cancer				---	---	---	---
Unknown	0	broad.mit.edu	37	16	69133241	69133241	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69133241delT								TMCO7 (14158 upstream) : HAS3 (6226 downstream)																																			---	---	---	---
SNTB2	6645	broad.mit.edu	37	16	69252327	69252328	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69252327_69252328delTT	uc002ewu.2	+							NM_006750	NP_006741			basic beta 2 syntrophin							cell junction|dystrophin-associated glycoprotein complex|membrane fraction|microtubule|transport vesicle membrane	actin binding|calmodulin binding|protein binding				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)														---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69694986	69694989	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69694986_69694989delTTTT	uc002exm.1	+						NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Intron|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron	NM_006599	NP_006590			nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NOB1	28987	broad.mit.edu	37	16	69785968	69785968	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69785968delA	uc002exs.2	-							NM_014062	NP_054781			nin one binding protein							nucleus	metal ion binding|protein binding				0																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69842961	69842961	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69842961delT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron	NM_007014	NP_008945			WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
AARS	16	broad.mit.edu	37	16	70312708	70312708	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70312708delA	uc002eyn.1	-							NM_001605	NP_001596			alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)													---	---	---	---
COG4	25839	broad.mit.edu	37	16	70548455	70548456	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70548455_70548456insA	uc002ezc.2	-						COG4_uc010cfu.2_Intron|COG4_uc002ezd.2_Intron|COG4_uc002eze.2_Intron	NM_015386	NP_056201			component of oligomeric golgi complex 4						Golgi organization|Golgi vesicle prefusion complex stabilization|protein transport|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0		Ovarian(137;0.0694)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	72563073	72563074	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72563073_72563074delTG	uc002fci.1	+											Homo sapiens cDNA FLJ38299 fis, clone FCBBF3017255.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	72722412	72722413	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72722412_72722413insT	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	73104609	73104610	+	IGR	INS	-	TC	TC	rs144216818	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73104609_73104610insTC								ZFHX3 (11372 upstream) : HTA (21638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74431321	74431322	+	IGR	INS	-	A	A	rs7194963	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74431321_74431322insA								LOC283922 (29168 upstream) : CLEC18B (11209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75815078	75815078	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75815078delA								TERF2IP (123750 upstream) : CNTNAP4 (496098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76089386	76089387	+	IGR	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76089386_76089387delTC								TERF2IP (398058 upstream) : CNTNAP4 (221789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	78041465	78041466	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78041465_78041466delAC								VAT1L (27464 upstream) : CLEC3A (14977 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78163607	78163607	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78163607delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	79023719	79023720	+	Intron	INS	-	TGTGTT	TGTGTT	rs145686653	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79023719_79023720insTGTGTT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	79600706	79600707	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79600706_79600707insA								WWOX (354143 upstream) : MAF (27039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80461958	80461958	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80461958delA								MAF (827336 upstream) : DYNLRB2 (112896 downstream)																																			---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81058306	81058307	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81058306_81058307delTT	uc002ffx.2	+						CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094			centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
GAN	8139	broad.mit.edu	37	16	81387847	81387849	+	Intron	DEL	AAA	-	-	rs139978939		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81387847_81387849delAAA	uc002fgo.2	+							NM_022041	NP_071324			gigaxonin						cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)																---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81696905	81696905	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81696905delA	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	81792283	81792284	+	IGR	DEL	TT	-	-	rs139360655		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81792283_81792284delTT								CMIP (46918 upstream) : PLCG2 (20646 downstream)																																			---	---	---	---
PLCG2	5336	broad.mit.edu	37	16	81929705	81929705	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81929705delC	uc002fgt.2	+						PLCG2_uc010chg.1_Intron	NM_002661	NP_002652			phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8																		---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82882187	82882188	+	Intron	DEL	TG	-	-	rs77857730		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82882187_82882188delTG	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
SLC38A8	146167	broad.mit.edu	37	16	84056552	84056552	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84056552delA	uc002fhg.1	-							NM_001080442	NP_001073911			solute carrier family 38, member 8						amino acid transport|sodium ion transport	integral to membrane					0																		---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84442180	84442180	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84442180delA	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron	NM_014861	NP_055676			ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84576886	84576886	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84576886delT								KIAA1609 (38598 upstream) : COTL1 (22320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85000860	85000860	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85000860delA								CRISPLD2 (57744 upstream) : ZDHHC7 (7207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85184289	85184306	+	IGR	DEL	TGTGTGTGTGTGTGTCTG	-	-	rs4783137	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85184289_85184306delTGTGTGTGTGTGTGTCTG								FAM92B (38175 upstream) : KIAA0182 (460723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85605725	85605726	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85605725_85605726delCA								FAM92B (459611 upstream) : KIAA0182 (39303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86258287	86258292	+	IGR	DEL	TGGTGA	-	-	rs11278810		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86258287_86258292delTGGTGA								IRF8 (302078 upstream) : LOC732275 (107164 downstream)																																			---	---	---	---
ZCCHC14	23174	broad.mit.edu	37	16	87445830	87445830	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87445830delG	uc002fjz.1	-	12	2113	c.2086delC	c.(2086-2088)CTGfs	p.L696fs	ZCCHC14_uc002fka.1_RNA|ZCCHC14_uc002fkb.2_Frame_Shift_Del_p.L472fs	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	696					cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)														---	---	---	---
KLHDC4	54758	broad.mit.edu	37	16	87771963	87771964	+	Intron	INS	-	CA	CA	rs146255573	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87771963_87771964insCA	uc002fki.2	-						KLHDC4_uc010cht.1_Intron|KLHDC4_uc002fkj.2_Intron|KLHDC4_uc002fkk.2_Intron|KLHDC4_uc002fkl.2_Intron|KLHDC4_uc010chu.1_Intron	NM_017566	NP_060036			kelch domain containing 4											pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0283)														---	---	---	---
ZFPM1	161882	broad.mit.edu	37	16	88558594	88558595	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88558594_88558595delTC	uc002fkv.2	+							NM_153813	NP_722520			zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89423852	89423852	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89423852delA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407			ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89430308	89430308	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89430308delA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407			ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
SPATA2L	124044	broad.mit.edu	37	16	89764373	89764374	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89764373_89764374insG	uc002foj.2	-	3	708_709	c.643_644insC	c.(643-645)CGAfs	p.R215fs	SPATA2L_uc002fok.2_Intron	NM_152339	NP_689552	Q8IUW3	SPA2L_HUMAN	spermatogenesis associated 2-like	215											0		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0272)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	410483	410483	+	IGR	DEL	G	-	-	rs112379300		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:410483delG								FAM101B (114752 upstream) : VPS53 (4247 downstream)																																			---	---	---	---
NXN	64359	broad.mit.edu	37	17	725521	725522	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:725521_725522insA	uc002fsa.2	-						NXN_uc002fsb.1_Intron|NXN_uc010vqd.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	772360	772360	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:772360delG	uc002fsa.2	-						NXN_uc002fsb.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
INPP5K	51763	broad.mit.edu	37	17	1406187	1406188	+	Intron	INS	-	T	T	rs57234309	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1406187_1406188insT	uc002fsr.2	-						INPP5K_uc002fss.2_Intron|INPP5K_uc002fsq.2_Intron|INPP5K_uc010cjr.2_Intron|INPP5K_uc010vql.1_Intron|INPP5K_uc010vqm.1_Intron	NM_016532	NP_057616			inositol polyphosphate-5-phosphatase K isoform						actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0																		---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1558922	1558924	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1558922_1558924delTTT	uc002fte.2	-							NM_006445	NP_006436			U5 snRNP-specific protein							catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)														---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1581619	1581619	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1581619delA	uc002fte.2	-							NM_006445	NP_006436			U5 snRNP-specific protein							catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)														---	---	---	---
TSR1	55720	broad.mit.edu	37	17	2227356	2227356	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2227356delA	uc002fuj.2	-	15					SRR_uc002fue.1_3'UTR|SRR_uc002fui.1_3'UTR	NM_018128	NP_060598			TSR1, 20S rRNA accumulation						ribosome assembly	nucleolus	protein binding			ovary(1)	1																		---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2560166	2560171	+	Intron	DEL	TCTGTT	-	-	rs145310274		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2560166_2560171delTCTGTT	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2568632	2568632	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2568632delT	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2570628	2570628	+	Intron	DEL	A	-	-	rs76296857		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2570628delA	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron|PAFAH1B1_uc010vqz.1_5'Flank	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2790369	2790371	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2790369_2790371delTTT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2823008	2823009	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2823008_2823009insT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3696355	3696355	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3696355delT	uc002fwo.3	-							NM_002208	NP_002199			integrin, alpha E precursor						cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)														---	---	---	---
C17orf85	55421	broad.mit.edu	37	17	3720329	3720330	+	Intron	DEL	AA	-	-	rs68087342		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3720329_3720330delAA	uc010ckl.1	-						C17orf85_uc002fwr.2_Intron|C17orf85_uc002fwq.2_Intron	NM_001114118	NP_001107590			ELG protein isoform a								nucleotide binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)														---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3947671	3947672	+	Intron	DEL	AA	-	-	rs34189065		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3947671_3947672delAA	uc002fxe.2	-						ZZEF1_uc002fxh.2_Intron|ZZEF1_uc002fxi.2_Intron|ZZEF1_uc002fxj.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3990635	3990635	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3990635delA	uc002fxe.2	-						ZZEF1_uc002fxk.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
CAMTA2	23125	broad.mit.edu	37	17	4875738	4875738	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4875738delG	uc002gah.1	-	16	2705	c.2597delC	c.(2596-2598)CCTfs	p.P866fs	CAMTA2_uc010cku.1_Frame_Shift_Del_p.P889fs|CAMTA2_uc002gag.1_Frame_Shift_Del_p.P865fs|CAMTA2_uc002gai.1_Frame_Shift_Del_p.P868fs|CAMTA2_uc010ckv.1_Frame_Shift_Del_p.P513fs	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	866					cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1																		---	---	---	---
RABEP1	9135	broad.mit.edu	37	17	5253728	5253728	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5253728delG	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron	NM_004703	NP_004694			rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
NUP88	4927	broad.mit.edu	37	17	5307292	5307293	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5307292_5307293insA	uc002gbo.1	-						NUP88_uc010vsx.1_Intron|NUP88_uc010cle.1_Intron|NUP88_uc010vsy.1_Intron	NM_002532	NP_002523			nucleoporin 88kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1																		---	---	---	---
RPAIN	84268	broad.mit.edu	37	17	5324579	5324580	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5324579_5324580delTT	uc002gbq.2	+						NUP88_uc002gbo.1_5'Flank|NUP88_uc010vsx.1_5'Flank|NUP88_uc010cle.1_5'Flank|NUP88_uc010vsy.1_5'Flank|RPAIN_uc010vsz.1_Intron|RPAIN_uc002gbp.1_Intron|RPAIN_uc010vta.1_Intron|RPAIN_uc010vtb.1_Intron|RPAIN_uc002gbs.2_Intron|RPAIN_uc002gbt.2_Intron|RPAIN_uc002gbu.2_Intron|RPAIN_uc002gbv.2_Intron|RPAIN_uc002gbr.2_Intron|RPAIN_uc002gbw.2_Intron	NM_001033002	NP_001028174			RPA interacting protein isoform b						DNA recombination|DNA repair|DNA-dependent DNA replication|protein import into nucleus|response to UV	cytoplasm|cytoplasm|nucleolus|PML body|PML body	metal ion binding|protein complex binding				0																		---	---	---	---
RPAIN	84268	broad.mit.edu	37	17	5336016	5336016	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5336016delA	uc002gbq.2	+	7					RPAIN_uc010vtb.1_3'UTR|RPAIN_uc002gbs.2_3'UTR|RPAIN_uc002gbt.2_3'UTR|RPAIN_uc002gbu.2_3'UTR|RPAIN_uc002gbv.2_RNA|RPAIN_uc002gbr.2_RNA|RPAIN_uc002gbw.2_3'UTR	NM_001033002	NP_001028174			RPA interacting protein isoform b						DNA recombination|DNA repair|DNA-dependent DNA replication|protein import into nucleus|response to UV	cytoplasm|cytoplasm|nucleolus|PML body|PML body	metal ion binding|protein complex binding				0																		---	---	---	---
MIS12	79003	broad.mit.edu	37	17	5392101	5392101	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5392101delT	uc002gcd.2	+						DERL2_uc002gcc.1_5'Flank|MIS12_uc002gce.2_Intron	NM_024039	NP_076944			MIS12 homolog						cell division|chromosome segregation|kinetochore assembly|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5568985	5568985	+	IGR	DEL	C	-	-	rs112249517		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5568985delC								NLRP1 (81153 upstream) : WSCD1 (403452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5801785	5801786	+	Intron	DEL	AA	-	-	rs71370097		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5801785_5801786delAA	uc002gcm.2	+											Homo sapiens hypothetical protein LOC339166, mRNA (cDNA clone IMAGE:5163423), partial cds.																														---	---	---	---
AIPL1	23746	broad.mit.edu	37	17	6340224	6340224	+	5'Flank	DEL	G	-	-	rs148736698	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6340224delG	uc002gcp.2	-						AIPL1_uc002gcq.2_5'Flank|AIPL1_uc002gcr.2_5'Flank|AIPL1_uc010clk.2_5'Flank|AIPL1_uc010cll.2_5'Flank|AIPL1_uc002gcs.2_5'Flank	NM_014336	NP_055151			aryl hydrocarbon receptor interacting						protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7111718	7111719	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7111718_7111719delCT	uc002get.3	-						DLG4_uc010cly.2_Intron|DLG4_uc010vto.1_Intron|DLG4_uc002geu.2_Intron	NM_001365	NP_001356			post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	7262562	7262564	+	IGR	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7262562_7262564delTTT								TMEM95 (2024 upstream) : TNK1 (21801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	7272872	7272872	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7272872delT								TMEM95 (12334 upstream) : TNK1 (11493 downstream)																																			---	---	---	---
SENP3	26168	broad.mit.edu	37	17	7474945	7474945	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7474945delT	uc002ghm.2	+	12					EIF4A1_uc002gho.1_Intron|EIF4A1_uc002ghr.1_5'Flank|EIF4A1_uc002ghq.1_5'Flank|EIF4A1_uc002ghp.1_5'Flank	NM_015670	NP_056485			SUMO1/sentrin/SMT3 specific protease 3						proteolysis	MLL1 complex|nucleolus	cysteine-type peptidase activity			ovary(1)|central_nervous_system(1)	2		Prostate(122;0.157)																---	---	---	---
EIF4A1	1973	broad.mit.edu	37	17	7480356	7480356	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7480356delT	uc002gho.1	+						EIF4A1_uc002ghr.1_Intron|EIF4A1_uc002ghq.1_Intron|EIF4A1_uc002ghp.1_Intron|SNORA67_uc010cml.1_5'Flank|CD68_uc002ghv.2_5'Flank|CD68_uc002ghu.2_5'Flank	NM_001416	NP_001407			eukaryotic translation initiation factor 4A						nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
CD68	968	broad.mit.edu	37	17	7484875	7484875	+	3'UTR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7484875delG	uc002ghv.2	+	6					CD68_uc002ghu.2_3'UTR|MPDU1_uc010vub.1_5'Flank|MPDU1_uc002ghw.2_5'Flank|MPDU1_uc002ghx.2_5'Flank|MPDU1_uc010vuc.1_5'Flank	NM_001251	NP_001242			CD68 antigen isoform A							endosome membrane|integral to membrane|lysosomal membrane|membrane fraction|plasma membrane					0																		---	---	---	---
MPDU1	9526	broad.mit.edu	37	17	7488326	7488326	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7488326delA	uc002ghw.2	+						MPDU1_uc010vub.1_Intron|MPDU1_uc002ghx.2_Intron|MPDU1_uc010vuc.1_Intron	NM_004870	NP_004861			mannose-P-dolichol utilization defect 1						dolichol-linked oligosaccharide biosynthetic process|protein folding	endoplasmic reticulum membrane|integral to membrane|mitochondrion	protein binding			central_nervous_system(1)	1																		---	---	---	---
FXR2	9513	broad.mit.edu	37	17	7496121	7496122	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7496121_7496122insG	uc002gia.1	-	14	1846_1847	c.1619_1620insC	c.(1618-1620)CCAfs	p.P540fs	SOX15_uc002ghy.1_5'Flank|SOX15_uc002ghz.1_5'Flank	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related	540						cytosolic large ribosomal subunit	protein binding|RNA binding				0				READ - Rectum adenocarcinoma(115;0.17)														---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7736095	7736096	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7736095_7736096insG	uc002giu.1	+							NM_020877	NP_065928			dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
CNTROB	116840	broad.mit.edu	37	17	7852808	7852809	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7852808_7852809insG	uc002gjq.2	+	20	3611_3612	c.2692_2693insG	c.(2692-2694)CGGfs	p.R898fs	CNTROB_uc002gjp.2_Frame_Shift_Ins_p.R920fs|CNTROB_uc002gjr.2_Frame_Shift_Ins_p.R801fs	NM_053051	NP_444279	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	898	Required for centrosome localization.				centriole replication|centrosome separation|cytokinesis	centriole	protein domain specific binding			breast(1)|central_nervous_system(1)	2		Prostate(122;0.173)																---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8455302	8455303	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8455302_8455303insA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron|MYH10_uc010cny.1_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8492450	8492450	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8492450delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8508327	8508327	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8508327delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8517213	8517213	+	Intron	DEL	A	-	-	rs112530084		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8517213delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	8981374	8981375	+	Intron	INS	-	ATCC	ATCC	rs111350777		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8981374_8981375insATCC	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
GAS7	8522	broad.mit.edu	37	17	10048180	10048180	+	Intron	DEL	A	-	-	rs112904693		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10048180delA	uc002gmg.1	-							NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
Unknown	0	broad.mit.edu	37	17	10291666	10291666	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10291666delT	uc002gml.1	+											Homo sapiens cDNA FLJ40181 fis, clone TESTI2018178.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	10664038	10664038	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10664038delT								TMEM220 (30392 upstream) : PIRT (61755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	10817662	10817662	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10817662delG								PIRT (76244 upstream) : SHISA6 (327078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	11072267	11072269	+	IGR	DEL	AAA	-	-	rs112292987		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11072267_11072269delAAA								PIRT (330849 upstream) : SHISA6 (72471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	11101155	11101156	+	IGR	INS	-	TTCA	TTCA	rs140315760	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11101155_11101156insTTCA								PIRT (359737 upstream) : SHISA6 (43584 downstream)																																			---	---	---	---
ZNF18	7566	broad.mit.edu	37	17	11888648	11888649	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11888648_11888649insT	uc002gng.1	-						ZNF18_uc002gnh.1_Intron|ZNF18_uc002gni.1_Intron	NM_144680	NP_653281			zinc finger protein 18						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	12070349	12070350	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12070349_12070350delAG								MAP2K4 (23299 upstream) : MYOCD (498857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	12081400	12081400	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12081400delA								MAP2K4 (34350 upstream) : MYOCD (487807 downstream)																																			---	---	---	---
TRIM16	10626	broad.mit.edu	37	17	15517511	15517512	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15517511_15517512insT	uc002gor.1	-						CDRT1_uc002gov.3_Intron					SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15938343	15938343	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15938343delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_Intron|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
PIGL	9487	broad.mit.edu	37	17	16149825	16149825	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16149825delA	uc002gpv.2	+						PIGL_uc010vwd.1_Intron	NM_004278	NP_004269			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)														---	---	---	---
TNFRSF13B	23495	broad.mit.edu	37	17	16851896	16851896	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16851896delT	uc002gqs.1	-						TNFRSF13B_uc010vwt.1_Intron|TNFRSF13B_uc002gqt.1_Intron|TNFRSF13B_uc010vwu.1_Intron	NM_012452	NP_036584			tumor necrosis factor receptor 13B						cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2														IgA_Deficiency_Selective				---	---	---	---
Unknown	0	broad.mit.edu	37	17	17360190	17360190	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17360190delA								NT5M (109215 upstream) : MED9 (20110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17363647	17363649	+	IGR	DEL	TAT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17363647_17363649delTAT								NT5M (112672 upstream) : MED9 (16651 downstream)																																			---	---	---	---
FLII	2314	broad.mit.edu	37	17	18152271	18152271	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18152271delA	uc002gsr.1	-						FLII_uc002gsq.1_Intron|FLII_uc010cpy.1_Intron|FLII_uc010vxn.1_Intron|FLII_uc010vxo.1_Intron|FLII_uc002gss.1_Intron	NM_002018	NP_002009			flightless I homolog						multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)|skin(1)	2	all_neural(463;0.228)																	---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19719998	19719998	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19719998delA	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082			unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
AKAP10	11216	broad.mit.edu	37	17	19809487	19809487	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19809487delA	uc002gwo.2	-	15						NM_007202	NP_009133			A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	20420310	20420310	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20420310delG								LGALS9B (49462 upstream) : CCDC144NL (346400 downstream)																																			---	---	---	---
CCDC144NL	339184	broad.mit.edu	37	17	20772809	20772810	+	Intron	INS	-	GG	GG	rs148295899		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20772809_20772810insGG	uc002gyf.2	-						uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306			coiled-coil domain containing 144 family,												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20834960	20834960	+	RNA	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20834960delA	uc002gyi.1	+	2		c.268delA								Homo sapiens cDNA clone IMAGE:6142464.																														---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21207047	21207048	+	Intron	DEL	CA	-	-	rs139663212		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21207047_21207048delCA	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731			mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)														---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21209822	21209823	+	Intron	DEL	AG	-	-	rs71993030		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21209822_21209823delAG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731			mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	21225471	21225472	+	IGR	INS	-	A	A	rs148666159		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21225471_21225472insA								MAP2K3 (6922 upstream) : KCNJ12 (54227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21264855	21264855	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21264855delC								MAP2K3 (46306 upstream) : KCNJ12 (14844 downstream)																																			---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21309595	21309596	+	Intron	INS	-	C	C	rs144963854		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21309595_21309596insC	uc002gyv.1	+							NM_021012	NP_066292			potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21334608	21334609	+	IGR	INS	-	T	T	rs11446604		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21334608_21334609insT								KCNJ12 (11429 upstream) : C17orf51 (96963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21507129	21507129	+	IGR	DEL	A	-	-	rs113637029		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21507129delA								C17orf51 (29398 upstream) : FAM27L (318241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21563911	21563911	+	IGR	DEL	T	-	-	rs112625646		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21563911delT								C17orf51 (86180 upstream) : FAM27L (261459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25297860	25297863	+	IGR	DEL	ACTA	-	-	rs147840595	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25297860_25297863delACTA								None (None upstream) : WSB1 (323243 downstream)																																			---	---	---	---
NLK	51701	broad.mit.edu	37	17	26512302	26512302	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26512302delT	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	26569964	26569965	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26569964_26569965insA								PYY2 (14881 upstream) : PPY2 (4505 downstream)																																			---	---	---	---
SARM1	23098	broad.mit.edu	37	17	26720582	26720582	+	Intron	DEL	A	-	-	rs79200423		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26720582delA	uc010crl.1	+						SARM1_uc010waj.1_Intron|SARM1_uc002hbe.1_Intron	NM_015077	NP_055892			sterile alpha and TIR motif containing 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	26751708	26751709	+	IGR	INS	-	A	A	rs141996647	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26751708_26751709insA								SLC46A1 (18480 upstream) : SLC13A2 (48955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27395247	27395247	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27395247delT								PIPOX (11011 upstream) : MYO18A (5281 downstream)																																			---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29157882	29157882	+	5'Flank	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29157882delA	uc002hfs.1	+							NM_024857	NP_079133			ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31183109	31183109	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31183109delT	uc002hho.1	-						MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron	NM_015194	NP_056009			myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	31275023	31275023	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31275023delT								TMEM98 (6358 upstream) : SPACA3 (43859 downstream)																																			---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31428871	31428871	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31428871delT	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31749762	31749762	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31749762delC	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	32729703	32729703	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32729703delG								CCL1 (39451 upstream) : C17orf102 (171439 downstream)																																			---	---	---	---
GAS2L2	246176	broad.mit.edu	37	17	34071837	34071837	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34071837delT	uc002hjv.1	-	6						NM_139285	NP_644814			growth arrest-specific 2 like 2						cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
GAS2L2	246176	broad.mit.edu	37	17	34073290	34073290	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34073290delG	uc002hjv.1	-	6	1254	c.1226delC	c.(1225-1227)CCTfs	p.P409fs		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	409					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	35097668	35097669	+	IGR	DEL	AG	-	-	rs66718564		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35097668_35097669delAG								MRM1 (132262 upstream) : LHX1 (196830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	35166196	35166196	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35166196delG								MRM1 (200790 upstream) : LHX1 (128303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	35240742	35240743	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35240742_35240743insG								MRM1 (275336 upstream) : LHX1 (53756 downstream)																																			---	---	---	---
LHX1	3975	broad.mit.edu	37	17	35300395	35300395	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35300395delC	uc002hnh.1	+	5	2184	c.1188delC	c.(1186-1188)CACfs	p.H396fs		NM_005568	NP_005559	P48742	LHX1_HUMAN	LIM homeobox protein 1	396					cerebellar Purkinje cell differentiation|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation|cervix development|comma-shaped body morphogenesis|dorsal/ventral pattern formation|ectoderm formation|embryonic pattern specification|embryonic retina morphogenesis in camera-type eye|embryonic viscerocranium morphogenesis|endoderm formation|forebrain regionalization|head development|motor axon guidance|negative regulation of transcription, DNA-dependent|nephric duct morphogenesis|nephron tubule epithelial cell differentiation|neuron migration|oviduct epithelium development|paramesonephric duct development|positive regulation of anterior head development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of embryonic development|positive regulation of gastrulation|positive regulation of transcription, DNA-dependent|post-embryonic development|primitive streak formation|renal vesicle morphogenesis|retina layer formation|S-shaped body morphogenesis|spinal cord association neuron differentiation|transcription from RNA polymerase II promoter|ureteric bud development|uterine epithelium development|vagina development	nucleus|protein complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(25;0.00607)																---	---	---	---
TADA2A	6871	broad.mit.edu	37	17	35827710	35827711	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35827710_35827711insT	uc002hnt.2	+						TADA2A_uc002hnv.2_Intron|TADA2A_uc002hnw.2_Intron|TADA2A_uc010cvb.2_Intron	NM_001488	NP_001479			transcriptional adaptor 2A isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4																		---	---	---	---
DUSP14	11072	broad.mit.edu	37	17	35872185	35872185	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35872185delA	uc002hnx.2	+						DUSP14_uc002hny.2_Intron|DUSP14_uc002hnz.2_Intron	NM_007026	NP_008957			dual specificity phosphatase 14								MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
HNF1B	6928	broad.mit.edu	37	17	36086152	36086153	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36086152_36086153delTC	uc002hok.3	-						HNF1B_uc010wdi.1_Intron	NM_000458	NP_000449			hepatocyte nuclear factor 1-beta isoform 1						endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)											Hereditary_Prostate_Cancer				---	---	---	---
MLLT6	4302	broad.mit.edu	37	17	36868998	36868998	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36868998delC	uc002hqi.3	+	8	788	c.775delC	c.(775-777)CCCfs	p.P259fs	MLLT6_uc010wdr.1_Frame_Shift_Del_p.P259fs|MLLT6_uc010cvm.1_Frame_Shift_Del_p.P259fs|MLLT6_uc002hqj.2_5'Flank	NM_005937	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	259					regulation of transcription, DNA-dependent	nucleus	protein binding|zinc ion binding			breast(3)|prostate(1)|lung(1)|skin(1)	6	Breast(7;4.43e-21)							T	MLL	AL								---	---	---	---
MED1	5469	broad.mit.edu	37	17	37600759	37600759	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37600759delA	uc002hrv.3	-						MED1_uc010wee.1_Intron|MED1_uc002hru.2_Intron	NM_004774	NP_004765			mediator complex subunit 1						androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)											HNSCC(31;0.082)			---	---	---	---
MED1	5469	broad.mit.edu	37	17	37604623	37604624	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37604623_37604624delAA	uc002hrv.3	-						MED1_uc010wee.1_Intron|MED1_uc002hru.2_Intron	NM_004774	NP_004765			mediator complex subunit 1						androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)											HNSCC(31;0.082)			---	---	---	---
IKZF3	22806	broad.mit.edu	37	17	37988230	37988230	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37988230delA	uc002hsu.2	-						IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron	NM_012481	NP_036613			aiolos isoform 1						B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	38370029	38370030	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38370029_38370030insA								RAPGEFL1 (18123 upstream) : WIPF2 (5544 downstream)																																			---	---	---	---
CDC6	990	broad.mit.edu	37	17	38444674	38444674	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38444674delT	uc002huj.1	+							NM_001254	NP_001245			cell division cycle 6 protein						cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3																		---	---	---	---
SMARCE1	6605	broad.mit.edu	37	17	38802119	38802119	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38802119delA	uc002hux.2	-						SMARCE1_uc010wff.1_Intron|SMARCE1_uc010wfg.1_Intron|SMARCE1_uc002huy.2_Intron|SMARCE1_uc010wfh.1_Intron|SMARCE1_uc010wfi.1_Intron|SMARCE1_uc002huz.1_Intron|SMARCE1_uc010wfj.1_5'Flank|SMARCE1_uc002hva.2_Intron	NM_003079	NP_003070			SWI/SNF-related matrix-associated						chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex	chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity				0		Breast(137;0.000812)																---	---	---	---
KRT24	192666	broad.mit.edu	37	17	38854446	38854446	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38854446delT	uc002hvd.2	-	8						NM_019016	NP_061889			keratin 24							cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.00526)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	39173540	39173540	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39173540delT								KRTAP3-1 (8174 upstream) : KRTAP1-5 (8741 downstream)																																			---	---	---	---
JUP	3728	broad.mit.edu	37	17	39821341	39821341	+	Intron	DEL	T	-	-	rs34833532		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39821341delT	uc010wfs.1	-							NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
FAM134C	162427	broad.mit.edu	37	17	40734988	40734988	+	Intron	DEL	T	-	-	rs35747013		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40734988delT	uc002ial.2	-						FAM134C_uc010wgq.1_Intron|FAM134C_uc002iam.1_Intron|FAM134C_uc010cyk.1_Intron	NM_178126	NP_835227			hypothetical protein LOC162427							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	40780036	40780039	+	IGR	DEL	TCTC	-	-	rs34799305		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40780036_40780039delTCTC								TUBG1 (12782 upstream) : TUBG2 (31227 downstream)																																			---	---	---	---
WNK4	65266	broad.mit.edu	37	17	40947885	40947887	+	In_Frame_Del	DEL	GAT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40947885_40947887delGAT	uc002ibj.2	+	16	3286_3288	c.3265_3267delGAT	c.(3265-3267)GATdel	p.D1090del	WNK4_uc010wgx.1_In_Frame_Del_p.D754del|CCDC56_uc010wgz.1_In_Frame_Del_p.H124del|CNTD1_uc002ibm.3_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	1090					intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)														---	---	---	---
AARSD1	80755	broad.mit.edu	37	17	41113018	41113018	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41113018delT	uc002icc.2	-						AARSD1_uc002icd.2_Intron|AARSD1_uc002ice.2_Intron|AARSD1_uc002icf.2_Intron|AARSD1_uc010whg.1_Intron|AARSD1_uc010cyu.1_Intron	NM_025267	NP_079543			alanyl-tRNA synthetase domain containing 1						alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	41447133	41447133	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41447133delA								TMEM106A (75544 upstream) : LOC100130581 (80 downstream)																																			---	---	---	---
LOC100130581	100130581	broad.mit.edu	37	17	41466488	41466489	+	5'Flank	INS	-	C	C	rs141326881		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41466488_41466489insC	uc010wib.1	-						LOC100130581_uc010wic.1_5'Flank|LOC100130581_uc010czf.2_5'Flank|LOC100130581_uc010wid.1_5'Flank|LOC100130581_uc010wie.1_5'Flank	NR_027412				Homo sapiens cDNA FLJ41591 fis, clone CTONG2022153.												0																		---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41585987	41585989	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41585987_41585989delTTT	uc002idu.1	+						DHX8_uc010wif.1_Intron|DHX8_uc010wig.1_Intron	NM_004941	NP_004932			DEAH (Asp-Glu-Ala-His) box polypeptide 8							catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	41705605	41705605	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41705605delA								ETV4 (81843 upstream) : MEOX1 (12162 downstream)																																			---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42512617	42512617	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42512617delA	uc002igw.1	-						GPATCH8_uc002igv.1_Intron|GPATCH8_uc010wiz.1_Intron	NM_001002909	NP_001002909			G patch domain containing 8							intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)														---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42797080	42797080	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42797080delT	uc002ihf.2	+						DBF4B_uc002ihd.1_Intron|DBF4B_uc010wjb.1_Intron|DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron|DBF4B_uc002ihg.2_Intron	NM_145663	NP_663696			DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
MAP3K14	9020	broad.mit.edu	37	17	43349730	43349730	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43349730delT	uc002iiw.1	-						MAP3K14_uc002iiu.1_Intron|MAP3K14_uc010daj.1_Intron|MAP3K14_uc002iiv.1_Intron	NM_003954	NP_003945			mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|I-kappaB kinase/NF-kappaB cascade|immune response|positive regulation of I-kappaB kinase/NF-kappaB cascade|T cell costimulation	cytosol	ATP binding|MAP kinase kinase kinase activity|NF-kappaB-inducing kinase activity|protein binding			central_nervous_system(3)|breast(2)|lung(1)|ovary(1)|stomach(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	43445896	43445897	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43445896_43445897delAA								MAP3K14 (51482 upstream) : ARHGAP27 (25372 downstream)																																			---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44248899	44248899	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44248899delC	uc002ikb.2	-	1	696	c.611delG	c.(610-612)GGTfs	p.G204fs	KIAA1267_uc002ikc.2_Frame_Shift_Del_p.G204fs|KIAA1267_uc002ikd.2_Frame_Shift_Del_p.G204fs|KIAA1267_uc010dav.2_Frame_Shift_Del_p.G204fs	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	204						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
WNT9B	7484	broad.mit.edu	37	17	44950172	44950172	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44950172delG	uc002ikw.1	+						WNT9B_uc002ikx.1_Intron	NM_003396	NP_003387			wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|collecting duct development|cornea development in camera-type eye|endoderm development|establishment of planar polarity involved in nephron morphogenesis|kidney rudiment formation|male genitalia development|mesonephric duct formation|metanephric tubule development|neuron differentiation|palate development|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|uterus morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway|Wnt receptor signaling pathway, planar cell polarity pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding			lung(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.0257)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	45283201	45283201	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45283201delC								CDC27 (16536 upstream) : MYL4 (3227 downstream)																																			---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45679204	45679204	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45679204delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_5'Flank	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
TBKBP1	9755	broad.mit.edu	37	17	45778744	45778745	+	Intron	DEL	CT	-	-	rs71141926		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45778744_45778745delCT	uc002ilu.2	+							NM_014726	NP_055541			TBK1 binding protein 1						innate immune response						0																		---	---	---	---
COPZ2	51226	broad.mit.edu	37	17	46116846	46116847	+	5'Flank	DEL	AG	-	-	rs112257401		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46116846_46116847delAG	uc002imy.2	-						uc010wld.1_5'Flank|MIR152_hsa-mir-152|MI0000462_5'Flank	NM_016429	NP_057513			coatomer protein complex, subunit zeta 2						intracellular protein transport|vesicle-mediated transport	cis-Golgi network|COPI vesicle coat					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	47150296	47150296	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47150296delT								IGF2BP1 (16791 upstream) : B4GALNT2 (59526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	47554461	47554462	+	IGR	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47554461_47554462delCA								PHB (62219 upstream) : NGFR (18193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	49032220	49032221	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49032220_49032221insC								TOB1 (86881 upstream) : SPAG9 (7315 downstream)																																			---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49054674	49054675	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49054674_49054675delAA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002ita.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
UTP18	51096	broad.mit.edu	37	17	49350960	49350960	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49350960delT	uc002its.2	+							NM_016001	NP_057085			UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	50359406	50359406	+	IGR	DEL	T	-	-	rs79769884		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50359406delT								CA10 (122029 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	50768114	50768115	+	IGR	INS	-	A	A	rs150184983	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50768114_50768115insA								CA10 (530737 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	50841013	50841013	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50841013delT								CA10 (603636 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	50856196	50856197	+	IGR	INS	-	G	G	rs72525908	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50856196_50856197insG								CA10 (618819 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51131343	51131343	+	IGR	DEL	A	-	-	rs115360482	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51131343delA								CA10 (893966 upstream) : KIF2B (768896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51194079	51194079	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51194079delT								CA10 (956702 upstream) : KIF2B (706160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51216214	51216214	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51216214delA								CA10 (978837 upstream) : KIF2B (684025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51724081	51724081	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51724081delT								None (None upstream) : KIF2B (176158 downstream)																																			---	---	---	---
STXBP4	252983	broad.mit.edu	37	17	53189257	53189260	+	Intron	DEL	GTTT	-	-	rs111438818		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53189257_53189260delGTTT	uc002iuf.1	+						STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604			syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	53336564	53336565	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53336564_53336565insT								STXBP4 (95115 upstream) : HLF (5756 downstream)																																			---	---	---	---
MMD	23531	broad.mit.edu	37	17	53471908	53471908	+	Intron	DEL	A	-	-	rs147641195		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53471908delA	uc002iui.2	-							NM_012329	NP_036461			monocyte to macrophage						cytolysis	integral to plasma membrane|late endosome membrane|lysosomal membrane|membrane fraction	receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	54175778	54175779	+	IGR	INS	-	AC	AC	rs139037719	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54175778_54175779insAC								PCTP (321031 upstream) : ANKFN1 (55057 downstream)																																			---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55395550	55395557	+	Intron	DEL	GAAGGTGG	-	-	rs28508393	by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55395550_55395557delGAAGGTGG	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
Unknown	0	broad.mit.edu	37	17	55850228	55850228	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55850228delG								MSI2 (92929 upstream) : MRPS23 (66616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	56213054	56213054	+	IGR	DEL	C	-	-	rs181254	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56213054delC								DYNLL2 (45436 upstream) : OR4D1 (19461 downstream)																																			---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56791346	56791346	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56791346delT	uc002iwu.2	+						RAD51C_uc010woa.1_Intron|RAD51C_uc010ddc.2_Intron|RAD51C_uc002iwv.2_Intron|RAD51C_uc002iww.2_Intron	NM_058216	NP_478123			RAD51 homolog C isoform 1						blood coagulation|DNA repair	mitochondrion|nucleoplasm|perinuclear region of cytoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)												Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2				---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	57005425	57005425	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57005425delA	uc002iwx.2	+						PPM1E_uc010ddd.2_Intron	NM_014906	NP_055721			protein phosphatase 1E						protein dephosphorylation	cytoplasm|nucleolus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(3)|lung(1)|skin(1)	5	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)															---	---	---	---
PRR11	55771	broad.mit.edu	37	17	57278909	57278909	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57278909delT	uc002ixf.1	+						PRR11_uc002ixg.1_Intron	NM_018304	NP_060774			proline rich 11											ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	57515862	57515864	+	IGR	DEL	TTT	-	-	rs66564647		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57515862_57515864delTTT								YPEL2 (36767 upstream) : DHX40 (127022 downstream)																																			---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57750998	57750998	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57750998delT	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850			clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							T	ALK|TFE3	ALCL|renal 								---	---	---	---
TUBD1	51174	broad.mit.edu	37	17	57963684	57963684	+	Intron	DEL	A	-	-	rs113094238		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57963684delA	uc002ixw.1	-						TUBD1_uc010ddf.1_Intron|TUBD1_uc010ddg.1_Intron|TUBD1_uc010ddh.1_Intron|TUBD1_uc010wok.1_Intron|TUBD1_uc002ixx.1_Intron|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345			delta-tubulin						cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)															---	---	---	---
CA4	762	broad.mit.edu	37	17	58241552	58241555	+	Intron	DEL	TTTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58241552_58241555delTTTC	uc010wou.1	+											Homo sapiens cDNA FLJ76600 complete cds, highly similar to Homo sapiens carbonic anhydrase IV (CA4), mRNA.						bicarbonate transport|one-carbon metabolic process	anchored to external side of plasma membrane|apical plasma membrane|brush border membrane|ER-Golgi intermediate compartment|membrane fraction|perinuclear region of cytoplasm|rough endoplasmic reticulum|secretory granule membrane|trans-Golgi network|transport vesicle membrane	carbonate dehydratase activity|protein binding|zinc ion binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.83e-12)|all cancers(12;6.83e-11)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)													---	---	---	---
USP32	84669	broad.mit.edu	37	17	58451546	58451546	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58451546delA	uc002iyo.1	-						USP32_uc010wov.1_Intron	NM_032582	NP_115971			ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)															---	---	---	---
PPM1D	8493	broad.mit.edu	37	17	58729547	58729548	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58729547_58729548delCT	uc002iyt.1	+						PPM1D_uc010ddm.1_Intron	NM_003620	NP_003611			protein phosphatase 1D						negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)															---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59946936	59946936	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59946936delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60237393	60237394	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60237393_60237394delAA								MED13 (94750 upstream) : TBC1D3P2 (104675 downstream)																																			---	---	---	---
MARCH10	162333	broad.mit.edu	37	17	60821555	60821555	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60821555delA	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345			ring finger protein 190								ligase activity|zinc ion binding				0																		---	---	---	---
MARCH10	162333	broad.mit.edu	37	17	60871506	60871507	+	Intron	INS	-	CAC	CAC	rs148676242	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60871506_60871507insCAC	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345			ring finger protein 190								ligase activity|zinc ion binding				0																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61278040	61278040	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61278040delT	uc002jal.3	+						TANC2_uc010wpe.1_Intron	NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	61540419	61540419	+	IGR	DEL	A	-	-	rs77543751		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61540419delA								CYB561 (16697 upstream) : ACE (14015 downstream)																																			---	---	---	---
POLG2	11232	broad.mit.edu	37	17	62474233	62474233	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62474233delA	uc002jei.2	-							NM_007215	NP_009146			DNA polymerase subunit gamma-2, mitochondrial						DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)															---	---	---	---
DDX5	1655	broad.mit.edu	37	17	62500585	62500585	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62500585delA	uc002jek.2	-						CCDC45_uc002jem.2_5'Flank|CCDC45_uc002jen.2_5'Flank|CCDC45_uc010wqb.1_5'Flank|DDX5_uc010deh.2_Intron|DDX5_uc002jej.2_Intron|DDX5_uc010wqa.1_Intron|DDX5_uc002jel.1_5'Flank	NM_004396	NP_004387			DEAD (Asp-Glu-Ala-Asp) box polypeptide 5						cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity			ovary(2)|lung(1)	3	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)					T	ETV4	prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	17	62929293	62929294	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62929293_62929294insA								LRRC37A3 (13707 upstream) : AMZ2P1 (33374 downstream)																																			---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63804768	63804769	+	Intron	INS	-	TC	TC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63804768_63804769insTC	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64470348	64470348	+	Intron	DEL	T	-	-	rs34330453		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64470348delT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65419108	65419108	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65419108delT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65548584	65548585	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65548584_65548585delTT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
NOL11	25926	broad.mit.edu	37	17	65735615	65735615	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65735615delT	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron|SNORA38B_uc010dev.2_5'Flank	NM_015462	NP_056277			nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66347077	66347077	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66347077delC	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775			Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
FAM20A	54757	broad.mit.edu	37	17	66535606	66535609	+	Intron	DEL	TCCT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66535606_66535609delTCCT	uc002jho.2	-						FAM20A_uc010wqp.1_Intron|PRKAR1A_uc002jhm.2_Intron|FAM20A_uc002jhn.2_Intron	NM_017565	NP_060035			family with sequence similarity 20, member A							extracellular region					0	Breast(10;1.64e-13)																	---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66871571	66871572	+	Intron	DEL	AA	-	-	rs4148027		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66871571_66871572delAA	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron	NM_007168	NP_009099			ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67160299	67160299	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67160299delA	uc010dfa.1	-						ABCA10_uc010wqs.1_Intron|ABCA10_uc010wqt.1_Intron	NM_080282	NP_525021			ATP-binding cassette, sub-family A, member 10						transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
MAP2K6	5608	broad.mit.edu	37	17	67492223	67492224	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67492223_67492224delTT	uc002jij.2	+						MAP2K6_uc002jii.2_Intron	NM_002758	NP_002749			mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)																	---	---	---	---
MAP2K6	5608	broad.mit.edu	37	17	67522251	67522251	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67522251delA	uc002jij.2	+							NM_002758	NP_002749			mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	68055699	68055699	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68055699delA	uc002jim.2	+											Homo sapiens mRNA; cDNA DKFZp313B0521 (from clone DKFZp313B0521).																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	68147344	68147344	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68147344delA								KCNJ16 (15600 upstream) : KCNJ2 (17470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68974700	68974703	+	IGR	DEL	GGGA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68974700_68974703delGGGA								KCNJ2 (798519 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69594591	69594591	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69594591delT								None (None upstream) : SOX9 (522570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70398457	70398458	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70398457_70398458delTG	uc002jix.2	-											Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																														---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71607362	71607363	+	Intron	DEL	CT	-	-	rs56104919	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71607362_71607363delCT	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72185499	72185500	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72185499_72185500delCT								C17orf54 (360823 upstream) : RPL38 (14295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72481261	72481261	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72481261delT								CD300A (330 upstream) : CD300LB (36052 downstream)																																			---	---	---	---
CD300E	342510	broad.mit.edu	37	17	72610005	72610005	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72610005delC	uc002jlb.1	-							NM_181449	NP_852114			CD300e molecule precursor							integral to membrane|plasma membrane	receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
RAB37	326624	broad.mit.edu	37	17	72712852	72712853	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72712852_72712853delAG	uc010dfu.2	+						RAB37_uc002jlc.2_Intron|RAB37_uc002jld.2_Intron	NM_175738	NP_783865			RAB37, member RAS oncogene family isoform 3						protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1																		---	---	---	---
EXOC7	23265	broad.mit.edu	37	17	74093813	74093816	+	Intron	DEL	GAAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74093813_74093816delGAAC	uc002jqs.2	-						EXOC7_uc010dgv.1_Intron|EXOC7_uc002jqq.2_Intron|EXOC7_uc010wsw.1_Intron|EXOC7_uc010wsx.1_Intron|EXOC7_uc002jqr.2_Intron|EXOC7_uc010wsv.1_Intron|EXOC7_uc002jqu.2_Intron	NM_001145297	NP_001138769			exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74148636	74148636	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74148636delA	uc002jqz.2	-						RNF157_uc002jra.2_Intron|uc002jqy.1_Intron	NM_052916	NP_443148			ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
RHBDF2	79651	broad.mit.edu	37	17	74494963	74494964	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74494963_74494964delTG	uc002jrq.1	-						RHBDF2_uc002jrp.1_Intron|uc002jrt.2_5'Flank	NM_024599	NP_078875			rhomboid, veinlet-like 6 isoform 1						negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0																		---	---	---	---
MFSD11	79157	broad.mit.edu	37	17	74737870	74737870	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74737870delA	uc002jta.2	+						MFSD11_uc002jtb.2_Intron|MFSD11_uc010dha.2_Intron|MFSD11_uc002jtc.2_Intron|MFSD11_uc002jtd.3_Intron|MFSD11_uc010dhb.2_Intron|MFSD11_uc002jte.2_Intron	NM_024311	NP_077287			major facilitator superfamily domain containing							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	75253484	75253484	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75253484delC								SEC14L1 (40305 upstream) : SEPT9 (24008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	75553120	75553120	+	5'Flank	DEL	A	-	-	rs71774831		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75553120delA	uc002jua.1	+											Homo sapiens cDNA FLJ38915 fis, clone NT2NE2008867.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	76580422	76580423	+	IGR	DEL	CC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76580422_76580423delCC								DNAH17 (111566 upstream) : CYTH1 (89708 downstream)																																			---	---	---	---
USP36	57602	broad.mit.edu	37	17	76825834	76825834	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76825834delT	uc002jvz.1	-						USP36_uc002jwa.1_Intron|USP36_uc002jwd.1_Intron	NM_025090	NP_079366			ubiquitin specific peptidase 36						ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	77019787	77019790	+	Intron	DEL	CACA	-	-	rs59199190		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77019787_77019790delCACA	uc002jwo.2	-						C1QTNF1_uc002jwp.2_5'Flank|C1QTNF1_uc002jwq.2_5'Flank|C1QTNF1_uc002jwr.3_5'Flank					Homo sapiens, clone IMAGE:5225774, mRNA.																														---	---	---	---
SGSH	6448	broad.mit.edu	37	17	78184283	78184284	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78184283_78184284delGA	uc002jxz.3	-	8	1563_1564	c.1476_1477delTC	c.(1474-1479)TCTCCCfs	p.S492fs	SGSH_uc002jya.3_Frame_Shift_Del_p.S289fs|SGSH_uc002jxy.2_3'UTR	NM_000199	NP_000190	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase precursor	492_493					proteoglycan metabolic process	lysosome	metal ion binding|N-sulfoglucosamine sulfohydrolase activity|sulfuric ester hydrolase activity			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
AATK	9625	broad.mit.edu	37	17	79095042	79095042	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79095042delC	uc010dia.2	-	11	2774	c.2694delG	c.(2692-2694)GGGfs	p.G898fs	AATK_uc010dhz.2_Intron	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	898						integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)															---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80073144	80073153	+	Intron	DEL	AAGAGGGGGC	-	-	rs71962125		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80073144_80073153delAAGAGGGGGC	uc002kdx.1	-						CCDC57_uc002kdy.2_Intron	NM_198082	NP_932348			coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	80257605	80257606	+	IGR	INS	-	TTC	TTC			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80257605_80257606insTTC								CSNK1D (26032 upstream) : CD7 (15140 downstream)																																			---	---	---	---
HEXDC	284004	broad.mit.edu	37	17	80377960	80377961	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80377960_80377961delAA	uc002kew.2	+						C17orf101_uc002ket.1_5'Flank|C17orf101_uc002keu.1_5'Flank|C17orf101_uc010dip.1_5'Flank|HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron					SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	81021685	81021686	+	IGR	INS	-	A	A	rs138243681	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81021685_81021686insA								B3GNTL1 (11999 upstream) : METRNL (15881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	120869	120869	+	RNA	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:120869delT	uc002kke.2	+	5		c.1107delT								Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																														---	---	---	---
THOC1	9984	broad.mit.edu	37	18	258093	258093	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:258093delA	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron	NM_005131	NP_005122			THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	335318	335319	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:335318_335319insA	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	2646360	2646360	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2646360delA								NDC80 (29727 upstream) : SMCHD1 (9526 downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2706611	2706612	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2706611_2706612insA	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2724883	2724883	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2724883delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3508765	3508766	+	Intron	DEL	CA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3508765_3508766delCA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3676693	3676693	+	Intron	DEL	T	-	-	rs66480452		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3676693delT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3741143	3741143	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3741143delA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
LOC642597	642597	broad.mit.edu	37	18	5198365	5198365	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5198365delT	uc010wzc.1	-							NM_001145194	NP_001138666			hypothetical protein LOC642597												0																		---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5460119	5460119	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5460119delT	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439			erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8184326	8184327	+	Intron	INS	-	A	A	rs145231368	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8184326_8184327insA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	8559165	8559166	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8559165_8559166delTT								PTPRM (152307 upstream) : RAB12 (50269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10272770	10272770	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10272770delA								VAPA (312753 upstream) : APCDD1 (181855 downstream)																																			---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10548537	10548539	+	Intron	DEL	TTT	-	-	rs1662154		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548537_10548539delTTT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10732040	10732040	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10732040delA	uc002kos.1	-											SubName: Full=cDNA FLJ45725 fis, clone HCHON2009766; Flags: Fragment;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	11523147	11523148	+	IGR	INS	-	CA	CA	rs140334588	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11523147_11523148insCA								FAM38B (821168 upstream) : GNAL (165988 downstream)																																			---	---	---	---
SEH1L	81929	broad.mit.edu	37	18	12979063	12979063	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12979063delT	uc002krr.2	+						SEH1L_uc002krq.2_Intron	NM_031216	NP_112493			sec13-like protein isoform 2						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14462771	14462771	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14462771delG								LOC284233 (120249 upstream) : CXADRP3 (15185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15127641	15127641	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15127641delC								ANKRD30B (274904 upstream) : LOC644669 (185914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15385208	15385209	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15385208_15385209delCT								LOC644669 (59290 upstream) : None (None downstream)																																			---	---	---	---
GREB1L	80000	broad.mit.edu	37	18	18929188	18929189	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18929188_18929189insT	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438			growth regulation by estrogen in breast							integral to membrane					0																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19378031	19378031	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19378031delT	uc002ktq.2	+						MIB1_uc002ktp.2_Intron	NM_020774	NP_065825			mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)															---	---	---	---
C18orf45	85019	broad.mit.edu	37	18	20876823	20876823	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20876823delA	uc002kuf.2	-	15					C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_RNA|C18orf45_uc002kug.2_RNA|C18orf45_uc002kuh.2_RNA|C18orf45_uc002kue.2_RNA	NM_032933	NP_116322			hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)																	---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21139924	21139924	+	Intron	DEL	A	-	-	rs112490232		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21139924delA	uc002kum.3	-						NPC1_uc010xaz.1_Intron|NPC1_uc010xba.1_Intron	NM_000271	NP_000262			Niemann-Pick disease, type C1 precursor						autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21465074	21465074	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21465074delC	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762			laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	21565125	21565125	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21565125delT								LAMA3 (30098 upstream) : TTC39C (7612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	22600849	22600849	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22600849delA								HRH4 (540929 upstream) : ZNF521 (41039 downstream)																																			---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22901719	22901719	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22901719delA	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276			zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24051110	24051110	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24051110delC	uc002kvw.2	-						KCTD1_uc010xbj.1_Intron|KCTD1_uc010xbk.1_Intron|KCTD1_uc002kvy.2_Intron	NM_001136205	NP_001129677			potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	26030161	26030161	+	IGR	DEL	A	-	-	rs113687176		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26030161delA								CDH2 (272716 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26993123	26993123	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26993123delA								None (None upstream) : MIR302F (885753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27675317	27675317	+	IGR	DEL	T	-	-	rs35233460		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27675317delT								None (None upstream) : MIR302F (203559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28113960	28113961	+	IGR	DEL	TT	-	-	rs11318941		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28113960_28113961delTT								MIR302F (235034 upstream) : DSC3 (456092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28181743	28181743	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28181743delT								MIR302F (302817 upstream) : DSC3 (388310 downstream)																																			---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29453418	29453418	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29453418delA	uc002kxc.3	-	14	2401	c.2037delT	c.(2035-2037)TTTfs	p.F679fs	KIAA1012_uc002kxb.3_Frame_Shift_Del_p.F625fs|KIAA1012_uc002kxd.3_RNA	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	679					ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29492624	29492624	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29492624delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron|KIAA1012_uc002kxe.2_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	30249381	30249381	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30249381delA								WBP11P1 (154785 upstream) : KLHL14 (3253 downstream)																																			---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30275527	30275527	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30275527delA	uc002kxm.1	-						KLHL14_uc010dmd.1_Intron	NM_020805	NP_065856			kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	32061399	32061400	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32061399_32061400delAA								NOL4 (257953 upstream) : DTNA (11854 downstream)																																			---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32405055	32405055	+	Intron	DEL	T	-	-	rs111758936		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32405055delT	uc010dmn.1	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
GALNT1	2589	broad.mit.edu	37	18	33215699	33215699	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33215699delT	uc010dmu.2	+						GALNT1_uc002kyz.3_Intron	NM_020474	NP_065207			polypeptide N-acetylgalactosaminyltransferase 1						protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	33330480	33330481	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33330480_33330481insT								GALNT1 (38683 upstream) : MIR187 (154300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33545164	33545164	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33545164delT								MIR187 (60275 upstream) : C18orf21 (7424 downstream)																																			---	---	---	---
SLC39A6	25800	broad.mit.edu	37	18	33690943	33690943	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33690943delA	uc010dmy.2	-							NM_012319	NP_036451			solute carrier family 39 (zinc transporter),							integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	33995391	33995392	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33995391_33995392insG	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34032120	34032120	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34032120delT	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
C18orf10	25941	broad.mit.edu	37	18	34402821	34402822	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34402821_34402822insA	uc002kzw.1	-						C18orf10_uc002kzv.1_Intron|C18orf10_uc010xci.1_Intron|C18orf10_uc002kzx.1_Intron|C18orf10_uc002kzy.3_Intron	NM_015476	NP_056291			tubulin polyglutamylase complex subunit 2							cytoplasm|microtubule				skin(1)	1																		---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34539244	34539244	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34539244delT	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_5'Flank|KIAA1328_uc010dnc.1_5'Flank	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	36293512	36293512	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36293512delT								None (None upstream) : LOC647946 (493376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36617013	36617013	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36617013delT								None (None upstream) : LOC647946 (169875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37872246	37872246	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37872246delT								LOC647946 (491964 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38317635	38317636	+	IGR	INS	-	T	T	rs148530503	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38317635_38317636insT								LOC647946 (937353 upstream) : KC6 (742602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38564407	38564407	+	IGR	DEL	T	-	-	rs111420694		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38564407delT								None (None upstream) : KC6 (495831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39750503	39750503	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39750503delA								PIK3C3 (89059 upstream) : RIT2 (572690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41731996	41731996	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41731996delA								SYT4 (874381 upstream) : SETBP1 (528142 downstream)																																			---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42298442	42298443	+	Intron	DEL	AG	-	-	rs34880717		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42298442_42298443delAG	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42485768	42485771	+	Intron	DEL	AATT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42485768_42485771delAATT	uc010dni.2	+							NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44272373	44272373	+	Intron	DEL	T	-	-	rs77603253		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44272373delT	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437			ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44274203	44274203	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44274203delT	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437			ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	44977357	44977358	+	Intron	INS	-	CA	CA	rs146290447	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44977357_44977358insCA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45512877	45512878	+	IGR	DEL	TA	-	-	rs59241792		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45512877_45512878delTA								SMAD2 (55362 upstream) : ZBTB7C (40870 downstream)																																			---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45845483	45845484	+	Intron	INS	-	TG	TG	rs143825394	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45845483_45845484insTG	uc010dnw.2	-						ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SMAD7	4092	broad.mit.edu	37	18	46470119	46470119	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46470119delA	uc002ldg.2	-						SMAD7_uc002ldf.2_5'Flank|SMAD7_uc010xde.1_Intron	NM_005904	NP_005895			SMAD family member 7						adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex	activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding				0	Colorectal(1;0.0518)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	47022027	47022027	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47022027delC								RPL17 (3121 upstream) : LIPG (66400 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47518830	47518830	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47518830delA	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936			myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48263665	48263665	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48263665delA								MAPK4 (5470 upstream) : MRO (57826 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	50152821	50152821	+	Intron	DEL	T	-	-	rs79565069		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50152821delT	uc002lfe.1	+							NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50554196	50554196	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50554196delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	51460412	51460412	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51460412delT								DCC (402630 upstream) : MBD2 (220163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	52456888	52456888	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52456888delA								C18orf26 (190164 upstream) : RAB27B (38952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54218207	54218208	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54218207_54218208insA								TCF4 (915022 upstream) : TXNL1 (51847 downstream)																																			---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54283634	54283634	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54283634delA	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron|TXNL1_uc002lgj.1_Intron	NM_004786	NP_004777			thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54438030	54438030	+	Intron	DEL	T	-	-	rs77195946		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54438030delT	uc002lgk.1	+						WDR7_uc010dpk.1_Intron|WDR7_uc002lgl.1_Intron	NM_015285	NP_056100			rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	55206603	55206604	+	IGR	INS	-	AC	AC	rs145734344	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55206603_55206604insAC								ONECUT2 (48074 upstream) : FECH (5470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55618823	55618823	+	IGR	DEL	T	-	-	rs35100190		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55618823delT								ATP8B1 (219784 upstream) : NEDD4L (92796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55686289	55686289	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55686289delC								ATP8B1 (287250 upstream) : NEDD4L (25330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	56459323	56459323	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56459323delA								MALT1 (41953 upstream) : ZNF532 (70738 downstream)																																			---	---	---	---
ZNF532	55205	broad.mit.edu	37	18	56646579	56646579	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56646579delA	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron|ZNF532_uc010xeh.1_Intron	NM_018181	NP_060651			zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	56850941	56850941	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56850941delT								SEC11C (24880 upstream) : GRP (36459 downstream)																																			---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59888172	59888172	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59888172delT	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_5'Flank	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59894503	59894503	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59894503delT	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	60110589	60110589	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60110589delT								TNFRSF11A (57087 upstream) : ZCCHC2 (80069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61049034	61049035	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61049034_61049035delAG								KDSR (14528 upstream) : VPS4B (7392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61132625	61132625	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61132625delA								VPS4B (42873 upstream) : SERPINB5 (11519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61912585	61912585	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61912585delT	uc002ljx.2	+						uc002ljy.2_Intron					Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	61987856	61987857	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61987856_61987857delTT	uc002ljx.2	+											Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	62668363	62668363	+	IGR	DEL	A	-	-	rs113396827		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62668363delA								C18orf20 (852103 upstream) : CDH7 (749125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62682375	62682375	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62682375delT								C18orf20 (866115 upstream) : CDH7 (735113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63594618	63594618	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63594618delT								CDH7 (46444 upstream) : CDH19 (576703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66024607	66024607	+	IGR	DEL	T	-	-	rs77940791		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66024607delT								DSEL (840640 upstream) : TMX3 (316320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66181069	66181069	+	IGR	DEL	G	-	-	rs71923333		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66181069delG								DSEL (997102 upstream) : TMX3 (159858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66292451	66292451	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66292451delT								None (None upstream) : TMX3 (48476 downstream)																																			---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67721312	67721312	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67721312delT	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron|RTTN_uc010dqp.2_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67758656	67758656	+	Intron	DEL	A	-	-	rs74317377		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67758656delA	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67836330	67836330	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67836330delT	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron|RTTN_uc002lkq.1_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	69643318	69643321	+	IGR	DEL	GTGT	-	-	rs112368997		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69643318_69643321delGTGT								None (None upstream) : CBLN2 (560594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71001547	71001556	+	Intron	DEL	TGTGTGTGTG	-	-	rs71865876		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71001547_71001556delTGTGTGTGTG	uc002llc.1	+											Homo sapiens cDNA clone IMAGE:4667929, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	71913998	71913999	+	IGR	DEL	CT	-	-	rs67333018		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71913998_71913999delCT								C18orf55 (87794 upstream) : CYB5A (6529 downstream)																																			---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74617099	74617099	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74617099delT	uc002lmi.2	+						ZNF236_uc002lmj.2_Intron	NM_007345	NP_031371			zinc finger protein 236						cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	75204268	75204268	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75204268delA								GALR1 (222174 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75981542	75981543	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75981542_75981543insA								GALR1 (999448 upstream) : SALL3 (758732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76798676	76798677	+	IGR	DEL	TG	-	-	rs111733904		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76798676_76798677delTG								SALL3 (40485 upstream) : ATP9B (30720 downstream)																																			---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	76870316	76870316	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76870316delA	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_5'Flank|ATP9B_uc002lmu.2_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77041498	77041498	+	Intron	DEL	A	-	-	rs35595923		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77041498delA	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77444926	77444927	+	Intron	DEL	GG	-	-	rs113059721		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77444926_77444927delGG	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706			CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)														---	---	---	---
C18orf22	79863	broad.mit.edu	37	18	77802768	77802769	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77802768_77802769delAA	uc002lns.2	+						C18orf22_uc010drh.2_Intron|C18orf22_uc010dri.1_Intron|C18orf22_uc002lnt.2_Intron	NM_024805	NP_079081			hypothetical protein LOC79863 precursor						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)														---	---	---	---
HCN2	610	broad.mit.edu	37	19	601315	601315	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:601315delA	uc002lpe.2	+							NM_001194	NP_001185			hyperpolarization activated cyclic						cell-cell signaling|muscle contraction	voltage-gated potassium channel complex	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MED16	10025	broad.mit.edu	37	19	876933	876933	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:876933delC	uc002lqd.1	-						MED16_uc010drw.1_Intron|MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Intron|MED16_uc010xfx.1_Intron|MED16_uc010xfy.1_Intron	NM_005481	NP_005472			mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
C19orf22	91300	broad.mit.edu	37	19	901632	901632	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:901632delT	uc002lqg.2	-						C19orf22_uc002lqh.2_Intron|C19orf22_uc002lqi.2_Intron|C19orf22_uc002lqj.2_Intron	NM_138774	NP_620129			hypothetical protein LOC91300							nucleus	nucleic acid binding			pancreas(1)	1		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)														---	---	---	---
ARID3A	1820	broad.mit.edu	37	19	968359	968359	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:968359delA	uc002lql.2	+							NM_005224	NP_005215			AT rich interactive domain 3A (BRIGHT- like)							cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MKNK2	2872	broad.mit.edu	37	19	2037631	2037632	+	3'UTR	DEL	TT	-	-	rs71737199		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2037631_2037632delTT	uc002lus.2	-	14					MKNK2_uc002luq.1_3'UTR|MKNK2_uc010xgu.1_3'UTR|MKNK2_uc010xgv.1_3'UTR|MKNK2_uc002lur.2_3'UTR|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009			MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2068173	2068174	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2068173_2068174insT								MKNK2 (16930 upstream) : MOBKL2A (2863 downstream)																																			---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2208187	2208187	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2208187delC	uc002lvb.3	+						DOT1L_uc002lvc.1_5'Flank	NM_032482	NP_115871			DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2558247	2558248	+	Intron	DEL	TG	-	-	rs144565304	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2558247_2558248delTG	uc002lwd.2	-							NM_052847	NP_443079			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2639230	2639231	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2639230_2639231delAA	uc002lwd.2	-							NM_052847	NP_443079			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF555	148254	broad.mit.edu	37	19	2851297	2851297	+	Intron	DEL	A	-	-	rs10713166		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2851297delA	uc002lwo.2	+						ZNF555_uc002lwn.3_Intron	NM_152791	NP_690004			zinc finger protein 555						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ITGB1BP3	27231	broad.mit.edu	37	19	3938842	3938842	+	Intron	DEL	G	-	-	rs7508648		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3938842delG	uc002lyz.3	+						ITGB1BP3_uc010xia.1_Intron	NM_170678	NP_733778			integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
CCDC94	55702	broad.mit.edu	37	19	4261827	4261827	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4261827delA	uc002lzv.3	+							NM_018074	NP_060544			coiled-coil domain containing 94												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
FSD1	79187	broad.mit.edu	37	19	4311683	4311683	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4311683delA	uc002lzy.2	+						FSD1_uc002lzz.2_Intron|FSD1_uc002maa.2_5'UTR	NM_024333	NP_077309			fibronectin type III and SPRY domain containing						cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SH3GL1	6455	broad.mit.edu	37	19	4363886	4363886	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4363886delG	uc002maj.2	-						SH3GL1_uc002mak.2_Intron|SH3GL1_uc010xig.1_Intron	NM_003025	NP_003016			SH3-domain GRB2-like 1						central nervous system development|endocytosis|signal transduction	early endosome membrane	lipid binding|protein binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)				T	MLL	AL								---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4694587	4694587	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4694587delG	uc002mba.2	-						DPP9_uc002mbb.2_3'UTR|DPP9_uc002mbc.2_3'UTR	NM_139159	NP_631898			dipeptidylpeptidase 9						proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)														---	---	---	---
UHRF1	29128	broad.mit.edu	37	19	4933248	4933248	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4933248delT	uc002mbo.2	+						UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_Intron|UHRF1_uc002mbp.2_Intron	NM_001048201	NP_001041666			ubiquitin-like with PHD and ring finger domains						cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	5386002	5386009	+	IGR	DEL	AGGAAGGA	-	-	rs111509028		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5386002_5386009delAGGAAGGA								PTPRS (45188 upstream) : ZNRF4 (69417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	5396444	5396445	+	IGR	INS	-	GCAGG	GCAGG	rs143093828	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5396444_5396445insGCAGG								PTPRS (55630 upstream) : ZNRF4 (58981 downstream)																																			---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5667025	5667025	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5667025delT	uc002mcf.2	+						SAFB_uc002mcg.2_Intron|SAFB_uc002mce.3_Intron|SAFB_uc010xir.1_Intron|SAFB_uc010xis.1_Intron|SAFB_uc010xit.1_Intron|SAFB_uc010xiu.1_Intron	NM_002967	NP_002958			scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)														---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7502956	7502957	+	5'Flank	DEL	CT	-	-	rs148698183	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7502956_7502957delCT	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron	NM_001130955	NP_001124427			Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)																---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7512065	7512065	+	Intron	DEL	T	-	-	rs59050162	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7512065delT	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427			Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)																---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7671043	7671043	+	Intron	DEL	C	-	-	rs71879481		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7671043delC	uc002mgv.3	+						KIAA1543_uc002mgu.3_Intron	NM_020902	NP_065953			NEZHA isoform 2						epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
CD209	30835	broad.mit.edu	37	19	7806378	7806378	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7806378delA	uc002mht.2	-	7					CD209_uc010xju.1_3'UTR|CD209_uc010dvp.2_3'UTR|CD209_uc002mhr.2_3'UTR|CD209_uc002mhs.2_3'UTR|CD209_uc002mhu.2_3'UTR|CD209_uc010dvq.2_3'UTR|CD209_uc002mhq.2_3'UTR|CD209_uc002mhv.2_3'UTR|CD209_uc002mhx.2_3'UTR|CD209_uc002mhw.2_3'UTR|CD209_uc010dvr.2_3'UTR	NM_021155	NP_066978			CD209 molecule isoform 1						cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding			skin(1)	1																		---	---	---	---
CD320	51293	broad.mit.edu	37	19	8372532	8372532	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8372532delG	uc002mjj.1	-						CD320_uc002mjk.1_Intron|CD320_uc002mjl.1_Intron	NM_016579	NP_057663			8D6 antigen isoform 1 precursor						regulation of cell growth	endoplasmic reticulum|integral to membrane	growth factor activity				0																		---	---	---	---
OR1M1	125963	broad.mit.edu	37	19	9202341	9202342	+	5'Flank	DEL	AA	-	-	rs113355974		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9202341_9202342delAA	uc010xkj.1	+							NM_001004456	NP_001004456			olfactory receptor, family 1, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10071664	10071664	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10071664delC	uc002mmq.1	-							NM_015719	NP_056534			collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10076810	10076810	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10076810delT	uc002mmq.1	-							NM_015719	NP_056534			collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
RAVER1	125950	broad.mit.edu	37	19	10428050	10428050	+	3'UTR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10428050delA	uc002moa.2	-	13					FDX1L_uc002mnx.1_5'Flank|FDX1L_uc002mny.1_5'Flank|RAVER1_uc002mnz.2_3'UTR	NM_133452	NP_597709			RAVER1							cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)															---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10544890	10544890	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10544890delT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron	NM_001111307	NP_001104777			phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10570559	10570559	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10570559delT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Intron|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_Intron	NM_001111307	NP_001104777			phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
LDLR	3949	broad.mit.edu	37	19	11230930	11230930	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11230930delC	uc002mqk.3	+						LDLR_uc010xlk.1_Intron|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Intron|LDLR_uc010xlo.1_Intron	NM_000527	NP_000518			low density lipoprotein receptor precursor						cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)													---	---	---	---
CNN1	1264	broad.mit.edu	37	19	11658537	11658537	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11658537delA	uc002msc.1	+						CNN1_uc010xmb.1_Intron|CNN1_uc010xmc.1_Intron	NM_001299	NP_001290			calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11940914	11940914	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11940914delA	uc002msp.1	+							NM_152357	NP_689570			zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF69	7620	broad.mit.edu	37	19	12014223	12014224	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12014223_12014224insA	uc002mst.3	+							NM_021915	NP_068734			zinc finger protein 69							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				Lung(535;0.011)														---	---	---	---
ZNF69	7620	broad.mit.edu	37	19	12014466	12014467	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12014466_12014467delCT	uc002mst.3	+	2	169_170	c.100_101delCT	c.(100-102)CTCfs	p.L34fs		NM_021915	NP_068734	Q9UC07	ZNF69_HUMAN	zinc finger protein 69	48	KRAB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				Lung(535;0.011)														---	---	---	---
ZNF20	7568	broad.mit.edu	37	19	12261910	12261910	+	Intron	DEL	T	-	-	rs35215456		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12261910delT	uc002mtg.1	-						ZNF625_uc010dyn.1_Intron|ZNF625_uc002mth.2_Intron	NM_021143	NP_066966			zinc finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
CALR	811	broad.mit.edu	37	19	13050676	13050676	+	Intron	DEL	T	-	-	rs111588637		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13050676delT	uc002mvu.2	+							NM_004343	NP_004334			calreticulin precursor						cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13171691	13171691	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13171691delT	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron					RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)													OREG0025285	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13199525	13199525	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13199525delT	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron					RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)															---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13208002	13208002	+	3'UTR	DEL	T	-	-	rs71719751		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13208002delT	uc010xmx.1	+	11					NFIX_uc002mwd.2_3'UTR|NFIX_uc002mwe.2_3'UTR|NFIX_uc002mwf.2_3'UTR					RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)															---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13395850	13395850	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13395850delC	uc010dze.2	-						CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	13684990	13684991	+	IGR	INS	-	ACAG	ACAG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13684990_13684991insACAG								CACNA1A (67716 upstream) : CCDC130 (157583 downstream)																																			---	---	---	---
ZSWIM4	65249	broad.mit.edu	37	19	13917484	13917484	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13917484delA	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560			zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)															---	---	---	---
DCAF15	90379	broad.mit.edu	37	19	14067112	14067112	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14067112delC	uc002mxt.2	+						PODNL1_uc010xnj.1_5'Flank|PODNL1_uc002mxs.2_5'Flank	NM_138353	NP_612362			DDB1 and CUL4 associated factor 15											central_nervous_system(1)	1																		---	---	---	---
SLC1A6	6511	broad.mit.edu	37	19	15070714	15070715	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15070714_15070715insT	uc002naa.1	-						SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Intron	NM_005071	NP_005062			solute carrier family 1 (high affinity						synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
SLC1A6	6511	broad.mit.edu	37	19	15080795	15080795	+	Intron	DEL	T	-	-	rs78920893		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15080795delT	uc002naa.1	-						SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Intron|SLC1A6_uc002nab.2_Intron|SLC1A6_uc002nac.2_Intron|SLC1A6_uc002nad.1_Intron	NM_005071	NP_005062			solute carrier family 1 (high affinity						synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	15599221	15599222	+	IGR	DEL	CA	-	-	rs114204328	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15599221_15599222delCA								PGLYRP2 (8906 upstream) : CYP4F22 (20114 downstream)																																			---	---	---	---
CALR3	125972	broad.mit.edu	37	19	16591362	16591362	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16591362delA	uc002ned.2	-						MED26_uc002nee.2_Intron	NM_145046	NP_659483			calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0																		---	---	---	---
MED26	9441	broad.mit.edu	37	19	16705532	16705532	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16705532delA	uc002nen.1	-						MED26_uc002nee.2_Intron	NM_004831	NP_004822			mediator complex subunit 26						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|RNA polymerase II transcription cofactor activity|transcription coactivator activity			ovary(2)	2																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16895744	16895744	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16895744delA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron					RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	16936514	16936514	+	IGR	DEL	A	-	-	rs72287578		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16936514delA								NWD1 (7741 upstream) : SIN3B (3704 downstream)																																			---	---	---	---
FAM129C	199786	broad.mit.edu	37	19	17643782	17643782	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17643782delA	uc010xpr.1	+						FAM129C_uc010xpq.1_Intron|FAM129C_uc010xps.1_Intron|FAM129C_uc010xpt.1_Intron	NM_173544	NP_775815			B-cell novel protein 1 isoform a												0																		---	---	---	---
FCHO1	23149	broad.mit.edu	37	19	17886616	17886617	+	Intron	INS	-	G	G	rs141975198	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17886616_17886617insG	uc010ebb.2	+						FCHO1_uc002nhg.3_Intron|FCHO1_uc002nhh.2_Intron|FCHO1_uc010xpw.1_Intron|FCHO1_uc002nhi.2_5'Flank|FCHO1_uc002nhj.2_5'Flank	NM_001161358	NP_001154830			FCH domain only 1 isoform b											breast(1)	1																OREG0025349	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17994332	17994332	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17994332delG	uc002nhr.3	+							NM_000453	NP_000444			solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
MAST3	23031	broad.mit.edu	37	19	18212176	18212178	+	Intron	DEL	CTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18212176_18212178delCTT	uc002nhz.3	+						IL12RB1_uc002nhx.1_5'Flank	NM_015016	NP_055831			microtubule associated serine/threonine kinase								ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)|stomach(1)	5																		---	---	---	---
UPF1	5976	broad.mit.edu	37	19	18975358	18975358	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18975358delT	uc002nkg.2	+						UPF1_uc002nkf.2_Intron|UPF1_uc002nkh.2_Intron	NM_002911	NP_002902			regulator of nonsense transcripts 1						cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SFRS14	10147	broad.mit.edu	37	19	19137052	19137052	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19137052delA	uc002nkx.2	-						SFRS14_uc002nkz.1_Intron|SFRS14_uc002nla.1_Intron|SFRS14_uc002nlb.2_Intron|SFRS14_uc010xqk.1_Intron	NM_014884	NP_055699			splicing factor, arginine/serine-rich 14						mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)															---	---	---	---
KIAA0892	23383	broad.mit.edu	37	19	19447108	19447109	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19447108_19447109insT	uc002nmk.3	+							NM_015329	NP_056144			hypothetical protein LOC23383 precursor						cell division|maintenance of mitotic sister chromatid cohesion	chromatin|nucleoplasm|SMC loading complex	protein N-terminus binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20635102	20635102	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20635102delT								ZNF826 (27340 upstream) : ZNF737 (85697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23300784	23300784	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23300784delT	uc002nrb.1	+											Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	24061349	24061351	+	IGR	DEL	AGA	-	-	rs67258339		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24061349_24061351delAGA								RPSAP58 (50432 upstream) : ZNF254 (154896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24537384	24537384	+	IGR	DEL	T	-	-	rs77972838		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24537384delT								LOC100101266 (191135 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27852050	27852051	+	IGR	INS	-	A	A	rs139076706		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27852050_27852051insA								None (None upstream) : LOC148189 (429351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27869241	27869241	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27869241delT								None (None upstream) : LOC148189 (412161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28503138	28503138	+	IGR	DEL	C	-	-	rs67329486		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28503138delC								LOC148189 (218290 upstream) : LOC148145 (952902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28834227	28834229	+	IGR	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28834227_28834229delAAA								LOC148189 (549379 upstream) : LOC148145 (621811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28890669	28890670	+	IGR	INS	-	CACACACACACA	CACACACACACA	rs141832722	by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28890669_28890670insCACACACACACA								LOC148189 (605821 upstream) : LOC148145 (565370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28915252	28915255	+	IGR	DEL	CACA	-	-	rs67479293		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28915252_28915255delCACA								LOC148189 (630404 upstream) : LOC148145 (540785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29968405	29968407	+	Intron	DEL	TTT	-	-	rs72150902		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29968405_29968407delTTT	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																														---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30441469	30441469	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30441469delT	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	31384326	31384327	+	IGR	DEL	AA	-	-	rs112959829		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31384326_31384327delAA								ZNF536 (335361 upstream) : DKFZp566F0947 (256456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32670631	32670632	+	IGR	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32670631_32670632delTC								TSHZ3 (830441 upstream) : ZNF507 (165882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32785844	32785845	+	IGR	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32785844_32785845insG								TSHZ3 (945654 upstream) : ZNF507 (50669 downstream)																																			---	---	---	---
DPY19L3	147991	broad.mit.edu	37	19	32927216	32927217	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32927216_32927217insT	uc002ntg.2	+						DPY19L3_uc002nth.1_Intron|DPY19L3_uc002nti.1_5'Flank	NM_207325	NP_997208			dpy-19-like 3							integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	33034360	33034360	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33034360delA								DPY19L3 (59124 upstream) : PDCD5 (37744 downstream)																																			---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33281512	33281512	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33281512delA	uc002ntq.2	+						TDRD12_uc002ntr.3_Intron					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34110863	34110864	+	5'Flank	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34110863_34110864delTG	uc002nus.3	+						CHST8_uc002nut.3_5'Flank	NM_001127895	NP_001121367			carbohydrate (N-acetylgalactosamine 4-0)						carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	34513459	34513459	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34513459delT								KCTD15 (206794 upstream) : LSM14A (149893 downstream)																																			---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34922918	34922919	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34922918_34922919insA	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490			SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)															---	---	---	---
ZNF30	90075	broad.mit.edu	37	19	35418657	35418658	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35418657_35418658delCT	uc010edp.1	+						ZNF30_uc002nxf.2_Intron|ZNF30_uc010edq.1_Intron|ZNF30_uc010edr.1_Intron	NM_194325	NP_919306			zinc finger protein 30 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)														---	---	---	---
GAPDHS	26330	broad.mit.edu	37	19	36027481	36027481	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36027481delA	uc002oaf.1	+							NM_014364	NP_055179			glyceraldehyde-3-phosphate dehydrogenase,						gluconeogenesis|glycolysis|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)													---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36572187	36572187	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36572187delT	uc002odc.2	+						WDR62_uc002odd.2_Intron	NM_173636	NP_775907			WD repeat domain 62 isoform 2						cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF567	163081	broad.mit.edu	37	19	37179363	37179363	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37179363delT	uc010xtl.1	+						ZNF567_uc002oeo.1_Intron|ZNF567_uc010xtk.1_Intron|ZNF567_uc002oep.3_5'Flank	NM_152603	NP_689816			zinc finger protein 567						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	37531931	37531931	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37531931delA								ZNF568 (43097 upstream) : ZNF420 (37451 downstream)																																			---	---	---	---
ZNF569	148266	broad.mit.edu	37	19	37916539	37916539	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37916539delT	uc002ogi.2	-						ZNF569_uc002ogh.2_Intron|ZNF569_uc002ogj.2_Intron	NM_152484	NP_689697			zinc finger protein 569						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
SARS2	54938	broad.mit.edu	37	19	39408522	39408522	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39408522delC	uc002oka.2	-						SARS2_uc002ojz.2_Intron|SARS2_uc010xup.1_Intron|SARS2_uc002okb.2_Intron|SARS2_uc010xuq.1_Intron|SARS2_uc010xur.1_Intron	NM_017827	NP_060297			seryl-tRNA synthetase 2 isoform b precursor						seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
PLEKHG2	64857	broad.mit.edu	37	19	39907069	39907069	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39907069delG	uc010xuz.1	+						PLEKHG2_uc010xuy.1_Intron|PLEKHG2_uc002olj.2_Intron|PLEKHG2_uc010xva.1_Intron	NM_022835	NP_073746			common-site lymphoma/leukemia guanine nucleotide						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41290746	41290747	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41290746_41290747delTT	uc010ehd.2	+						RAB4B_uc002opc.1_Intron|RAB4B_uc002opd.1_Intron|RAB4B_uc002ope.1_Intron|RAB4B_uc002opf.1_Intron	NM_080732	NP_542770			EGL nine (C.elegans) homolog 2						cell redox homeostasis|estrogen receptor signaling pathway|positive regulation of protein catabolic process|regulation of cell growth|response to hypoxia	cytoplasm|nucleus	ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|oxygen sensor activity			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	42203963	42203968	+	IGR	DEL	ACACAC	-	-	rs9304599		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42203963_42203968delACACAC								CEACAM7 (11867 upstream) : CEACAM5 (8562 downstream)																																			---	---	---	---
CEACAM3	1084	broad.mit.edu	37	19	42310943	42310943	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42310943delT	uc002orn.1	+						CEACAM3_uc010eia.1_Intron|CEACAM3_uc002oro.1_Intron	NM_001815	NP_001806			carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1																		---	---	---	---
DMRTC2	63946	broad.mit.edu	37	19	42352414	42352414	+	Intron	DEL	A	-	-	rs79959130		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42352414delA	uc002ors.2	+						DMRTC2_uc002orr.1_Intron|DMRTC2_uc010xwe.1_Intron	NM_001040283	NP_001035373			DMRT-like family C2						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
XRCC1	7515	broad.mit.edu	37	19	44055917	44055918	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44055917_44055918delAG	uc002owt.2	-						XRCC1_uc010xwp.1_Intron	NM_006297	NP_006288			X-ray repair cross complementing protein 1						base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(2)|large_intestine(1)|prostate(1)|breast(1)	7		Prostate(69;0.0153)											Other_BER_factors					---	---	---	---
Unknown	0	broad.mit.edu	37	19	44197658	44197658	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44197658delT								PLAUR (23156 upstream) : IRGC (22556 downstream)																																			---	---	---	---
ZNF234	10780	broad.mit.edu	37	19	44662403	44662403	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44662403delT	uc002oym.2	+	6					ZNF234_uc002oyl.3_3'UTR	NM_006630	NP_006621			zinc finger protein 234						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	45127521	45127523	+	Intron	DEL	TCC	-	-	rs35551910		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45127521_45127523delTCC	uc002ozk.2	+											SubName: Full=LOC147710 protein; Flags: Fragment;																														---	---	---	---
PVRL2	5819	broad.mit.edu	37	19	45384941	45384942	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45384941_45384942insA	uc002ozw.1	+							NM_001042724	NP_001036189			poliovirus receptor related 2 isoform delta						adherens junction organization|adhesion to symbiont|cell junction assembly|homophilic cell adhesion|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|susceptibility to natural killer cell mediated cytotoxicity|susceptibility to T cell mediated cytotoxicity|viral envelope fusion with host membrane|virion attachment, binding of host cell surface coreceptor	cell surface|integral to membrane|zonula adherens	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45438353	45438353	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45438353delA								APOC1P1 (4072 upstream) : APOC4 (7142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45637425	45637425	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45637425delT	uc002pas.2	+											Homo sapiens leucine rich repeat containing 68, mRNA (cDNA clone IMAGE:5573062), partial cds.																														---	---	---	---
ERCC2	2068	broad.mit.edu	37	19	45863039	45863040	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45863039_45863040delTT	uc002pbj.2	-						ERCC2_uc002pbh.2_5'Flank|ERCC2_uc002pbi.2_Intron|ERCC2_uc010ejz.2_Intron|ERCC2_uc002pbk.2_Intron|ERCC2_uc002pbl.3_Intron	NM_000400	NP_000391			excision repair cross-complementing rodent						cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction	cytoplasm|holo TFIIH complex|MMXD complex	5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding			lung(2)|pancreas(1)	3		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)				Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
PPP1R13L	10848	broad.mit.edu	37	19	45899209	45899209	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45899209delA	uc002pbn.2	-						PPP1R13L_uc002pbm.2_5'Flank|PPP1R13L_uc002pbo.2_Intron|PPP1R13L_uc002pbp.2_Intron	NM_006663	NP_006654			protein phosphatase 1, regulatory subunit 13						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription corepressor activity|transcription factor binding			skin(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)														---	---	---	---
QPCTL	54814	broad.mit.edu	37	19	46204848	46204849	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46204848_46204849insA	uc010xxr.1	+						QPCTL_uc010ekn.2_Intron	NM_017659	NP_060129			glutaminyl-peptide cyclotransferase-like isoform						peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase|proteolysis	Golgi membrane|integral to membrane	acyltransferase activity|glutaminyl-peptide cyclotransferase activity|peptidase activity|protein binding|zinc ion binding			skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	46530004	46530004	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46530004delA								PGLYRP1 (3681 upstream) : IGFL4 (13002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	47075041	47075041	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47075041delT	uc002pev.1	-											SubName: Full=cDNA FLJ37185 fis, clone BRALZ2001743, moderately similar to Serine/threonine-protein phosphatase 5;          EC=3.1.3.16;																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	47330412	47330413	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47330412_47330413insT								SLC1A5 (38570 upstream) : SNAR-E (3429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	47794120	47794122	+	IGR	DEL	AAA	-	-	rs143445362	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47794120_47794122delAAA								PRR24 (15141 upstream) : C5AR1 (18982 downstream)																																			---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47869997	47869998	+	Intron	INS	-	T	T	rs113188823		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47869997_47869998insT	uc010xyn.1	+						DHX34_uc010elc.1_Intron	NM_014681	NP_055496			DEAH (Asp-Glu-Ala-His) box polypeptide 34							intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)														---	---	---	---
EHD2	30846	broad.mit.edu	37	19	48219901	48219901	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48219901delG	uc002phj.3	+	2	282	c.32delG	c.(31-33)CGGfs	p.R11fs	EHD2_uc010xyu.1_Intron	NM_014601	NP_055416	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	11					blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding			ovary(1)|skin(1)	2		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)														---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48653517	48653517	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48653517delT	uc002pia.1	-						LIG1_uc010xze.1_Intron|LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron	NM_000234	NP_000225			DNA ligase I						anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)								NER					---	---	---	---
SPHK2	56848	broad.mit.edu	37	19	49130901	49130901	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49130901delG	uc002pjr.2	+						SPHK2_uc010xzt.1_Intron|SPHK2_uc002pjs.2_Intron|SPHK2_uc002pjt.2_Intron|SPHK2_uc002pju.2_Intron|SPHK2_uc002pjv.2_Intron|SPHK2_uc002pjw.2_Intron|SPHK2_uc010xzu.1_Intron	NM_020126	NP_064511			sphingosine kinase 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)														---	---	---	---
PLEKHA4	57664	broad.mit.edu	37	19	49365224	49365224	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49365224delA	uc002pkx.2	-						PLEKHA4_uc002pkw.1_5'Flank|PLEKHA4_uc010eml.2_Intron	NM_020904	NP_065955			pleckstrin homology domain containing family A							cytoplasm|membrane	1-phosphatidylinositol binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)														---	---	---	---
TULP2	7288	broad.mit.edu	37	19	49399502	49399502	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49399502delC	uc002pkz.2	-							NM_003323	NP_003314			tubby like protein 2						visual perception	cytoplasm|extracellular region				ovary(1)|kidney(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)														---	---	---	---
NUCB1	4924	broad.mit.edu	37	19	49409198	49409202	+	Intron	DEL	CACTC	-	-	rs71903082		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49409198_49409202delCACTC	uc002plb.3	+						NUCB1_uc002pla.2_Intron|NUCB1_uc002plc.2_Intron	NM_006184	NP_006175			nucleobindin 1 precursor							ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)														---	---	---	---
DHDH	27294	broad.mit.edu	37	19	49434630	49434630	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49434630delT	uc002ple.1	+							NM_014475	NP_055290			dimeric dihydrodiol dehydrogenase						carbohydrate metabolic process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)														---	---	---	---
SNRNP70	6625	broad.mit.edu	37	19	49604874	49604877	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49604874_49604877delTTTT	uc002pmk.2	+						SNRNP70_uc002pmh.1_Intron|SNRNP70_uc002pmi.1_Intron|SNRNP70_uc002pml.2_Intron|SNRNP70_uc002pmm.2_Intron	NM_003089	NP_003080			U1 small nuclear ribonucleoprotein 70 kDa						nuclear mRNA splicing, via spliceosome|regulation of RNA splicing	nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	49715837	49715838	+	IGR	INS	-	CTTC	CTTC	rs76677262		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49715837_49715838insCTTC								TRPM4 (746 upstream) : SLC6A16 (77056 downstream)																																			---	---	---	---
BCL2L12	83596	broad.mit.edu	37	19	50170493	50170493	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50170493delG	uc002ppa.2	+						IRF3_uc002pot.1_5'Flank|IRF3_uc010end.1_5'Flank|IRF3_uc002pox.1_5'Flank|IRF3_uc002poy.1_5'Flank|IRF3_uc002pou.2_5'Flank|IRF3_uc002pov.2_5'Flank|IRF3_uc002pow.2_5'Flank|IRF3_uc002poz.1_5'Flank|IRF3_uc010ene.1_5'Flank|BCL2L12_uc002ppb.2_Intron	NM_138639	NP_619580			BCL2-like 12 isoform 1						apoptosis					central_nervous_system(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)														---	---	---	---
PRMT1	3276	broad.mit.edu	37	19	50177601	50177601	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50177601delT	uc010enf.1	+						PRMT1_uc002ppc.1_5'Flank|PRMT1_uc002ppd.2_5'Flank|PRMT1_uc002ppe.2_5'Flank|PRMT1_uc002ppf.2_5'Flank|PRMT1_uc002ppg.2_5'Flank	NM_001536	NP_001527			HMT1 hnRNP methyltransferase-like 2 isoform 1							cytoplasm	protein methyltransferase activity			ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)														---	---	---	---
PRMT1	3276	broad.mit.edu	37	19	50183041	50183041	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50183041delC	uc010enf.1	+						PRMT1_uc002ppc.1_Intron|PRMT1_uc002ppd.2_Intron|PRMT1_uc002ppe.2_Intron|PRMT1_uc002ppf.2_Intron|PRMT1_uc002ppg.2_Intron|PRMT1_uc010yba.1_5'Flank	NM_001536	NP_001527			HMT1 hnRNP methyltransferase-like 2 isoform 1							cytoplasm	protein methyltransferase activity			ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)														---	---	---	---
MED25	81857	broad.mit.edu	37	19	50333435	50333435	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50333435delC	uc002ppw.1	+	7	832	c.779delC	c.(778-780)GCCfs	p.A260fs	MED25_uc010ybe.1_Intron|MED25_uc002ppx.1_Frame_Shift_Del_p.A41fs	NM_030973	NP_112235	Q71SY5	MED25_HUMAN	mediator complex subunit 25	260	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)														---	---	---	---
SIGLEC11	114132	broad.mit.edu	37	19	50462070	50462070	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50462070delG	uc010ybh.1	-	7	1284	c.1193delC	c.(1192-1194)CCAfs	p.P398fs	SIGLEC11_uc010ybi.1_Frame_Shift_Del_p.P398fs	NM_052884	NP_443116	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11 isoform 1	398	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|central_nervous_system(2)|pancreas(1)	6		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)														---	---	---	---
MYBPC2	4606	broad.mit.edu	37	19	50951238	50951239	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50951238_50951239insT	uc002psf.2	+							NM_004533	NP_004524			myosin binding protein C, fast type						cell adhesion|muscle filament sliding	cytosol|myosin filament	actin binding|structural constituent of muscle			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51197571	51197571	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51197571delG	uc002psx.1	-							NM_016148	NP_057232			SH3 and multiple ankyrin repeat domains 1						cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52020158	52020158	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52020158delT								SIGLEC12 (15115 upstream) : SIGLEC6 (2626 downstream)																																			---	---	---	---
FPR3	2359	broad.mit.edu	37	19	52319510	52319510	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52319510delT	uc002pxt.1	+							NM_002030	NP_002021			formyl peptide receptor-like 2						cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity			lung(4)|breast(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	52685026	52685027	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52685026_52685027delGT								ZNF836 (10130 upstream) : PPP2R1A (8164 downstream)																																			---	---	---	---
ZNF137	7696	broad.mit.edu	37	19	53102005	53102006	+	RNA	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53102005_53102006insA	uc002pzt.2	+	2		c.1425_1426insA				NR_023311				Homo sapiens zinc finger protein 137, mRNA (cDNA clone IMAGE:40016639).												0				GBM - Glioblastoma multiforme(134;0.0212)|OV - Ovarian serous cystadenocarcinoma(262;0.0221)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53428515	53428515	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53428515delT								ZNF320 (27569 upstream) : ZNF321 (1873 downstream)																																			---	---	---	---
MIR1323	100302255	broad.mit.edu	37	19	54172530	54172530	+	5'Flank	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54172530delG	hsa-mir-1323|MI0003786	+																							0																		---	---	---	---
MIR527	574497	broad.mit.edu	37	19	54255824	54255824	+	5'Flank	DEL	T	-	-	rs68052952		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54255824delT	hsa-mir-527|MI0003179	+																							0																		---	---	---	---
PRKCG	5582	broad.mit.edu	37	19	54393516	54393517	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54393516_54393517insT	uc002qcq.1	+						PRKCG_uc010eqz.1_Intron|PRKCG_uc010yef.1_Intron|PRKCG_uc010yeg.1_Intron|PRKCG_uc010yeh.1_Intron	NM_002739	NP_002730			protein kinase C, gamma						activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)														---	---	---	---
NLRP7	199713	broad.mit.edu	37	19	55446085	55446085	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55446085delT	uc002qih.3	-						NLRP7_uc002qig.3_Intron|NLRP7_uc002qii.3_Intron|NLRP7_uc010esk.2_Intron|NLRP7_uc010esl.2_Intron	NM_206828	NP_996611			NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57469352	57469355	+	IGR	DEL	AGGA	-	-	rs73070779		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57469352_57469355delAGGA								MIMT1 (109430 upstream) : USP29 (162154 downstream)																																			---	---	---	---
AURKC	6795	broad.mit.edu	37	19	57745123	57745123	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57745123delT	uc002qoe.2	+						AURKC_uc002qoc.2_Intron|AURKC_uc002qod.2_Intron|AURKC_uc010etv.2_Intron	NM_001015878	NP_001015878			aurora kinase C isoform 1						cell cycle|cytokinesis	condensed chromosome|cytoplasm|midbody|spindle midzone	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)														---	---	---	---
ZSCAN1	284312	broad.mit.edu	37	19	58543388	58543390	+	5'Flank	DEL	AAC	-	-	rs149320625	by1000genomes;byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58543388_58543390delAAC	uc002qrc.1	+						ZSCAN1_uc002qra.1_5'Flank|ZSCAN1_uc002qrb.1_5'Flank	NM_182572	NP_872378			zinc finger and SCAN domain containing 1						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)														---	---	---	---
TBC1D20	128637	broad.mit.edu	37	20	436895	436895	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:436895delA	uc002wds.2	-						TBC1D20_uc002wdv.2_Intron|TBC1D20_uc002wdt.2_Intron|TBC1D20_uc002wdu.2_Intron	NM_144628	NP_653229			TBC1 domain family, member 20						interspecies interaction between organisms	integral to membrane|intracellular	Rab GTPase activator activity			central_nervous_system(1)	1		all_epithelial(17;0.228)|Breast(17;0.231)																---	---	---	---
SIRPG	55423	broad.mit.edu	37	20	1612056	1612056	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1612056delA	uc002wfm.1	-						SIRPG_uc002wfn.1_Intron|SIRPG_uc002wfo.1_Intron|uc002wfp.1_Intron	NM_018556	NP_061026			signal-regulatory protein gamma isoform 1						blood coagulation|cell adhesion|cell junction assembly|cell-cell signaling|intracellular signal transduction|leukocyte migration|negative regulation of cell proliferation|positive regulation of cell proliferation|positive regulation of cell-cell adhesion|positive regulation of T cell activation	integral to membrane|intracellular|plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	1857844	1857845	+	IGR	INS	-	CT	CT	rs62192684		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1857844_1857845insCT								SIRPG (219419 upstream) : SIRPA (16968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1993623	1993623	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1993623delA								PDYN (18920 upstream) : STK35 (88905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	2423382	2423382	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2423382delA								TGM6 (9983 upstream) : SNRPB (18899 downstream)																																			---	---	---	---
IDH3B	3420	broad.mit.edu	37	20	2643791	2643792	+	Intron	DEL	AA	-	-	rs11476625		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2643791_2643792delAA	uc002wgp.2	-						IDH3B_uc002wgq.2_Intron|IDH3B_uc002wgr.2_Intron|IDH3B_uc010zpz.1_Intron	NM_006899	NP_008830			isocitrate dehydrogenase 3, beta subunit isoform						isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	electron carrier activity|isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0					NADH(DB00157)													---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2928696	2928696	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2928696delT	uc010zqb.1	+						VPS16_uc002whh.2_Intron|PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc010zqd.1_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron					SubName: Full=cDNA FLJ60525, highly similar to Receptor-type tyrosine-protein phosphatase alpha (EC 3.1.3.48);						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3076947	3076947	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3076947delT								AVP (11577 upstream) : UBOX5 (11273 downstream)																																			---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3146039	3146039	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3146039delC	uc002wia.1	-						ProSAPiP1_uc002wib.1_Intron	NM_014731	NP_055546			ProSAPiP1 protein							cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3694626	3694626	+	IGR	DEL	T	-	-	rs11475302		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3694626delT								SIGLEC1 (6851 upstream) : HSPA12B (18730 downstream)																																			---	---	---	---
PRNT	149830	broad.mit.edu	37	20	4714057	4714057	+	Intron	DEL	A	-	-	rs77300761		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4714057delA	uc002wlb.2	-						PRNT_uc010zqp.1_Intron|PRNT_uc010zqq.1_Intron	NR_024268				Homo sapiens mRNA for putative M8 protein, isoform 2.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5026647	5026647	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5026647delA								SLC23A2 (35708 upstream) : C20orf30 (22483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5032324	5032324	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5032324delT								SLC23A2 (41385 upstream) : C20orf30 (16806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5722347	5722347	+	IGR	DEL	A	-	-	rs113693503		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5722347delA								GPCPD1 (130675 upstream) : C20orf196 (8696 downstream)																																			---	---	---	---
TRMT6	51605	broad.mit.edu	37	20	5924808	5924808	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5924808delT	uc002wmh.1	-	4	580	c.458delA	c.(457-459)AAAfs	p.K153fs	TRMT6_uc010zra.1_5'UTR|TRMT6_uc010gbn.1_5'UTR|TRMT6_uc010gbo.1_RNA	NM_015939	NP_057023	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6	153					regulation of translational initiation|tRNA processing	nucleus	protein binding|translation initiation factor activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	7291030	7291030	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7291030delA								BMP2 (530120 upstream) : HAO1 (572601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7615076	7615076	+	IGR	DEL	T	-	-	rs145191665		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7615076delT								BMP2 (854166 upstream) : HAO1 (248555 downstream)																																			---	---	---	---
HAO1	54363	broad.mit.edu	37	20	7894665	7894665	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7894665delA	uc002wmw.1	-						HAO1_uc010gbu.2_Intron	NM_017545	NP_060015			hydroxyacid oxidase 1						cellular nitrogen compound metabolic process|fatty acid alpha-oxidation|glycolate catabolic process|glyoxylate metabolic process	peroxisomal matrix	FMN binding|glycolate oxidase activity|glyoxylate oxidase activity			ovary(3)	3																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8152644	8152644	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8152644delT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8287850	8287850	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8287850delG	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9200111	9200112	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9200111_9200112insA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
C20orf103	24141	broad.mit.edu	37	20	9495651	9495651	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9495651delA	uc002wni.1	+						C20orf103_uc010zrc.1_Intron	NM_012261	NP_036393			chromosome 20 open reading frame 103 precursor							integral to membrane				upper_aerodigestive_tract(1)|lung(1)|breast(1)	3			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
PAK7	57144	broad.mit.edu	37	20	9716045	9716045	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9716045delA	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074			p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	9852736	9852737	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9852736_9852737delGT								PAK7 (33049 upstream) : ANKRD5 (162960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10996443	10996443	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10996443delA								JAG1 (341749 upstream) : BTBD3 (875034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12532107	12532107	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12532107delT								BTBD3 (624865 upstream) : SPTLC3 (457520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12545651	12545652	+	IGR	DEL	AA	-	-	rs67781311		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12545651_12545652delAA								BTBD3 (638409 upstream) : SPTLC3 (443975 downstream)																																			---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13049399	13049401	+	Intron	DEL	AAA	-	-	rs74181402		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13049399_13049401delAAA	uc002wod.1	+							NM_018327	NP_060797			serine palmitoyltransferase, long chain base						sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13128335	13128335	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13128335delT	uc002wod.1	+							NM_018327	NP_060797			serine palmitoyltransferase, long chain base						sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
ISM1	140862	broad.mit.edu	37	20	13200601	13200601	+	5'Flank	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13200601delG	uc010gce.1	+						uc002woe.1_RNA	NM_080826	NP_543016			isthmin 1 homolog precursor							extracellular region					0																		---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13945395	13945395	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13945395delT	uc010gcf.2	-						SEL1L2_uc002woq.3_Intron|SEL1L2_uc010zrl.1_Intron|SEL1L2_uc002wor.2_Intron	NM_025229	NP_079505			sel-1 suppressor of lin-12-like 2 precursor							integral to membrane	binding			ovary(2)	2																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14039293	14039295	+	Intron	DEL	TTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14039293_14039295delTTT	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14079924	14079925	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14079924_14079925delAA	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15170489	15170490	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15170489_15170490delTT	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	16004708	16004708	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16004708delC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	16676637	16676637	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16676637delT								KIF16B (122559 upstream) : SNRPB2 (33992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	18466245	18466245	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18466245delA								POLR3F (961 upstream) : RBBP9 (945 downstream)																																			---	---	---	---
DTD1	92675	broad.mit.edu	37	20	18699879	18699880	+	Intron	INS	-	TA	TA	rs146023150	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18699879_18699880insTA	uc002wrf.3	+							NM_080820	NP_543010			D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18796529	18796529	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18796529delA	uc002wrj.1	-											full-length cDNA clone CS0DI003YB20 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20317995	20318002	+	Intron	DEL	TGGGTGGA	-	-	rs111753471		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20317995_20318002delTGGGTGGA	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21128602	21128603	+	Intron	INS	-	TGTG	TGTG	rs140129874	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21128602_21128603insTGTG	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	21420663	21420663	+	IGR	DEL	T	-	-	rs71893145		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21420663delT								NKX2-4 (42616 upstream) : NKX2-2 (71001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21436880	21436881	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21436880_21436881insT								NKX2-4 (58833 upstream) : NKX2-2 (54783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21449096	21449097	+	IGR	DEL	GG	-	-	rs112319550		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21449096_21449097delGG								NKX2-4 (71049 upstream) : NKX2-2 (42567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22146637	22146637	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22146637delT								PAX1 (450017 upstream) : LOC284788 (234334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22302834	22302835	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22302834_22302835insA								PAX1 (606214 upstream) : LOC284788 (78136 downstream)																																			---	---	---	---
CD93	22918	broad.mit.edu	37	20	23066469	23066469	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23066469delC	uc002wsv.2	-	1	509	c.361delG	c.(361-363)GAGfs	p.E121fs		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	121	Extracellular (Potential).|C-type lectin.				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	23757764	23757765	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23757764_23757765delTT								CST1 (26190 upstream) : CST2 (46639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23886179	23886180	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23886179_23886180delGT								CST5 (25799 upstream) : GGTLC1 (79511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24697907	24697908	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24697907_24697908insT								TMEM90B (50740 upstream) : CST7 (231958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25159938	25159938	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25159938delA								LOC284798 (30512 upstream) : ENTPD6 (16401 downstream)																																			---	---	---	---
ABHD12	26090	broad.mit.edu	37	20	25349760	25349760	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25349760delA	uc002wus.1	-						ABHD12_uc002wuq.2_Intron|ABHD12_uc002wur.2_Intron|ABHD12_uc002wut.1_Intron|ABHD12_uc002wuu.1_Intron	NM_001042472	NP_001035937			abhydrolase domain containing 12 isoform a							integral to membrane	acylglycerol lipase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25856337	25856339	+	IGR	DEL	GAT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25856337_25856339delGAT								FAM182B (7551 upstream) : LOC100134868 (134096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25862448	25862449	+	IGR	DEL	GA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25862448_25862449delGA								FAM182B (13662 upstream) : LOC100134868 (127986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26213040	26213041	+	IGR	INS	-	A	A	rs77211147		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26213040_26213041insA								MIR663 (24126 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29562213	29562215	+	IGR	DEL	GTG	-	-	rs73620363		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29562213_29562215delGTG								None (None upstream) : FRG1B (49664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29608472	29608472	+	IGR	DEL	G	-	-	rs113600748		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29608472delG								None (None upstream) : FRG1B (3407 downstream)																																			---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29617419	29617420	+	Intron	INS	-	T	T	rs147393502	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29617419_29617420insT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29652356	29652356	+	3'UTR	DEL	T	-	-	rs111401906		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29652356delT	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29824964	29824965	+	IGR	INS	-	GGAAT	GGAAT	rs62641485		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29824964_29824965insGGAAT								FRG1B (171056 upstream) : DEFB115 (20502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29858189	29858189	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29858189delA								DEFB115 (10754 upstream) : DEFB116 (32827 downstream)																																			---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30729932	30729932	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30729932delA	uc002wxj.2	+						TM9SF4_uc010ztr.1_Intron|TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.2_Intron|TM9SF4_uc010gdz.2_Intron	NM_014742	NP_055557			transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
COMMD7	149951	broad.mit.edu	37	20	31316255	31316256	+	Intron	DEL	AC	-	-	rs112717200		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31316255_31316256delAC	uc002wya.3	-						COMMD7_uc010ged.2_Intron|COMMD7_uc002wyb.2_Intron	NM_053041	NP_444269			COMM domain containing 7 isoform 1						negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|tumor necrosis factor-mediated signaling pathway		NF-kappaB binding			breast(1)	1																		---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31362024	31362024	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31362024delT	uc002wyc.2	+						DNMT3B_uc010ztx.1_Intron|DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron	NM_006892	NP_008823			DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31366749	31366756	+	Intron	DEL	GATGGATG	-	-	rs143438514		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31366749_31366756delGATGGATG	uc002wyc.2	+						DNMT3B_uc010ztx.1_Intron|DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_5'Flank	NM_006892	NP_008823			DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
CDK5RAP1	51654	broad.mit.edu	37	20	31987854	31987854	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31987854delA	uc010gek.2	-						CDK5RAP1_uc002wyy.2_Intron|CDK5RAP1_uc002wyz.2_Intron|CDK5RAP1_uc002wza.2_Intron|CDK5RAP1_uc010gel.2_Intron|CDK5RAP1_uc010gem.2_Intron|CDK5RAP1_uc002wzc.1_Intron|CDK5RAP1_uc010gen.2_Intron	NM_016408	NP_057492			CDK5 regulatory subunit associated protein 1						brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
PXMP4	11264	broad.mit.edu	37	20	32300255	32300258	+	Intron	DEL	TTTT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32300255_32300258delTTTT	uc002wzv.2	-						PXMP4_uc002wzw.2_Intron|PXMP4_uc010zuh.1_Intron	NM_007238	NP_009169			peroxisomal membrane protein 4 isoform a							integral to membrane|membrane fraction|mitochondrial inner membrane|peroxisomal membrane	protein transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32311501	32311501	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32311501delT								PXMP4 (3365 upstream) : ZNF341 (8307 downstream)																																			---	---	---	---
CHMP4B	128866	broad.mit.edu	37	20	32399502	32399502	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32399502delC	uc002xaa.2	+							NM_176812	NP_789782			chromatin modifying protein 4B						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33163118	33163118	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33163118delC	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
HMGB3L1	128872	broad.mit.edu	37	20	33421797	33421797	+	RNA	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33421797delT	uc002xax.2	-	1		c.469delA				NR_002165				Homo sapiens high-mobility group (nonhistone chromosomal) protein 4-like, mRNA (cDNA clone IMAGE:40002762).												0																		---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33656344	33656344	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33656344delT	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34096147	34096147	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34096147delT	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117			centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
C20orf152	140894	broad.mit.edu	37	20	34574253	34574253	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34574253delT	uc002xes.1	+						C20orf152_uc002xer.1_Intron|C20orf152_uc010gfp.1_Intron					SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34726805	34726805	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34726805delT	uc002xev.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_Intron|EPB41L1_uc002xez.2_Intron	NM_012156	NP_036288			erythrocyte membrane protein band 4.1-like 1						cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)															OREG0025898	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DSN1	79980	broad.mit.edu	37	20	35398343	35398344	+	Intron	INS	-	AG	AG	rs147257254	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35398343_35398344insAG	uc010gfr.2	-						DSN1_uc002xfz.2_Intron|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_Intron|DSN1_uc010zvs.1_Intron|DSN1_uc002xgc.2_Intron|DSN1_uc002xgb.2_Intron	NM_001145316	NP_001138788			DSN1, MIND kinetochore complex component,						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35445891	35445893	+	Intron	DEL	AAA	-	-	rs75011336		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35445891_35445893delAAA	uc002xgd.1	-						C20orf117_uc002xge.1_5'Flank	NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35463715	35463716	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35463715_35463716insT	uc002xgd.1	-							NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35632424	35632424	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35632424delT	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf132	140699	broad.mit.edu	37	20	35742230	35742233	+	Intron	DEL	TCTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35742230_35742233delTCTG	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron	NM_152503	NP_689716			hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
SRC	6714	broad.mit.edu	37	20	35994291	35994291	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35994291delT	uc002xgx.2	+						SRC_uc002xgy.2_Intron	NM_005417	NP_005408			proto-oncogene tyrosine-protein kinase SRC						axon guidance|bone resorption|cell junction assembly|cellular membrane organization|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular protein kinase cascade|leukocyte migration|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of integrin activation|Ras protein signal transduction|regulation of bone resorption|regulation of vascular permeability|response to interleukin-1|signal complex assembly|T cell costimulation	caveola|cytosol|mitochondrial inner membrane	ATP binding|heme binding|integrin binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|SH3/SH2 adaptor activity			large_intestine(10)|lung(1)|central_nervous_system(1)|endometrium(1)	13		Myeloproliferative disorder(115;0.00878)			Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	36068005	36068005	+	IGR	DEL	T	-	-	rs11476095		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36068005delT								SRC (34186 upstream) : BLCAP (77815 downstream)																																			---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36541266	36541267	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36541266_36541267delCT	uc002xhk.3	+							NM_080607	NP_542174			V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36572311	36572311	+	Intron	DEL	C	-	-	rs33961791		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572311delC	uc002xhk.3	+							NM_080607	NP_542174			V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RPRD1B	58490	broad.mit.edu	37	20	36687671	36687672	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36687671_36687672insT	uc002xho.3	+							NM_021215	NP_067038			Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	36831715	36831715	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36831715delT								TGM2 (38015 upstream) : KIAA1755 (7192 downstream)																																			---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37136349	37136349	+	Intron	DEL	T	-	-	rs79116799	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37136349delT	uc002xiw.2	+						RALGAPB_uc010zvz.1_Intron|RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron|RALGAPB_uc002xja.1_5'Flank	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	37698288	37698290	+	IGR	DEL	AAA	-	-	rs5841313		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37698288_37698290delAAA								DHX35 (29925 upstream) : LOC339568 (144134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37764902	37764903	+	IGR	INS	-	TG	TG	rs149004653	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37764902_37764903insTG								DHX35 (96539 upstream) : LOC339568 (77521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37813436	37813436	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37813436delT								DHX35 (145073 upstream) : LOC339568 (28988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39071511	39071512	+	IGR	DEL	TG	-	-	rs9798531		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39071511_39071512delTG								None (None upstream) : MAFB (243007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39550480	39550480	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39550480delA								MAFB (232604 upstream) : TOP1 (106982 downstream)																																			---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39898218	39898219	+	Intron	INS	-	T	T	rs67991044		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39898218_39898219insT	uc002xjs.1	-						ZHX3_uc002xjq.1_5'Flank|ZHX3_uc002xjr.1_Intron|ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc002xjv.1_Intron|ZHX3_uc002xjw.1_Intron	NM_015035	NP_055850			zinc fingers and homeoboxes 3						negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41608215	41608215	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41608215delA	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	42525514	42525514	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42525514delT								GTSF1L (169872 upstream) : TOX2 (17978 downstream)																																			---	---	---	---
TOX2	84969	broad.mit.edu	37	20	42662880	42662880	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42662880delT	uc002xlf.3	+						TOX2_uc010ggo.2_Intron|TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron|TOX2_uc002xlg.2_Intron	NM_001098798	NP_001092268			TOX high mobility group box family member 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	42715424	42715424	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42715424delT								TOX2 (17172 upstream) : JPH2 (24913 downstream)																																			---	---	---	---
STK4	6789	broad.mit.edu	37	20	43600644	43600644	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43600644delA	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Intron	NM_006282	NP_006273			serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	43713550	43713550	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43713550delA								STK4 (4959 upstream) : KCNS1 (7401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	43765975	43765975	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43765975delT								WFDC12 (12869 upstream) : PI3 (37565 downstream)																																			---	---	---	---
WFDC8	90199	broad.mit.edu	37	20	44184633	44184633	+	Intron	DEL	A	-	-	rs78363134		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44184633delA	uc002xow.2	-						WFDC8_uc002xox.2_Intron	NM_181510	NP_852611			WAP four-disulfide core domain 8 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44560715	44560718	+	5'Flank	DEL	AAAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44560715_44560718delAAAA	uc002xqs.2	+							NM_022104	NP_071387			phosphorylated CTD interacting factor 1							nucleus				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	44621893	44621893	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44621893delA								ZNF335 (21060 upstream) : MMP9 (15654 downstream)																																			---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44926840	44926840	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44926840delA	uc010ghk.1	-							NM_021248	NP_067071			cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44938260	44938261	+	5'Flank	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44938260_44938261insC	uc010ghk.1	-							NM_021248	NP_067071			cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45228423	45228423	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45228423delT	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45231823	45231823	+	Intron	DEL	A	-	-	rs78028785		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45231823delA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45300157	45300157	+	Intron	DEL	A	-	-	rs144166777		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45300157delA	uc002xsg.1	-						SLC13A3_uc010gho.1_Intron|SLC13A3_uc002xsi.3_5'Flank	NM_001011554	NP_001011554			solute carrier family 13 member 3 isoform b							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45644794	45644794	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45644794delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45789429	45789429	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45789429delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46215943	46215944	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46215943_46215944insT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	46429708	46429708	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46429708delG								SULF2 (14348 upstream) : LOC284749 (558946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46607687	46607687	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46607687delC								SULF2 (192327 upstream) : LOC284749 (380967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47961859	47961859	+	IGR	DEL	A	-	-	rs73625442		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47961859delA								C20orf199 (56066 upstream) : KCNB1 (26646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48230556	48230556	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48230556delG								PTGIS (45849 upstream) : B4GALT5 (18929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49504922	49504922	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49504922delA								BCAS4 (11209 upstream) : ADNP (1961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49602058	49602058	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49602058delT								MOCS3 (24238 upstream) : KCNG1 (18136 downstream)																																			---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50273875	50273876	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50273875_50273876insA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50286409	50286409	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50286409delA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	52406797	52406797	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52406797delT								ZNF217 (195996 upstream) : SUMO1P1 (84245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52431048	52431048	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52431048delA								ZNF217 (220247 upstream) : SUMO1P1 (59994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53323509	53323509	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53323509delA								DOK5 (55800 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53620520	53620520	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53620520delT								DOK5 (352811 upstream) : CBLN4 (951977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53717366	53717366	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53717366delT								DOK5 (449657 upstream) : CBLN4 (855131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54134316	54134317	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54134316_54134317insA								DOK5 (866607 upstream) : CBLN4 (438180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54372419	54372420	+	IGR	DEL	AA	-	-	rs34528195		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54372419_54372420delAA								None (None upstream) : CBLN4 (200077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54541173	54541173	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54541173delA								None (None upstream) : CBLN4 (31324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54903351	54903352	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54903351_54903352delAA								MC3R (78480 upstream) : C20orf108 (30631 downstream)																																			---	---	---	---
GCNT7	140687	broad.mit.edu	37	20	55094613	55094617	+	Intron	DEL	TTTTT	-	-	rs33996449		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55094613_55094617delTTTTT	uc010zzg.1	-							NM_080615	NP_542182			glucosaminyl (N-acetyl) transferase family							Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	55150582	55150582	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55150582delT								C20orf107 (39008 upstream) : TFAP2C (53776 downstream)																																			---	---	---	---
PMEPA1	56937	broad.mit.edu	37	20	56230042	56230042	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56230042delC	uc002xyq.2	-						PMEPA1_uc002xyr.2_Intron|PMEPA1_uc002xys.2_Intron|PMEPA1_uc002xyt.2_Intron	NM_020182	NP_064567			transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1																OREG0026069	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	20	56487906	56487906	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56487906delG								PMEPA1 (201365 upstream) : C20orf85 (238077 downstream)																																			---	---	---	---
PPP4R1L	55370	broad.mit.edu	37	20	56862129	56862129	+	Intron	DEL	T	-	-	rs66635333		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56862129delT	uc002xyy.1	-						PPP4R1L_uc010gjn.1_Intron					SubName: Full=cDNA FLJ50842, moderately similar to Serine/threonine-protein phosphatase 4regulatory subunit 1;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	57195722	57195727	+	IGR	DEL	ACACAT	-	-	rs146808621	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57195722_57195727delACACAT								APCDD1L (105773 upstream) : STX16 (30582 downstream)																																			---	---	---	---
STX16	8675	broad.mit.edu	37	20	57248581	57248583	+	Intron	DEL	CAT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57248581_57248583delCAT	uc002xzi.2	+						STX16_uc010zzq.1_Intron|STX16_uc002xzk.2_Intron|STX16_uc002xzm.2_Intron|STX16_uc002xzj.2_Intron|STX16_uc002xzl.2_Intron	NM_001001433	NP_001001433			syntaxin 16 isoform a						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|microsome|SNARE complex	SNAP receptor activity			ovary(1)	1	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	57495688	57495688	+	IGR	DEL	T	-	-	rs112658012		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57495688delT								GNAS (9439 upstream) : TH1L (60623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57853010	57853011	+	IGR	INS	-	TTGT	TTGT	rs143470791	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57853010_57853011insTTGT								ZNF831 (18845 upstream) : EDN3 (22488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57929337	57929337	+	IGR	DEL	T	-	-	rs11477300		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57929337delT								EDN3 (28291 upstream) : PHACTR3 (223227 downstream)																																			---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58288801	58288801	+	Intron	DEL	T	-	-	rs80230376		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58288801delT	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron	NM_080672	NP_542403			phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	58913262	58913263	+	Intron	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58913262_58913263delTG	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59262352	59262353	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59262352_59262353delAA								MIR646 (378727 upstream) : CDH4 (565206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59733668	59733668	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59733668delT								MIR646 (850043 upstream) : CDH4 (93891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59781561	59781561	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59781561delT								MIR646 (897936 upstream) : CDH4 (45998 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60282218	60282218	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60282218delG	uc002ybn.1	+						CDH4_uc002ybo.1_Intron|CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60399417	60399418	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60399417_60399418delAA	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	60536883	60536883	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60536883delT								MIR1257 (8165 upstream) : TAF4 (12972 downstream)																																			---	---	---	---
GATA5	140628	broad.mit.edu	37	20	61052315	61052316	+	5'Flank	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61052315_61052316delTT	uc002ycx.1	-							NM_080473	NP_536721			GATA binding protein 5						blood coagulation|intestinal epithelial cell differentiation|positive regulation of transcription from RNA polymerase II promoter	nucleoplasm	sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding				0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)															---	---	---	---
SLCO4A1	28231	broad.mit.edu	37	20	61304517	61304517	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61304517delG	uc002ydc.1	+											Homo sapiens mRNA for organic anion transporter OATP-E, complete cds.						sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)															---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62070158	62070159	+	Intron	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62070158_62070159insC	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)													---	---	---	---
RTEL1	51750	broad.mit.edu	37	20	62320366	62320366	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62320366delG	uc002yfu.1	+						RTEL1_uc011abc.1_Intron|RTEL1_uc002yft.1_Intron|RTEL1_uc011abd.1_Intron|RTEL1_uc011abe.1_Intron|RTEL1_uc002yfw.2_Intron|RTEL1_uc002yfx.1_5'Flank	NM_016434	NP_057518			regulator of telomere elongation helicase 1						DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)															---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62656406	62656406	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62656406delT	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601			PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9655803	9655804	+	IGR	INS	-	A	A	rs78775969		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9655803_9655804insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10417854	10417854	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10417854delA								None (None upstream) : TPTE (488889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10435925	10435925	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10435925delT								None (None upstream) : TPTE (470818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10469320	10469320	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10469320delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10560706	10560706	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10560706delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10744332	10744332	+	IGR	DEL	G	-	-	rs111628632		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10744332delG								None (None upstream) : TPTE (162411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10807081	10807100	+	IGR	DEL	GGAATGGAGTGGAATGGAGT	-	-	rs75071634		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10807081_10807100delGGAATGGAGTGGAATGGAGT								None (None upstream) : TPTE (99643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10815072	10815081	+	IGR	DEL	AATGGAATGC	-	-	rs150426227		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10815072_10815081delAATGGAATGC								None (None upstream) : TPTE (91662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10906284	10906285	+	IGR	INS	-	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10906284_10906285insC								None (None upstream) : TPTE (458 downstream)																																			---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10910947	10910947	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10910947delT	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11037486	11037487	+	Intron	DEL	AG	-	-	rs147195770		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037486_11037487delAG	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11059001	11059003	+	Intron	DEL	AAG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11059001_11059003delAAG	uc002yit.1	-						BAGE_uc002yiw.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	11137924	11137935	+	IGR	DEL	TCTTTCTTTCTC	-	-	rs71182431		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11137924_11137935delTCTTTCTTTCTC								BAGE (38987 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14343742	14343743	+	IGR	INS	-	AG	AG			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14343742_14343743insAG								None (None upstream) : C21orf99 (66744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14375336	14375336	+	IGR	DEL	T	-	-	rs143097557	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14375336delT								None (None upstream) : C21orf99 (35151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14746192	14746192	+	IGR	DEL	A	-	-	rs112615010		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14746192delA								C21orf99 (255623 upstream) : POTED (236306 downstream)																																			---	---	---	---
LIPI	149998	broad.mit.edu	37	21	15578985	15578985	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15578985delA	uc002yjm.2	-							NM_198996	NP_945347			lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16255940	16255940	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16255940delA								SAMSN1 (300217 upstream) : NRIP1 (77616 downstream)																																			---	---	---	---
USP25	29761	broad.mit.edu	37	21	17203605	17203605	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17203605delA	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
USP25	29761	broad.mit.edu	37	21	17238573	17238573	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17238573delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	17259617	17259617	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17259617delT								USP25 (7240 upstream) : C21orf34 (183225 downstream)																																			---	---	---	---
C21orf34	388815	broad.mit.edu	37	21	17566944	17566945	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17566944_17566945insT	uc002ykb.2	+						C21orf34_uc010glc.2_Intron|C21orf34_uc002ykc.2_RNA	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	17985349	17985350	+	IGR	DEL	TT	-	-	rs78125669		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17985349_17985350delTT								C21orf34 (3255 upstream) : CXADR (899980 downstream)																																			---	---	---	---
CXADR	1525	broad.mit.edu	37	21	18882691	18882691	+	5'Flank	DEL	C	-	-	rs71992719		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18882691delC	uc002yki.2	+						CXADR_uc002ykh.1_5'Flank|CXADR_uc010gld.1_5'Flank|CXADR_uc010gle.1_5'Flank	NM_001338	NP_001329			coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20055820	20055821	+	Intron	INS	-	TG	TG	rs138038345	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20055820_20055821insTG	uc010glf.1	-						uc002ykx.2_Intron					Homo sapiens, clone IMAGE:5392784, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20328826	20328826	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20328826delA								TMPRSS15 (552856 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20661225	20661228	+	IGR	DEL	ATAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20661225_20661228delATAC								TMPRSS15 (885255 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20961803	20961803	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20961803delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21215275	21215276	+	IGR	DEL	AA	-	-	rs72471383		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21215275_21215276delAA								None (None upstream) : C21orf131 (899638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21577165	21577165	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21577165delA								None (None upstream) : C21orf131 (537749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21724158	21724159	+	IGR	INS	-	T	T	rs141929732		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21724158_21724159insT								None (None upstream) : C21orf131 (390755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23141928	23141928	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23141928delT	uc002yle.2	+											Homo sapiens, clone IMAGE:5547749, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	24821348	24821348	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24821348delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25650476	25650477	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25650476_25650477delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27124278	27124278	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27124278delT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031			GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
APP	351	broad.mit.edu	37	21	27394038	27394038	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27394038delA	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475			amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
ADAMTS1	9510	broad.mit.edu	37	21	28215013	28215013	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28215013delA	uc002ymf.2	-							NM_006988	NP_008919			ADAM metallopeptidase with thrombospondin type 1						integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)														---	---	---	---
N6AMT1	29104	broad.mit.edu	37	21	30248595	30248595	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30248595delT	uc002ymo.1	-	6					N6AMT1_uc002ymp.1_3'UTR|N6AMT1_uc002ymq.1_Intron	NM_013240	NP_037372			N-6 adenine-specific DNA methyltransferase 1						positive regulation of cell growth	protein complex	nucleic acid binding|protein binding|protein methyltransferase activity				0																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32643558	32643558	+	Intron	DEL	A	-	-	rs111662882		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32643558delA	uc002yow.1	-						TIAM1_uc011adk.1_Intron|TIAM1_uc011adl.1_Intron|TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32646887	32646887	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32646887delC	uc002yow.1	-						TIAM1_uc011adk.1_Intron|TIAM1_uc011adl.1_Intron|TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32793444	32793445	+	Intron	DEL	AA	-	-	rs71318276		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32793444_32793445delAA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33074822	33074822	+	Intron	DEL	A	-	-	rs72441176		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33074822delA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.2_Intron	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
HUNK	30811	broad.mit.edu	37	21	33272759	33272762	+	Intron	DEL	ACAC	-	-	rs10540286		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33272759_33272762delACAC	uc002yph.2	+							NM_014586	NP_055401			hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2																		---	---	---	---
URB1	9875	broad.mit.edu	37	21	33749844	33749844	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33749844delA	uc002ypn.2	-						SNORA80_uc002ypo.2_5'Flank	NM_014825	NP_055640			URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34100099	34100100	+	Intron	INS	-	A	A	rs145812696	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34100099_34100100insA	uc002yqh.2	-						SYNJ1_uc011ads.1_5'Flank|SYNJ1_uc002yqf.2_Intron|SYNJ1_uc002yqg.2_Intron|SYNJ1_uc002yqi.2_Intron|uc002yqj.1_5'Flank|uc002yqk.2_5'Flank	NM_003895	NP_003886			synaptojanin 1 isoform a								inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5																OREG0003585	type=REGULATORY REGION|Gene=AK056384|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
Unknown	0	broad.mit.edu	37	21	34420632	34420632	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34420632delA								OLIG2 (19132 upstream) : OLIG1 (21818 downstream)																																			---	---	---	---
DONSON	29980	broad.mit.edu	37	21	35267946	35267947	+	Intron	INS	-	GT	GT	rs146422087	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35267946_35267947insGT	uc002ysn.1	-											Homo sapiens full length insert cDNA clone ZD90F06.						multicellular organismal development	nucleus				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ATP5O	539	broad.mit.edu	37	21	35276748	35276748	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35276748delA	uc002ytl.2	-						DONSON_uc002ysn.1_Intron	NM_001697	NP_001688			mitochondrial ATP synthase, O subunit precursor						ATP catabolic process|mitochondrial ATP synthesis coupled proton transport|respiratory electron transport chain	mitochondrial proton-transporting ATP synthase complex|plasma membrane|proton-transporting ATP synthase complex, catalytic core F(1)	drug binding|hydrogen ion transporting ATP synthase activity, rotational mechanism			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	36122278	36122278	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36122278delT	uc002yug.2	+											Homo sapiens cDNA: FLJ22133 fis, clone HEP20529.																														---	---	---	---
RUNX1	861	broad.mit.edu	37	21	37064319	37064319	+	Intron	DEL	T	-	-	rs71706356		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37064319delT	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	37204035	37204036	+	Intron	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37204035_37204036delCT	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37586724	37586724	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37586724delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_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	21	37958207	37958218	+	IGR	DEL	CCTTCCTTCCTC	-	-	rs148186753	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37958207_37958218delCCTTCCTTCCTC								CLDN14 (9340 upstream) : SIM2 (113773 downstream)																																			---	---	---	---
HLCS	3141	broad.mit.edu	37	21	38210627	38210630	+	Intron	DEL	CACC	-	-	rs150404706	by1000genomes;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38210627_38210630delCACC	uc010gnb.2	-						HLCS_uc002yvs.2_Intron	NM_000411	NP_000402			holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)													---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38569584	38569584	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38569584delA	uc002yvz.2	+						TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron	NM_001001894	NP_001001894			tetratricopeptide repeat domain 3						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	40310173	40310174	+	IGR	DEL	CT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40310173_40310174delCT								ETS2 (113297 upstream) : PSMG1 (237216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40516169	40516169	+	IGR	DEL	A	-	-	rs68109209		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40516169delA								ETS2 (319293 upstream) : PSMG1 (31221 downstream)																																			---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40584804	40584804	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40584804delA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron|BRWD1_uc010god.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
WRB	7485	broad.mit.edu	37	21	40768612	40768613	+	Intron	DEL	AA	-	-	rs71806408		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40768612_40768613delAA	uc002yxs.2	+						WRB_uc002yxt.3_Intron|WRB_uc010goj.2_Intron	NM_004627	NP_004618			tryptophan rich basic protein isoform 1							integral to membrane|nucleolus					0		Prostate(19;1.2e-06)																---	---	---	---
SH3BGR	6450	broad.mit.edu	37	21	40866460	40866460	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40866460delT	uc002yya.2	+						SH3BGR_uc002yxz.2_Intron	NM_007341	NP_031367			SH3-binding domain and glutamic acid-rich						protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity				0		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	41110819	41110819	+	IGR	DEL	T	-	-	rs112203012		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41110819delT								B3GALT5 (76004 upstream) : IGSF5 (6515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	42228408	42228408	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42228408delC								DSCAM (9369 upstream) : C21orf130 (285019 downstream)																																			---	---	---	---
BACE2	25825	broad.mit.edu	37	21	42585701	42585701	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42585701delA	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_012105	NP_036237			beta-site APP-cleaving enzyme 2 isoform A						membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)																---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43187462	43187462	+	5'Flank	DEL	T	-	-	rs112658598		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43187462delT	uc002yzn.1	-							NM_020639	NP_065690			ankyrin repeat domain 3							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43246208	43246208	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43246208delC	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43254676	43254677	+	Intron	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43254676_43254677delAG	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43280532	43280536	+	Intron	DEL	TTTTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43280532_43280536delTTTTG	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44023238	44023239	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44023238_44023239insA	uc002zbk.1	-											Homo sapiens, clone IMAGE:5189363, mRNA.																														---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45499777	45499777	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45499777delA	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc011afa.1_5'Flank	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
KRTAP10-5	386680	broad.mit.edu	37	21	46000366	46000366	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46000366delG	uc002zfl.1	-	1	116	c.90delC	c.(88-90)CCCfs	p.P30fs	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198694	NP_941967	P60370	KR105_HUMAN	keratin associated protein 10-5	30	1.|22 X 5 AA repeats of C-C-X(3).					keratin filament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	46158198	46158198	+	IGR	DEL	T	-	-	rs67677812		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46158198delT								C21orf29 (26703 upstream) : UBE2G2 (30758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	46667414	46667414	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46667414delA	uc002zgz.1	+											Homo sapiens C21orf89 protein (C21orf89) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	46983441	46983442	+	IGR	DEL	AA	-	-	rs8132317	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46983441_46983442delAA								SLC19A1 (19116 upstream) : PCBP3 (80241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	47468897	47468898	+	IGR	INS	-	GG	GG	rs142205683	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47468897_47468898insGG								COL6A1 (43934 upstream) : COL6A2 (49135 downstream)																																			---	---	---	---
LSS	4047	broad.mit.edu	37	21	47644797	47644797	+	Intron	DEL	G	-	-	rs11701877		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47644797delG	uc002zij.2	-						LSS_uc011afv.1_Intron|LSS_uc002zil.2_Intron|LSS_uc002zik.2_Intron	NM_001001438	NP_001001438			lanosterol synthase isoform 1						cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	16935747	16935747	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16935747delA								OR11H1 (485943 upstream) : CCT8L2 (135901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17236829	17236829	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17236829delT								psiTPTE22 (57308 upstream) : XKR3 (27484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17374203	17374203	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17374203delA								HSFYL1 (63978 upstream) : GAB4 (68626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17375815	17375816	+	IGR	INS	-	A	A	rs145883088		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17375815_17375816insA								HSFYL1 (65590 upstream) : GAB4 (67013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17392546	17392547	+	IGR	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17392546_17392547insA								HSFYL1 (82321 upstream) : GAB4 (50282 downstream)																																			---	---	---	---
IL17RA	23765	broad.mit.edu	37	22	17576589	17576589	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17576589delA	uc002zly.2	+						IL17RA_uc010gqt.2_Intron	NM_014339	NP_055154			interleukin 17A receptor precursor						fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)												OREG0026280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CECR6	27439	broad.mit.edu	37	22	17598108	17598109	+	3'UTR	INS	-	GGAGA	GGAGA	rs139590477	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17598108_17598109insGGAGA	uc002zmb.2	-	1					CECR6_uc002zma.2_3'UTR	NM_031890	NP_114096			cat eye syndrome chromosome region, candidate 6												0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17911099	17911100	+	Intron	INS	-	T	T	rs139517696	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17911099_17911100insT	uc010gqv.1	+							NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18329162	18329163	+	Intron	INS	-	A	A	rs141609478	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18329162_18329163insA	uc002zng.3	-						MICAL3_uc011agl.1_Intron|MICAL3_uc002znh.2_Intron|MICAL3_uc002znj.1_Intron|MICAL3_uc002znk.1_Intron|MICAL3_uc002znl.1_Intron	NM_015241	NP_056056			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19189912	19189912	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19189912delC	uc002zpb.2	-						CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron|CLTCL1_uc011agt.1_Intron|CLTCL1_uc011agu.1_Intron|CLTCL1_uc010grm.1_Intron|CLTCL1_uc002zpe.2_Intron|CLTCL1_uc002zpd.1_Intron	NM_007098	NP_009029			clathrin, heavy polypeptide-like 1 isoform 1						anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19323614	19323614	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19323614delA	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron	NM_003325	NP_003316			HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	19574266	19574266	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19574266delA								LOC150185 (19904 upstream) : SEPT5 (127721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	19688583	19688583	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19688583delA								LOC150185 (134221 upstream) : SEPT5 (13404 downstream)																																			---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20052869	20052870	+	3'UTR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20052869_20052870delTT	uc010grw.1	+	10					C22orf25_uc002zrb.1_3'UTR|C22orf25_uc002zrc.1_3'UTR|C22orf25_uc002zrd.1_3'UTR|C22orf25_uc011ahe.1_RNA|C22orf25_uc011ahf.1_3'UTR|C22orf25_uc011ahg.1_3'UTR|C22orf25_uc002zrg.2_3'UTR|C22orf25_uc011ahh.1_3'UTR|C22orf25_uc002zrf.2_3'UTR|C22orf25_uc011ahi.1_3'UTR|C22orf25_uc010gry.1_RNA|C22orf25_uc002zrh.1_3'UTR	NM_152906	NP_690870			hypothetical protein LOC128989												0	Colorectal(54;0.0533)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	20192155	20192155	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20192155delC	uc002zrs.1	-						LOC150197_uc002zrt.2_5'Flank					Homo sapiens cDNA FLJ35233 fis, clone PROST2001540.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	20283701	20283702	+	IGR	DEL	TT	-	-	rs68109051		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20283701_20283702delTT								RTN4R (27885 upstream) : DGCR6L (18100 downstream)																																			---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21192409	21192411	+	Intron	DEL	AAA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21192409_21192411delAAA	uc002zsz.3	-						PI4KA_uc010gsq.1_Intron	NM_058004	NP_477352			phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	21316407	21316407	+	Intron	DEL	T	-	-	rs78800285		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21316407delT	uc002zti.1	+											Homo sapiens cDNA clone IMAGE:40134315.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	21915871	21915871	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21915871delA								PI4KAP2 (44091 upstream) : UBE2L3 (6086 downstream)																																			---	---	---	---
PPIL2	23759	broad.mit.edu	37	22	22045978	22045979	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22045978_22045979delAA	uc010gtj.1	+						PPIL2_uc002zvh.3_Intron|PPIL2_uc002zvi.3_Intron|PPIL2_uc002zvg.3_Intron|PPIL2_uc011aij.1_Intron|PPIL2_uc002zvk.3_Intron	NM_148175	NP_680480			peptidylprolyl isomerase-like 2 isoform a						blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)																	---	---	---	---
BCR	613	broad.mit.edu	37	22	23554825	23554825	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23554825delT	uc002zww.2	+						BCR_uc002zwx.2_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
BCR	613	broad.mit.edu	37	22	23634962	23634962	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23634962delG	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	22	23945410	23945411	+	IGR	INS	-	T	T	rs139933610	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23945410_23945411insT								IGLL1 (22915 upstream) : C22orf43 (5229 downstream)																																			---	---	---	---
RGL4	266747	broad.mit.edu	37	22	24040565	24040566	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24040565_24040566delTT	uc002zxn.2	+						LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron|RGL4_uc002zxo.2_Intron|RGL4_uc002zxp.1_Intron|RGL4_uc002zxq.2_Intron	NM_153615	NP_705843			ral guanine nucleotide dissociation						small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle	guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24807190	24807191	+	Intron	INS	-	G	G	rs74267210		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24807190_24807191insG	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145			cytospin A						cell cycle|cell division						0																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26688111	26688112	+	Intron	INS	-	AAGG	AAGG	rs638297	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26688111_26688112insAAGG	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_5'Flank|SEZ6L_uc010gvc.1_5'Flank	NM_021115	NP_066938			seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
TPST2	8459	broad.mit.edu	37	22	26933832	26933832	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26933832delT	uc003acv.2	-						TPST2_uc003acw.2_Intron|TPST2_uc003acx.2_Intron	NM_003595	NP_003586			tyrosylprotein sulfotransferase 2						peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27361828	27361828	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27361828delA								MIAT (246879 upstream) : MN1 (782438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27899117	27899121	+	IGR	DEL	TTTTG	-	-	rs113333229		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27899117_27899121delTTTTG								MIAT (784168 upstream) : MN1 (245145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28019881	28019882	+	IGR	INS	-	GTTT	GTTT	rs148980845	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28019881_28019882insGTTT								MIAT (904932 upstream) : MN1 (124384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28116625	28116626	+	IGR	INS	-	T	T	rs5762332	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28116625_28116626insT								None (None upstream) : MN1 (27640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	29819372	29819372	+	IGR	DEL	T	-	-	rs67350067		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29819372delT								AP1B1 (34803 upstream) : RFPL1S (13634 downstream)																																			---	---	---	---
PATZ1	23598	broad.mit.edu	37	22	31740114	31740114	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31740114delA	uc003akq.2	-						PATZ1_uc003akp.2_Intron|PATZ1_uc003akr.2_Intron|PATZ1_uc003aks.2_Intron|uc003akt.2_5'Flank	NM_014323	NP_055138			POZ (BTB) and AT hook containing zinc finger 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	soft_tissue(2)	2																		---	---	---	---
C22orf28	51493	broad.mit.edu	37	22	32795522	32795522	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32795522delT	uc003amm.2	-						C22orf28_uc011ama.1_Intron	NM_014306	NP_055121			hypothetical protein LOC51493						cell-matrix adhesion|substrate adhesion-dependent cell spreading|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|tRNA-splicing ligase complex	ATP binding|metal ion binding|RNA ligase (ATP) activity|vinculin binding				0																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33018287	33018287	+	Intron	DEL	G	-	-	rs988670	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33018287delG	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33386294	33386295	+	Intron	INS	-	ATGA	ATGA	rs67505827		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33386294_33386295insATGA	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33391653	33391653	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33391653delT	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34145111	34145112	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34145111_34145112delTT	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|uc003ang.2_Intron|uc003anh.2_Intron	NM_004737	NP_004728			like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34227738	34227741	+	Intron	DEL	ACAC	-	-	rs144221715		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34227738_34227741delACAC	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron	NM_004737	NP_004728			like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	34355051	34355051	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34355051delG								LARGE (36467 upstream) : None (None downstream)																																			---	---	---	---
HMGXB4	10042	broad.mit.edu	37	22	35659263	35659263	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35659263delT	uc003anl.2	+						HMGXB4_uc011amh.1_Intron|HMGXB4_uc003ank.2_Intron	NM_001003681	NP_001003681			high-mobility group protein 2-like 1						endosome to lysosome transport|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	NURF complex	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	36002197	36002197	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36002197delT								RASD2 (52154 upstream) : MB (615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36621289	36621290	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36621289_36621290delAA								APOL4 (20410 upstream) : APOL2 (966 downstream)																																			---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36702363	36702363	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36702363delG	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36712840	36712840	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36712840delA	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
CACNG2	10369	broad.mit.edu	37	22	36997258	36997259	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36997258_36997259insT	uc003aps.1	-							NM_006078	NP_006069			voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0																		---	---	---	---
IFT27	11020	broad.mit.edu	37	22	37161540	37161541	+	Intron	DEL	AA	-	-	rs67738997		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37161540_37161541delAA	uc003apv.1	-						IFT27_uc003apu.1_Intron|IFT27_uc003apw.1_Intron	NM_006860	NP_006851			RAB, member of RAS oncogene family-like 4						small GTPase mediated signal transduction	intraflagellar transport particle B|microtubule-based flagellum	GTP binding				0																		---	---	---	---
KCTD17	79734	broad.mit.edu	37	22	37457531	37457531	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37457531delC	uc010gxb.2	+						KCTD17_uc011amv.1_Intron|KCTD17_uc010gxc.2_Intron	NM_024681	NP_078957			potassium channel tetramerisation domain							voltage-gated potassium channel complex	identical protein binding|voltage-gated potassium channel activity				0																		---	---	---	---
IL2RB	3560	broad.mit.edu	37	22	37528367	37528367	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37528367delC	uc003aqv.1	-							NM_000878	NP_000869			interleukin 2 receptor beta precursor						interspecies interaction between organisms|positive regulation of survival gene product expression|protein complex assembly	external side of plasma membrane|integral to plasma membrane	interleukin-2 receptor activity				0					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)													---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37914128	37914128	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37914128delG	uc003asx.1	-						CARD10_uc003ast.1_Intron|CARD10_uc003asy.1_Intron	NM_014550	NP_055365			caspase recruitment domain protein 10						activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
GALR3	8484	broad.mit.edu	37	22	38216513	38216513	+	5'Flank	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38216513delT	uc003aub.1	+							NM_003614	NP_003605			galanin receptor 3						feeding behavior|learning or memory|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity				0	Melanoma(58;0.045)																	---	---	---	---
BAIAP2L2	80115	broad.mit.edu	37	22	38481524	38481524	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38481524delT	uc003auw.2	-						SLC16A8_uc003auu.2_5'Flank|BAIAP2L2_uc003auv.2_Intron	NM_025045	NP_079321			BAI1-associated protein 2-like 2						filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding			pancreas(1)	1	Melanoma(58;0.045)																	---	---	---	---
LOC646851	646851	broad.mit.edu	37	22	39006197	39006198	+	Intron	DEL	AT	-	-	rs113735937		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39006197_39006198delAT	uc011anx.1	-						LOC646851_uc011anw.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348086;												0																		---	---	---	---
CBX6	23466	broad.mit.edu	37	22	39263028	39263028	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39263028delC	uc003awl.2	-	5	488	c.425delG	c.(424-426)GGCfs	p.G142fs		NM_014292	NP_055107	O95503	CBX6_HUMAN	chromobox homolog 6	142					chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	PcG protein complex					0	Melanoma(58;0.04)																	---	---	---	---
APOBEC3A	200315	broad.mit.edu	37	22	39354396	39354397	+	Intron	INS	-	TCCC	TCCC	rs144420983	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39354396_39354397insTCCC	uc003awn.2	+						APOBEC3A_uc011aob.1_Intron|APOBEC3A_uc011aoc.1_Intron	NM_145699	NP_663745			phorbolin 1						cellular response to xenobiotic stimulus|defense response to virus|DNA cytosine deamination|DNA demethylation|innate immune response|negative regulation of transposition|negative regulation of viral genome replication	cytoplasm|nucleus	cytidine deaminase activity|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
ENTHD1	150350	broad.mit.edu	37	22	40191415	40191415	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40191415delT	uc003ayg.2	-							NM_152512	NP_689725			ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)																	---	---	---	---
EP300	2033	broad.mit.edu	37	22	41547630	41547631	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41547630_41547631insA	uc003azl.3	+							NM_001429	NP_001420			E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
XRCC6	2547	broad.mit.edu	37	22	42041703	42041704	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42041703_42041704delTT	uc003bao.1	+						XRCC6_uc003bap.1_Intron|XRCC6_uc011apc.1_Intron|XRCC6_uc003baq.1_Intron|XRCC6_uc003bar.1_Intron|XRCC6_uc003bas.1_Intron	NM_001469	NP_001460			ATP-dependent DNA helicase II, 70 kDa subunit						DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5													Direct_reversal_of_damage|NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	22	42731260	42731262	+	IGR	DEL	CTC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42731260_42731262delCTC								TCF20 (119815 upstream) : NFAM1 (45153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	42892830	42892830	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42892830delA								NFAM1 (64429 upstream) : SERHL (3755 downstream)																																			---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44166703	44166703	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44166703delA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622			CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)																---	---	---	---
PNPLA3	80339	broad.mit.edu	37	22	44346851	44346852	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44346851_44346852insA	uc010gzm.1	+											Synthetic construct DNA, clone: pF1KB8717, Homo sapiens PNPLA3 gene for patatin-like phospholipase domain containing 3, without stop codon, in Flexi system.						triglyceride biosynthetic process|triglyceride catabolic process	integral to membrane	diolein transacylation activity|mono-olein transacylation activity|phospholipase A2 activity|triglyceride lipase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44508839	44508842	+	Intron	DEL	TAAG	-	-	rs62227672		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44508839_44508842delTAAG	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44725321	44725322	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44725321_44725322delAC								KIAA1644 (16590 upstream) : LDOC1L (163128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	45009075	45009075	+	IGR	DEL	A	-	-	rs71188470		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45009075delA								NCRNA00207 (40746 upstream) : PRR5 (55518 downstream)																																			---	---	---	---
PPARA	5465	broad.mit.edu	37	22	46626949	46626949	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46626949delT	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bhb.1_Intron|PPARA_uc010hac.1_Intron	NM_005036	NP_005027			peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	46942795	46942795	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46942795delT								CELSR1 (9728 upstream) : GRAMD4 (79863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	47860470	47860470	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47860470delG	uc003bih.2	-											Homo sapiens, clone IMAGE:5180210, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48138347	48138348	+	Intron	DEL	AA	-	-	rs35673895		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48138347_48138348delAA	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	49678094	49678095	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49678094_49678095delAG								FAM19A5 (530352 upstream) : C22orf34 (130081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49709345	49709345	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49709345delA								FAM19A5 (561603 upstream) : C22orf34 (98831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49793181	49793182	+	IGR	INS	-	CAC	CAC	rs147492631	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49793181_49793182insCAC								FAM19A5 (645439 upstream) : C22orf34 (14994 downstream)																																			---	---	---	---
ZBED4	9889	broad.mit.edu	37	22	50279276	50279276	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50279276delA	uc003bix.2	+	2	2436	c.1966delA	c.(1966-1968)AAAfs	p.K656fs		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	656						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50673003	50673003	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50673003delC	uc003bkb.1	-						TUBGCP6_uc010har.1_Intron|TUBGCP6_uc010has.1_Intron	NM_020461	NP_065194			tubulin, gamma complex associated protein 6						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
SAPS2	9701	broad.mit.edu	37	22	50857139	50857140	+	Intron	DEL	AG	-	-	rs7293044	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50857139_50857140delAG	uc003blb.1	+						SAPS2_uc003bky.1_Intron|SAPS2_uc003bkz.1_Intron|SAPS2_uc003blc.2_Intron|SAPS2_uc003bla.1_Intron	NM_014678	NP_055493			SAPS domain family, member 2							cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)														---	---	---	---
SAPS2	9701	broad.mit.edu	37	22	50879410	50879410	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50879410delC	uc003blb.1	+	23	2977	c.2555delC	c.(2554-2556)GCCfs	p.A852fs	SAPS2_uc003bky.1_Frame_Shift_Del_p.A819fs|SAPS2_uc003bkz.1_Frame_Shift_Del_p.A818fs|SAPS2_uc003blc.2_Frame_Shift_Del_p.A845fs|SAPS2_uc003bla.1_Frame_Shift_Del_p.A819fs|SAPS2_uc003bld.1_Frame_Shift_Del_p.A378fs	NM_014678	NP_055493	O75170	PP6R2_HUMAN	SAPS domain family, member 2	852						cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	50930173	50930173	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50930173delA								MIOX (1423 upstream) : LMF2 (11203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	67539	67539	+	IGR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67539delC								None (None upstream) : PLCXD1 (125453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	228115	228117	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:228115_228117delAGA	uc004cpd.1	-	1	679_681	c.68_70delTCT	c.(67-72)TTCTCC>TCC	p.F23del	uc004cpe.1_In_Frame_Del_p.F136del	NM_012227	NP_036359			pseudoautosomal GTP-binding protein-like																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	465661	465677	+	IGR	DEL	TCCTTCCTTCCTTCCTG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:465661_465677delTCCTTCCTTCCTTCCTG								PPP2R3B (118034 upstream) : SHOX (119402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	469281	469282	+	IGR	DEL	AG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:469281_469282delAG								PPP2R3B (121654 upstream) : SHOX (115797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	722137	722138	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:722137_722138insT								SHOX (101992 upstream) : CRLF2 (592749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	826038	826039	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:826038_826039delAC								SHOX (205893 upstream) : CRLF2 (488848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	860948	860948	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:860948delG								SHOX (240803 upstream) : CRLF2 (453939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2121207	2121208	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2121207_2121208delTT								ASMT (359234 upstream) : DHRSX (16349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2130880	2130880	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2130880delA								ASMT (368907 upstream) : DHRSX (6677 downstream)																																			---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2326743	2326743	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2326743delA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	2487032	2487032	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2487032delT								DHRSX (68017 upstream) : CD99 (122196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2563446	2563447	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2563446_2563447insT	uc004cqj.1	+											Homo sapiens cDNA FLJ13471 fis, clone PLACE1003566.																														---	---	---	---
CD99	4267	broad.mit.edu	37	X	2612561	2612561	+	Intron	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2612561delG	uc004cqm.2	+						CD99_uc010nda.2_Intron|CD99_uc004cqn.2_Intron|CD99_uc004cqo.2_Intron	NM_002414	NP_002405			CD99 antigen isoform a precursor						cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1																		---	---	---	---
PRKX	5613	broad.mit.edu	37	X	3539377	3539377	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3539377delA	uc010nde.2	-							NM_005044	NP_005035			protein kinase, X-linked								ATP binding|cAMP-dependent protein kinase activity			skin(2)|lung(1)	3		all_lung(23;0.000396)|Lung NSC(23;0.00123)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	5197160	5197161	+	IGR	INS	-	AGGAAGGA	AGGAAGGA	rs10701505		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5197160_5197161insAGGAAGGA								None (None upstream) : NLGN4X (610923 downstream)																																			---	---	---	---
STS	412	broad.mit.edu	37	X	7177636	7177636	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7177636delT	uc004cry.3	+	5	889	c.644delT	c.(643-645)GTTfs	p.V215fs		NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor	215	Helical.				female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)									Ichthyosis				---	---	---	---
STS	412	broad.mit.edu	37	X	7193957	7193957	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7193957delT	uc004cry.3	+							NM_000351	NP_000342			steryl-sulfatase precursor						female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)									Ichthyosis				---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9665501	9665501	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9665501delT	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron|TBL1X_uc004css.2_Intron	NM_001139466	NP_001132938			transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
WWC3	55841	broad.mit.edu	37	X	10047741	10047741	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10047741delA	uc004csx.3	+						WWC3_uc010nds.2_Intron|WWC3_uc010ndt.2_5'Flank	NM_015691	NP_056506			WWC family member 3											ovary(4)	4																		---	---	---	---
WWC3	55841	broad.mit.edu	37	X	10094410	10094410	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10094410delT	uc004csx.3	+						WWC3_uc010nds.2_Intron|WWC3_uc010ndt.2_Intron	NM_015691	NP_056506			WWC family member 3											ovary(4)	4																		---	---	---	---
MSL3	10943	broad.mit.edu	37	X	11793085	11793085	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11793085delT	uc004cuw.2	+						MSL3_uc004cux.2_Intron|MSL3_uc011mig.1_Intron|MSL3_uc011mih.1_Intron|MSL3_uc004cuy.2_Intron	NM_078629	NP_523353			male-specific lethal 3-like 1 isoform a						histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12701630	12701631	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12701630_12701631insA	uc004cuz.1	+	6	1003_1004	c.497_498insA	c.(496-498)GCAfs	p.A166fs	FRMPD4_uc011mij.1_Frame_Shift_Ins_p.A158fs	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	166					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																		---	---	---	---
GEMIN8	54960	broad.mit.edu	37	X	14039512	14039512	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14039512delA	uc004cwb.2	-						GEMIN8_uc004cwc.2_Intron|GEMIN8_uc004cwd.2_Intron	NM_017856	NP_060326			gem (nuclear organelle) associated protein 8						spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0																		---	---	---	---
FANCB	2187	broad.mit.edu	37	X	14868854	14868854	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14868854delA	uc004cwg.1	-						FANCB_uc004cwh.1_Intron	NM_001018113	NP_001018123			Fanconi anemia complementation group B						DNA repair	nucleoplasm				lung(1)	1	Hepatocellular(33;0.183)												Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FANCB	2187	broad.mit.edu	37	X	14883337	14883337	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14883337delT	uc004cwg.1	-	3	564	c.296delA	c.(295-297)AATfs	p.N99fs	FANCB_uc004cwh.1_Frame_Shift_Del_p.N99fs	NM_001018113	NP_001018123	Q8NB91	FANCB_HUMAN	Fanconi anemia complementation group B	99					DNA repair	nucleoplasm				lung(1)	1	Hepatocellular(33;0.183)												Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FIGF	2277	broad.mit.edu	37	X	15364176	15364176	+	3'UTR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15364176delG	uc004cwt.1	-	7						NM_004469	NP_004460			vascular endothelial growth factor D						angiogenesis|cell differentiation|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of mast cell chemotaxis|vascular endothelial growth factor receptor signaling pathway	extracellular space|membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity|platelet-derived growth factor receptor binding			ovary(1)|breast(1)|central_nervous_system(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
BMX	660	broad.mit.edu	37	X	15561054	15561054	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15561054delA	uc004cww.2	+						BMX_uc004cwx.3_Intron|BMX_uc004cwy.3_Intron	NM_203281	NP_975010			BMX non-receptor tyrosine kinase						cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)																	---	---	---	---
ACE2	59272	broad.mit.edu	37	X	15584646	15584646	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15584646delA	uc004cxa.1	-						ACE2_uc004cxb.2_Intron	NM_021804	NP_068576			angiotensin I converting enzyme 2 precursor						angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)													---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16871712	16871713	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16871712_16871713insA	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron|RBBP7_uc010nez.2_3'UTR	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18597856	18597856	+	Intron	DEL	A	-	-	rs12013924		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18597856delA	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18613311	18613312	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18613311_18613312insA	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18662778	18662778	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18662778delC	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18664273	18664273	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18664273delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18665265	18665265	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18665265delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
PHKA2	5256	broad.mit.edu	37	X	18942294	18942294	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18942294delT	uc004cyv.3	-						PHKA2_uc010nfg.1_Intron	NM_000292	NP_000283			phosphorylase kinase, alpha 2 (liver)						glucose metabolic process|glycogen catabolic process	cytosol|phosphorylase kinase complex|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(1)|central_nervous_system(1)	2	Hepatocellular(33;0.183)																	---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19014007	19014007	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19014007delT	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19014281	19014281	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19014281delA	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19017412	19017412	+	Intron	DEL	G	-	-	rs142903941	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19017412delG	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
PDHA1	5160	broad.mit.edu	37	X	19363864	19363866	+	Intron	DEL	CCC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19363864_19363866delCCC	uc004czg.3	+						PDHA1_uc004czh.3_Intron|PDHA1_uc011mjc.1_Intron|PDHA1_uc011mjd.1_Intron|PDHA1_uc010nfk.2_Intron	NM_000284	NP_000275			pyruvate dehydrogenase E1 alpha 1 precursor						glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)													---	---	---	---
MAP3K15	389840	broad.mit.edu	37	X	19389185	19389186	+	Intron	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19389185_19389186delAA	uc004czk.1	-						MAP3K15_uc004czj.1_Intron|MAP3K15_uc004czi.1_Intron	NM_001001671	NP_001001671			mitogen-activated protein kinase kinase kinase								ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21545055	21545055	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21545055delG	uc004czx.1	+	10	1064	c.1028delG	c.(1027-1029)AGAfs	p.R343fs	CNKSR2_uc004czw.2_Frame_Shift_Del_p.R343fs|CNKSR2_uc011mjn.1_Frame_Shift_Del_p.R294fs|CNKSR2_uc011mjo.1_Frame_Shift_Del_p.R343fs|CNKSR2_uc004czy.2_5'UTR	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	343	DUF1170.				regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21613201	21613201	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21613201delT	uc004czx.1	+						CNKSR2_uc004czw.2_Intron|CNKSR2_uc011mjn.1_Intron|CNKSR2_uc011mjo.1_Intron|CNKSR2_uc004czy.2_Intron	NM_014927	NP_055742			connector enhancer of kinase suppressor of Ras						regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
KLHL34	257240	broad.mit.edu	37	X	21675046	21675046	+	Frame_Shift_Del	DEL	C	-	-	rs139183650	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21675046delC	uc004czz.1	-	1	1403	c.861delG	c.(859-861)GGGfs	p.G287fs		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	287										ovary(1)	1																		---	---	---	---
PTCHD1	139411	broad.mit.edu	37	X	23397692	23397692	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23397692delT	uc004dal.3	+						PTCHD1_uc010nfu.1_Intron	NM_173495	NP_775766			patched domain containing 1						cognition|smoothened signaling pathway	integral to membrane|plasma membrane	hedgehog receptor activity			ovary(4)|kidney(1)|skin(1)	6																		---	---	---	---
CXorf58	254158	broad.mit.edu	37	X	23945136	23945136	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23945136delA	uc004daz.1	+						CXorf58_uc011mju.1_Intron	NM_152761	NP_689974			hypothetical protein LOC254158												0																		---	---	---	---
PCYT1B	9468	broad.mit.edu	37	X	24576282	24576282	+	3'UTR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24576282delG	uc004dbi.2	-	8					PCYT1B_uc004dbk.3_3'UTR|PCYT1B_uc004dbj.2_3'UTR	NM_004845	NP_004836			choline phosphate cytidylyltransferase 1 beta							endoplasmic reticulum	choline-phosphate cytidylyltransferase activity				0					Choline(DB00122)													---	---	---	---
CXorf21	80231	broad.mit.edu	37	X	30578281	30578281	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30578281delA	uc004dcg.1	-	3	468	c.192delT	c.(190-192)TTTfs	p.F64fs		NM_025159	NP_079435	Q9HAI6	CX021_HUMAN	hypothetical protein LOC80231	64										ovary(1)	1																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31950371	31950371	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31950371delT	uc004dda.1	-						DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc010ngn.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	35077922	35077922	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35077922delT								FAM47B (114888 upstream) : MAGEB16 (738537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35171139	35171142	+	IGR	DEL	ACAC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35171139_35171142delACAC								FAM47B (208105 upstream) : MAGEB16 (645317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38806239	38806240	+	IGR	DEL	AA	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38806239_38806240delAA								MID1IP1 (140458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	40374789	40374790	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40374789_40374790insT								BCOR (338207 upstream) : ATP6AP2 (65426 downstream)																																			---	---	---	---
MED14	9282	broad.mit.edu	37	X	40588551	40588551	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40588551delT	uc004dex.3	-						MED14_uc010nhe.1_Intron	NM_004229	NP_004220			mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40691634	40691636	+	Intron	DEL	GGG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40691634_40691636delGGG	uc004dfa.1	-						LOC100132831_uc011mkp.1_RNA					Homo sapiens cDNA FLJ31962 fis, clone NT2RP7007594.																														---	---	---	---
USP9X	8239	broad.mit.edu	37	X	40999815	40999815	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40999815delT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
CASK	8573	broad.mit.edu	37	X	41429005	41429005	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41429005delA	uc004dfl.3	-						CASK_uc004dfj.3_Intron|CASK_uc004dfk.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron	NM_003688	NP_003679			calcium/calmodulin-dependent serine protein						cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6																		---	---	---	---
GPR82	27197	broad.mit.edu	37	X	41586948	41586949	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41586948_41586949delTT	uc004dfs.1	+	3	909_910	c.669_670delTT	c.(667-672)TCTTTTfs	p.S223fs	CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR82_uc004dft.2_Frame_Shift_Del_p.S223fs|GPR82_uc004dfu.1_RNA	NM_080817	NP_543007	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	223_224	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	45623220	45623220	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45623220delA								MIR222 (16690 upstream) : ZNF673 (683404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	47578336	47578336	+	Intron	DEL	G	-	-	rs5953088	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47578336delG	uc004dio.1	+											Homo sapiens cDNA FLJ36789 fis, clone ADRGL2004459.																														---	---	---	---
SHROOM4	57477	broad.mit.edu	37	X	50378789	50378792	+	Intron	DEL	AAAG	-	-	rs5915290	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50378789_50378792delAAAG	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron|SHROOM4_uc004dpf.1_Intron	NM_020717	NP_065768			shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	52574759	52574759	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52574759delG								XAGE1D (330808 upstream) : SSX8 (77226 downstream)																																			---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53245132	53245133	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53245132_53245133insG	uc004drz.2	-	7	1340_1341	c.807_808insC	c.(805-810)CCCACAfs	p.P269fs	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Frame_Shift_Ins_p.P202fs|KDM5C_uc004dsa.2_Frame_Shift_Ins_p.P268fs	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	269_270					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18								N|F|S		clear cell renal carcinoma								---	---	---	---
FAM120C	54954	broad.mit.edu	37	X	54107631	54107631	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54107631delA	uc004dsz.3	-						FAM120C_uc011moh.1_Intron	NM_017848	NP_060318			hypothetical protein LOC54954											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	57703526	57703526	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57703526delT								ZXDB (79620 upstream) : ZXDA (230672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	58494457	58494458	+	IGR	DEL	AC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58494457_58494458delAC								ZXDA (557390 upstream) : None (None downstream)																																			---	---	---	---
ZC4H2	55906	broad.mit.edu	37	X	64139033	64139033	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64139033delG	uc004dvu.2	-	4	538	c.450delC	c.(448-450)CCCfs	p.P150fs	ZC4H2_uc004dvv.2_Frame_Shift_Del_p.P127fs|ZC4H2_uc011mov.1_Frame_Shift_Del_p.P127fs|ZC4H2_uc011mow.1_Intron|ZC4H2_uc004dvw.1_3'UTR	NM_018684	NP_061154	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	150							metal ion binding|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	64548401	64548402	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64548401_64548402insT								ZC4H2 (293808 upstream) : ZC3H12B (160304 downstream)																																			---	---	---	---
BCYRN1	618	broad.mit.edu	37	X	70535193	70535194	+	Intron	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70535193_70535194insT	uc011mpt.1	-							NR_001568				Homo sapiens brain cytoplasmic RNA 1 (non-protein coding) (BCYRN1), non-coding RNA.												0																		---	---	---	---
ACRC	93953	broad.mit.edu	37	X	70812449	70812450	+	Intron	DEL	TT	-	-	rs71886942		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70812449_70812450delTT	uc004eae.2	+						BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189			ACRC protein							nucleus				ovary(3)	3	Renal(35;0.156)																	---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71788554	71788554	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71788554delA	uc004eau.2	-						HDAC8_uc011mqe.1_5'Flank|HDAC8_uc011mqf.1_Intron|HDAC8_uc011mqg.1_Intron|HDAC8_uc011mqh.1_Intron|HDAC8_uc010nlk.1_Intron|HDAC8_uc004eav.2_Intron|HDAC8_uc004eaw.2_Intron	NM_018486	NP_060956			histone deacetylase 8						chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)													---	---	---	---
CHIC1	53344	broad.mit.edu	37	X	72797172	72797172	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72797172delT	uc004ebk.3	+						CHIC1_uc010nlo.2_Intron|CHIC1_uc011mql.1_Intron|CHIC1_uc004ebl.3_Intron	NM_001039840	NP_001034929			cysteine-rich hydrophobic domain 1							cytoplasmic membrane-bounded vesicle|plasma membrane					0	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	74387595	74387596	+	IGR	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74387595_74387596delTT								ABCB7 (11463 upstream) : UPRT (106365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	74964416	74964416	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74964416delT								ZDHHC15 (221079 upstream) : MAGEE2 (38407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	75851756	75851756	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75851756delT								MAGEE1 (200012 upstream) : MIR384 (287942 downstream)																																			---	---	---	---
ATP7A	538	broad.mit.edu	37	X	77264922	77264922	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77264922delT	uc004ecx.3	+						ATP7A_uc004ecw.2_3'UTR	NM_000052	NP_000043			ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	80185321	80185321	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80185321delA	uc004eec.1	+	1	394	c.220delA	c.(220-222)AAAfs	p.K74fs						SubName: Full=cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1; SubName: Full=Voltage-dependent anion channel 1, isoform CRA_a;																														---	---	---	---
RPS6KA6	27330	broad.mit.edu	37	X	83320142	83320143	+	Intron	INS	-	TA	TA			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83320142_83320143insTA	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron	NM_014496	NP_055311			ribosomal protein S6 kinase polypeptide 6						axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
RPS6KA6	27330	broad.mit.edu	37	X	83361835	83361836	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83361835_83361836insA	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron	NM_014496	NP_055311			ribosomal protein S6 kinase polypeptide 6						axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
APOOL	139322	broad.mit.edu	37	X	84309335	84309336	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84309335_84309336delTT	uc004eem.2	+						APOOL_uc010nmp.2_Intron	NM_198450	NP_940852			apolipoprotein O-like precursor							extracellular region					0																		---	---	---	---
ZNF711	7552	broad.mit.edu	37	X	84524996	84524996	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84524996delT	uc004eeo.2	+						ZNF711_uc004eep.2_Intron|ZNF711_uc004eeq.2_Intron|ZNF711_uc011mqy.1_Intron	NM_021998	NP_068838			zinc finger protein 711						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
POF1B	79983	broad.mit.edu	37	X	84534382	84534383	+	3'UTR	INS	-	C	C	rs112147894	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84534382_84534383insC	uc004eer.2	-	17						NM_024921	NP_079197			premature ovarian failure, 1B								actin binding				0																		---	---	---	---
CHM	1121	broad.mit.edu	37	X	85134074	85134074	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85134074delA	uc004eet.2	-						CHM_uc011mqz.1_Intron	NM_000390	NP_000381			choroideremia isoform a						intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)																---	---	---	---
DACH2	117154	broad.mit.edu	37	X	86087097	86087097	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86087097delT	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.2_Intron|DACH2_uc011mra.1_Intron|DACH2_uc010nmr.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																		---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91134309	91134309	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91134309delT	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron|PCDH11X_uc004efh.1_Intron|PCDH11X_uc004efj.1_3'UTR	NM_032968	NP_116750			protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96502621	96502621	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96502621delA	uc004efu.3	+						DIAPH2_uc004eft.3_Intron	NM_006729	NP_006720			diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
TRMT2B	79979	broad.mit.edu	37	X	100273829	100273829	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100273829delT	uc004egq.2	-						TRMT2B_uc004egp.2_Intron|TRMT2B_uc004egr.2_Intron|TRMT2B_uc004egs.2_Intron|TRMT2B_uc004egt.2_Intron|TRMT2B_uc004egu.2_Intron|TRMT2B_uc004egv.2_Intron	NM_024917	NP_079193			TRM2 tRNA methyltransferase 2 homolog B								tRNA (uracil-5-)-methyltransferase activity			ovary(1)	1																		---	---	---	---
GPRASP1	9737	broad.mit.edu	37	X	101912486	101912486	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101912486delT	uc004ejj.3	+	5	4446	c.3645delT	c.(3643-3645)AGTfs	p.S1215fs	GPRASP1_uc004eji.3_Frame_Shift_Del_p.S1215fs|GPRASP1_uc010nod.2_Frame_Shift_Del_p.S1215fs	NM_014710	NP_055525	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting	1215	OPRD1-binding.					cytoplasm	protein binding			ovary(1)|lung(1)	2																		---	---	---	---
CXorf57	55086	broad.mit.edu	37	X	105905170	105905170	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105905170delT	uc004emi.3	+						CXorf57_uc004emj.3_Intron	NM_018015	NP_060485			hypothetical protein LOC55086											ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
RNF128	79589	broad.mit.edu	37	X	105937256	105937256	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105937256delT	uc004emk.2	+	1	189	c.24delT	c.(22-24)AGTfs	p.S8fs		NM_024539	NP_078815	Q8TEB7	RN128_HUMAN	ring finger protein 128 isoform 2	Error:Variant_position_missing_in_Q8TEB7_after_alignment						endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TBC1D8B	54885	broad.mit.edu	37	X	106097566	106097566	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106097566delT	uc004emo.2	+						MORC4_uc004emp.3_Intron	NM_017752	NP_060222			TBC1 domain family, member 8B (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
COL4A5	1287	broad.mit.edu	37	X	107819103	107819103	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107819103delT	uc004enz.1	+						COL4A5_uc011mso.1_Intron	NM_033380	NP_203699			type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110416183	110416184	+	Intron	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110416183_110416184delTC	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron|PAK3_uc004eoz.2_Intron|PAK3_uc011mst.1_Intron|PAK3_uc010npv.1_Intron|PAK3_uc010npw.1_Intron	NM_001128173	NP_001121645			p21-activated kinase 3 isoform d						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10															TSP Lung(19;0.15)			---	---	---	---
AMOT	154796	broad.mit.edu	37	X	112023978	112023978	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112023978delA	uc004eps.2	-						AMOT_uc004epr.2_Intron|AMOT_uc011mtc.1_Intron|hsa-mir-4329|MI0015901_RNA	NM_133265	NP_573572			angiomotin isoform 2						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																		---	---	---	---
IL13RA2	3598	broad.mit.edu	37	X	114251579	114251579	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114251579delT	uc004epx.2	-						IL13RA2_uc010nqd.1_Intron	NM_000640	NP_000631			interleukin 13 receptor, alpha 2 precursor							extracellular space|integral to membrane|soluble fraction	cytokine receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114877908	114877908	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114877908delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_Intron|PLS3_uc011mtl.1_Intron	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
AGTR2	186	broad.mit.edu	37	X	115303402	115303402	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115303402delT	uc004eqh.3	+							NM_000686	NP_000677			angiotensin II receptor, type 2						behavior|blood vessel remodeling|brain development|G-protein signaling, coupled to cGMP nucleotide second messenger|intracellular protein kinase cascade|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of heart rate|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of apoptosis|positive regulation of nitric-oxide synthase activity|positive regulation of phosphoprotein phosphatase activity|positive regulation of vasodilation|regulation of systemic arterial blood pressure by circulatory renin-angiotensin		angiotensin type II receptor activity|receptor antagonist activity			ovary(2)|lung(1)	3																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117743229	117743229	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117743229delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
IL13RA1	3597	broad.mit.edu	37	X	117883814	117883814	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117883814delA	uc004eqs.2	+						IL13RA1_uc004eqr.1_Intron|IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551			interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0																		---	---	---	---
SLC25A5	292	broad.mit.edu	37	X	118605036	118605036	+	3'UTR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118605036delT	uc004erh.3	+	4					LOC100303728_uc004ere.1_5'Flank|LOC100303728_uc004erg.1_5'Flank	NM_001152	NP_001143			adenine nucleotide translocator 2						chromosome segregation|energy reserve metabolic process|interspecies interaction between organisms|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane|mitochondrial nucleoid|MMXD complex	adenine transmembrane transporter activity|protein binding			ovary(1)	1					Clodronate(DB00720)													---	---	---	---
CXorf56	63932	broad.mit.edu	37	X	118694020	118694020	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118694020delA	uc004erk.1	-						CXorf56_uc004erj.1_Intron|CXorf56_uc011mtu.1_Intron	NM_022101	NP_071384			hypothetical protein LOC63932								protein binding				0																		---	---	---	---
NKAP	79576	broad.mit.edu	37	X	119068556	119068556	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119068556delT	uc004esh.2	-						NKAP_uc004esg.2_Intron	NM_024528	NP_078804			NFKB activating protein						negative regulation of transcription, DNA-dependent|Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	120993859	120993859	+	IGR	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120993859delG								GLUD2 (810065 upstream) : None (None downstream)																																			---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123697632	123697633	+	Intron	INS	-	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123697632_123697633insG	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
RBMX2	51634	broad.mit.edu	37	X	129546261	129546262	+	Intron	DEL	TT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129546261_129546262delTT	uc004evt.2	+							NM_016024	NP_057108			RNA binding motif protein, X-linked 2								nucleotide binding|RNA binding			breast(3)|ovary(1)	4																		---	---	---	---
GPC4	2239	broad.mit.edu	37	X	132439923	132439923	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132439923delG	uc004exc.1	-	6	1244	c.1032delC	c.(1030-1032)CCCfs	p.P344fs	GPC4_uc011mvg.1_Frame_Shift_Del_p.P274fs	NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4 precursor	344					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
HPRT1	3251	broad.mit.edu	37	X	133632480	133632480	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133632480delT	uc004exl.3	+						HPRT1_uc010nrs.2_Intron	NM_000194	NP_000185			hypoxanthine phosphoribosyltransferase 1						adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP catabolic process|GMP salvage|grooming behavior|guanine salvage|hypoxanthine salvage|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|protein homotetramerization|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	guanine phosphoribosyltransferase activity|hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity				0	Acute lymphoblastic leukemia(192;0.000127)				Mercaptopurine(DB01033)|Thioguanine(DB00352)													---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135322706	135322706	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135322706delA	uc004ezt.2	-						MAP7D3_uc004ezs.2_Intron|MAP7D3_uc011mwc.1_Intron|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135322790	135322790	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135322790delT	uc004ezt.2	-						MAP7D3_uc004ezs.2_Intron|MAP7D3_uc011mwc.1_Intron|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
VGLL1	51442	broad.mit.edu	37	X	135630679	135630679	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135630679delA	uc004ezy.2	+						MIR934_hsa-mir-934|MI0005756_5'Flank	NM_016267	NP_057351			vestigial like 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138909001	138909001	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138909001delA	uc004faz.2	-						ATP11C_uc004fba.2_Intron	NM_173694	NP_775965			ATPase, class VI, type 11C isoform a						ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
CXorf66	347487	broad.mit.edu	37	X	139040421	139040421	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139040421delT	uc004fbb.2	-							NM_001013403	NP_001013421			hypothetical protein LOC347487 precursor							integral to membrane					0																		---	---	---	---
SPANXC	64663	broad.mit.edu	37	X	140355351	140355351	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140355351delA	uc004fbl.2	-											Homo sapiens nuclear-associated protein SPAN-Xa (SPANX) mRNA, complete cds.							cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)																	---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147985845	147985846	+	Intron	INS	-	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147985845_147985846insA	uc004fcp.2	+						AFF2_uc004fco.2_3'UTR|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron|AFF2_uc011mxc.1_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149898766	149898766	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149898766delT	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819			myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150794092	150794092	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150794092delT	uc004fev.3	+							NM_173493	NP_775764			PAS domain containing 1							nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAGEA6	4105	broad.mit.edu	37	X	151870319	151870319	+	3'UTR	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151870319delC	uc004ffq.1	+	3					MAGEA6_uc004ffr.1_3'UTR|MAGEA2_uc010nto.2_Intron	NM_005363	NP_005354			melanoma antigen family A, 6								protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153216186	153216186	+	Intron	DEL	C	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153216186delC	uc004fjp.2	-							NM_005334	NP_005325			host cell factor 1						cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	154045564	154045564	+	RNA	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154045564delT	uc004fmr.1	-	1		c.224delA								full-length cDNA clone CS0DM009YP14 of Fetal liver of Homo sapiens (human).																														---	---	---	---
VBP1	7411	broad.mit.edu	37	X	154464693	154464693	+	Intron	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154464693delT	uc004fnc.2	+						VBP1_uc004fnd.2_Intron	NM_003372	NP_003363			von Hippel-Lindau binding protein 1						'de novo' posttranslational protein folding	nucleus|prefoldin complex	unfolded protein binding				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
Unknown	0	broad.mit.edu	37	Y	3720506	3720506	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:3720506delT								TGIF2LY (272426 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	8002232	8002232	+	IGR	DEL	T	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:8002232delT								TTTY12 (323511 upstream) : TTTY18 (549179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9368302	9368303	+	IGR	DEL	TG	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9368302_9368303delTG								TSPY1 (20913 upstream) : RBMY3AP (80027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9926066	9926067	+	IGR	DEL	GT	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9926066_9926067delGT								TTTY22 (275212 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9960320	9960321	+	IGR	INS	-	A	A	rs148334492		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9960320_9960321insA								TTTY22 (309466 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10066471	10066471	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10066471delA								TTTY22 (415617 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13285777	13285777	+	IGR	DEL	T	-	-	rs113216904		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13285777delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13371026	13371027	+	IGR	DEL	TC	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13371026_13371027delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13448188	13448192	+	IGR	DEL	TCCAT	-	-	rs148695425		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13448188_13448192delTCCAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13896559	13896560	+	IGR	INS	-	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13896559_13896560insT								None (None upstream) : TTTY15 (877738 downstream)																																			---	---	---	---
UTY	7404	broad.mit.edu	37	Y	15448218	15448218	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15448218delA	uc004fsx.1	-						UTY_uc004fsw.1_Intron|UTY_uc010nwx.1_Intron|UTY_uc004fsy.2_Intron|UTY_uc004fsz.2_Intron	NM_007125	NP_009056			tetratricopeptide repeat protein isoform 3						chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
RBMY2EP	159125	broad.mit.edu	37	Y	23557683	23557683	+	Intron	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:23557683delA	uc004fun.1	-							NR_001574				Homo sapiens RNA binding motif protein, Y-linked, family 2, member E pseudogene (RBMY2EP), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	28774180	28774180	+	IGR	DEL	A	-	-			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28774180delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	58970661	58970662	+	IGR	INS	-	T	T	rs141723260		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58970661_58970662insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	58994226	58994226	+	IGR	DEL	C	-	-	rs149664455		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58994226delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59002387	59002388	+	IGR	INS	-	TTA	TTA	rs140674030		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59002387_59002388insTTA								None (None upstream) : None (None downstream)																																			---	---	---	---
SAMD11	148398	broad.mit.edu	37	1	865640	865640	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:865640G>A	uc001abw.1	+	3	258	c.178G>A	c.(178-180)GGG>AGG	p.G60R	SAMD11_uc001abv.1_Missense_Mutation_p.G60R	NM_152486	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	60						nucleus					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)														---	---	---	---
CPSF3L	54973	broad.mit.edu	37	1	1248290	1248290	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1248290C>T	uc001aee.1	-	12	1229	c.1171G>A	c.(1171-1173)GCA>ACA	p.A391T	CPSF3L_uc009vjy.1_RNA|CPSF3L_uc001aef.1_Missense_Mutation_p.A397T|CPSF3L_uc009vjz.1_Missense_Mutation_p.A369T|CPSF3L_uc010nyj.1_Missense_Mutation_p.A362T|CPSF3L_uc001aeg.1_Missense_Mutation_p.A267T|CPSF3L_uc001aeh.1_Missense_Mutation_p.A290T|CPSF3L_uc001aei.1_Missense_Mutation_p.A293T|CPSF3L_uc001aej.1_Missense_Mutation_p.A218T|CPSF3L_uc001aek.1_Missense_Mutation_p.A133T	NM_017871	NP_060341	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor	391						Golgi apparatus|nucleus	hydrolase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)														---	---	---	---
VWA1	64856	broad.mit.edu	37	1	1374474	1374474	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1374474G>A	uc001afs.2	+	3	865	c.645G>A	c.(643-645)CCG>CCA	p.P215P	VWA1_uc001afr.2_Silent_p.P3P	NM_022834	NP_073745	Q6PCB0	VWA1_HUMAN	von Willebrand factor A domain containing 1	215	Fibronectin type-III 1.					basement membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
GNB1	2782	broad.mit.edu	37	1	1721834	1721834	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1721834G>A	uc001aif.2	-	9	1031	c.699C>T	c.(697-699)TGC>TGT	p.C233C	GNB1_uc009vky.2_Silent_p.C133C	NM_002074	NP_002065	P62873	GBB1_HUMAN	guanine nucleotide-binding protein, beta-1	233	WD 5.				cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				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;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)														---	---	---	---
GNB1	2782	broad.mit.edu	37	1	1735888	1735888	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1735888G>A	uc001aif.2	-	7	732	c.400C>T	c.(400-402)CGC>TGC	p.R134C	GNB1_uc009vky.2_Missense_Mutation_p.R34C	NM_002074	NP_002065	P62873	GBB1_HUMAN	guanine nucleotide-binding protein, beta-1	134					cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				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;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)														---	---	---	---
PEX10	5192	broad.mit.edu	37	1	2340015	2340015	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2340015G>A	uc001ajh.2	-	3	545	c.476C>T	c.(475-477)GCG>GTG	p.A159V	PEX10_uc001ajg.2_Missense_Mutation_p.A159V	NM_002617	NP_002608	O60683	PEX10_HUMAN	peroxisome biogenesis factor 10 isoform 2	159					protein import into peroxisome matrix|protein import into peroxisome matrix	integral to peroxisomal membrane|peroxisomal membrane	protein binding|protein C-terminus binding|zinc ion binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)														---	---	---	---
TPRG1L	127262	broad.mit.edu	37	1	3545135	3545135	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3545135T>C	uc001akm.2	+	5	868	c.787T>C	c.(787-789)TAC>CAC	p.Y263H	TPRG1L_uc009vlj.2_Missense_Mutation_p.Y204H	NM_182752	NP_877429	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	263						cell junction|synaptic vesicle					0	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)														---	---	---	---
TP73	7161	broad.mit.edu	37	1	3648049	3648049	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3648049C>T	uc001akp.2	+	13	1617	c.1507C>T	c.(1507-1509)CCA>TCA	p.P503S	TP73_uc001akq.2_Intron|TP73_uc001akr.2_Missense_Mutation_p.P454S|TP73_uc009vlk.1_Missense_Mutation_p.S404F|TP73_uc001aks.2_Intron|TP73_uc010nzk.1_Missense_Mutation_p.P432S|TP73_uc010nzl.1_Missense_Mutation_p.P52S	NM_005427	NP_005418	O15350	P73_HUMAN	tumor protein p73 isoform a	503	SAM.				cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)														---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	6021992	6021992	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6021992G>T	uc001alq.1	-	6	801	c.535C>A	c.(535-537)CTC>ATC	p.L179I	NPHP4_uc001als.1_RNA|NPHP4_uc009vlt.1_RNA|NPHP4_uc001alt.1_RNA	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	179					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PLEKHG5	57449	broad.mit.edu	37	1	6529456	6529456	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6529456G>A	uc001ano.1	-	19	2257	c.2156C>T	c.(2155-2157)ACG>ATG	p.T719M	PLEKHG5_uc001ann.1_Missense_Mutation_p.T700M|PLEKHG5_uc001anq.1_Missense_Mutation_p.T740M|PLEKHG5_uc001anp.1_Missense_Mutation_p.T740M|PLEKHG5_uc001anj.1_Missense_Mutation_p.T224M|PLEKHG5_uc009vma.1_Missense_Mutation_p.T503M|PLEKHG5_uc010nzr.1_Missense_Mutation_p.T732M|PLEKHG5_uc001ank.1_Missense_Mutation_p.T663M|PLEKHG5_uc009vmb.1_Missense_Mutation_p.T663M|PLEKHG5_uc001anl.1_Missense_Mutation_p.T663M|PLEKHG5_uc001anm.1_Missense_Mutation_p.T663M|PLEKHG5_uc001anr.1_5'Flank	NM_001042663	NP_001036128	O94827	PKHG5_HUMAN	pleckstrin homology domain containing family G	719	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
ZBTB48	3104	broad.mit.edu	37	1	6646788	6646788	+	Missense_Mutation	SNP	C	T	T	rs144980289		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6646788C>T	uc009vmc.1	+	5	1201	c.1078C>T	c.(1078-1080)CGC>TGC	p.R360C	ZBTB48_uc001anx.2_Missense_Mutation_p.R360C|ZBTB48_uc009vmd.1_Missense_Mutation_p.R360C|ZBTB48_uc001any.1_5'UTR	NM_005341	NP_005332	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	360	C2H2-type 3.					cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
ZBTB48	3104	broad.mit.edu	37	1	6648915	6648915	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6648915G>A	uc009vmc.1	+						ZBTB48_uc001anx.2_Intron|ZBTB48_uc009vmd.1_Intron|ZBTB48_uc001any.1_Intron	NM_005341	NP_005332			zinc finger and BTB domain containing 48							cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
DNAJC11	55735	broad.mit.edu	37	1	6698400	6698400	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6698400G>A	uc001aof.2	-	12	1384	c.1278C>T	c.(1276-1278)AGC>AGT	p.S426S	DNAJC11_uc010nzt.1_Intron|DNAJC11_uc001aog.2_Silent_p.S374S|DNAJC11_uc010nzu.1_Silent_p.S336S	NM_018198	NP_060668	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	426	Potential.				protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9099929	9099929	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9099929C>T	uc001apo.2	-	7	1107	c.815G>A	c.(814-816)CGC>CAC	p.R272H	SLC2A5_uc010nzy.1_Missense_Mutation_p.R213H|SLC2A5_uc010nzz.1_Missense_Mutation_p.R157H|SLC2A5_uc010oaa.1_Missense_Mutation_p.R228H|SLC2A5_uc010oab.1_Missense_Mutation_p.R272H	NM_003039	NP_003030	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated	272	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TMEM201	199953	broad.mit.edu	37	1	9658528	9658528	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9658528G>A	uc001apz.2	+	4	463	c.451G>A	c.(451-453)GAG>AAG	p.E151K	TMEM201_uc001apy.2_Missense_Mutation_p.E151K	NM_001130924	NP_001124396	Q5SNT2	TM201_HUMAN	transmembrane protein 201 isoform 1	151						integral to membrane|nuclear inner membrane					0	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9809613	9809613	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9809613G>T	uc001aqh.2	-	7	1650	c.891C>A	c.(889-891)GCC>GCA	p.A297A	CLSTN1_uc001aqi.2_Silent_p.A287A|CLSTN1_uc010oag.1_Silent_p.A297A	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	297	Extracellular (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
EXOSC10	5394	broad.mit.edu	37	1	11141161	11141161	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11141161C>T	uc001asa.2	-	11	1465	c.1415G>A	c.(1414-1416)CGG>CAG	p.R472Q	EXOSC10_uc001asb.2_Missense_Mutation_p.R472Q|EXOSC10_uc009vmy.1_Missense_Mutation_p.R472Q	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1	472					CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11308060	11308060	+	Missense_Mutation	SNP	C	T	T	rs150146024		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11308060C>T	uc001asd.2	-	7	1053	c.932G>A	c.(931-933)CGT>CAT	p.R311H		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	311					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
MFN2	9927	broad.mit.edu	37	1	12052667	12052667	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12052667C>T	uc001atn.3	+	4	684	c.231C>T	c.(229-231)GAC>GAT	p.D77D	MFN2_uc009vni.2_Silent_p.D77D	NM_014874	NP_055689	O95140	MFN2_HUMAN	mitofusin 2	77	Cytoplasmic (Potential).				blood coagulation|mitochondrial fusion|mitochondrial membrane organization|mitochondrion localization|negative regulation of Ras protein signal transduction|negative regulation of smooth muscle cell proliferation|protein targeting to mitochondrion	cytosol|integral to membrane|intrinsic to mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16257436	16257436	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257436G>T	uc001axk.1	+	11	4905	c.4701G>T	c.(4699-4701)GAG>GAT	p.E1567D	SPEN_uc010obp.1_Missense_Mutation_p.E1526D	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1567					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
C1orf89	79363	broad.mit.edu	37	1	16560154	16560154	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16560154G>A	uc001ayd.2	-	2	640	c.218C>T	c.(217-219)GCC>GTC	p.A73V		NM_030907	NP_112169	Q9BU20	RSG1_HUMAN	hypothetical protein LOC79363	73	Small GTPase-like.				cellular protein localization|cilium assembly|exocytosis|protein transport|regulation of exocytosis|regulation of vesicle fusion|small GTPase mediated signal transduction	cilium|microtubule basal body	GTP binding				0		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.2e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17567233	17567233	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17567233C>T	uc001bah.1	+	15	1828	c.1736C>T	c.(1735-1737)GCG>GTG	p.A579V	PADI1_uc010oco.1_Missense_Mutation_p.A136V|PADI1_uc010ocp.1_Intron|PADI1_uc010ocq.1_Missense_Mutation_p.A50V|PADI1_uc009vpb.1_Intron	NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	579					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)													---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19439239	19439239	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19439239G>A	uc001bbi.2	-	78	11584	c.11580C>T	c.(11578-11580)TCC>TCT	p.S3860S	UBR4_uc001bbj.1_3'UTR	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3860					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
AKR7A3	22977	broad.mit.edu	37	1	19610581	19610581	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610581A>G	uc001bbv.1	-	6	820	c.743T>C	c.(742-744)GTG>GCG	p.V248A		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	248					cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21551914	21551914	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21551914G>A	uc001bek.2	-	17	1944	c.1869C>T	c.(1867-1869)GAC>GAT	p.D623D	ECE1_uc001bem.2_Silent_p.D607D|ECE1_uc001bej.2_Silent_p.D611D|ECE1_uc001bei.2_Silent_p.D620D|ECE1_uc010odl.1_Silent_p.D623D	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	623	Extracellular (Potential).				bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21586818	21586818	+	Silent	SNP	G	A	A	rs13306314	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21586818G>A	uc001bek.2	-	5	636	c.561C>T	c.(559-561)AAC>AAT	p.N187N	ECE1_uc001bem.2_Silent_p.N171N|ECE1_uc001bej.2_Silent_p.N175N|ECE1_uc001bei.2_Silent_p.N184N|ECE1_uc010odl.1_Silent_p.N187N|ECE1_uc009vqa.1_Silent_p.N187N	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	187	Extracellular (Potential).				bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22032982	22032982	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22032982G>A	uc001bfb.2	-	17	2427	c.2189C>T	c.(2188-2190)CCG>CTG	p.P730L	USP48_uc001bfa.2_Missense_Mutation_p.P268L|USP48_uc010odq.1_Missense_Mutation_p.P742L|USP48_uc009vqc.2_Missense_Mutation_p.P664L|USP48_uc001bfc.2_Missense_Mutation_p.P730L|USP48_uc001bfd.1_5'Flank	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	730	DUSP 3.				ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
CELA3A	10136	broad.mit.edu	37	1	22332154	22332154	+	Splice_Site	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22332154G>A	uc001bfl.2	+	4	247	c.228_splice	c.e4-1	p.S76_splice	CELA3B_uc009vqf.2_Splice_Site_p.S75_splice	NM_005747	NP_005738			elastase 3A, pancreatic preproprotein						cholesterol metabolic process|digestion|proteolysis		serine-type endopeptidase activity			haematopoietic_and_lymphoid_tissue(1)	1																OREG0013211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
WNT4	54361	broad.mit.edu	37	1	22446903	22446903	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22446903G>A	uc001bfs.3	-	5	800	c.696C>T	c.(694-696)CAC>CAT	p.H232H	WNT4_uc010odt.1_Silent_p.H169H	NM_030761	NP_110388	P56705	WNT4_HUMAN	wingless-type MMTV integration site family,	232					adrenal gland development|androgen biosynthetic process|anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|dermatome development|endoderm development|epithelial to mesenchymal transition|establishment of protein localization in plasma membrane|female gonad development|female sex determination|liver development|male gonad development|mesonephric tubule development|metanephric mesenchymal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of male gonad development|negative regulation of testicular blood vessel morphogenesis|negative regulation of testosterone biosynthetic process|negative regulation of transcription, DNA-dependent|oocyte development|paramesonephric duct development|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of collagen biosynthetic process|positive regulation of cortisol biosynthetic process|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|protein palmitoylation|renal vesicle formation|smooth muscle cell differentiation|somatotropin secreting cell differentiation|tertiary branching involved in mammary gland duct morphogenesis|thyroid-stimulating hormone-secreting cell differentiation|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|extracellular space|Golgi apparatus|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|signal transducer activity|transcription corepressor activity			ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)														---	---	---	---
ZBTB40	9923	broad.mit.edu	37	1	22850903	22850903	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22850903C>T	uc001bft.2	+	18	4002	c.3491C>T	c.(3490-3492)ACG>ATG	p.T1164M	ZBTB40_uc001bfu.2_Missense_Mutation_p.T1164M|ZBTB40_uc009vqi.1_Missense_Mutation_p.T1052M	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1164					bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)														---	---	---	---
IL28RA	163702	broad.mit.edu	37	1	24486061	24486061	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24486061G>A	uc001bis.2	-	5	586	c.573C>T	c.(571-573)AGC>AGT	p.S191S	IL28RA_uc001bir.2_Silent_p.S191S|IL28RA_uc001bit.2_Silent_p.S191S|IL28RA_uc001biu.2_Silent_p.S107S	NM_170743	NP_734464	Q8IU57	I28RA_HUMAN	interleukin 28 receptor, alpha isoform 1	191	Extracellular (Potential).				cytokine-mediated signaling pathway|negative regulation of cell proliferation|regulation of defense response to virus by host	interleukin-28 receptor complex	protein binding|receptor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00117)|all_lung(284;0.00151)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.21e-24)|Colorectal(126;6.61e-08)|COAD - Colon adenocarcinoma(152;3.56e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00918)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.185)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27101213	27101213	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27101213C>T	uc001bmv.1	+	18	4868	c.4495C>T	c.(4495-4497)CAG>TAG	p.Q1499*	ARID1A_uc001bmt.1_Nonsense_Mutation_p.Q1498*|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Nonsense_Mutation_p.Q1116*|ARID1A_uc001bmx.1_Nonsense_Mutation_p.Q345*|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1499					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
FAM46B	115572	broad.mit.edu	37	1	27332480	27332480	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27332480T>C	uc010ofj.1	-	2	1405	c.1233A>G	c.(1231-1233)CAA>CAG	p.Q411Q		NM_052943	NP_443175	Q96A09	FA46B_HUMAN	hypothetical protein LOC115572	411										central_nervous_system(1)	1		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27876367	27876367	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27876367G>A	uc009vsy.2	-	6	3229	c.2260C>T	c.(2260-2262)CAG>TAG	p.Q754*	AHDC1_uc009vsz.1_Nonsense_Mutation_p.Q754*	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	754	Gly-rich.						DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27878443	27878443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27878443G>A	uc009vsy.2	-	6	1153	c.184C>T	c.(184-186)CGC>TGC	p.R62C	AHDC1_uc009vsz.1_Missense_Mutation_p.R62C|AHDC1_uc001boh.1_Intron	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	62	Pro-rich.						DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)														---	---	---	---
OPRD1	4985	broad.mit.edu	37	1	29185773	29185773	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29185773G>A	uc001brf.1	+	2	777	c.535G>A	c.(535-537)GTT>ATT	p.V179I		NM_000911	NP_000902	P41143	OPRD_HUMAN	opioid receptor, delta 1	179	Helical; Name=4; (Potential).				immune response|protein import into nucleus, translocation	integral to plasma membrane	delta-opioid receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Butorphanol(DB00611)|Codeine(DB00318)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Loperamide(DB00836)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pimozide(DB01100)|Propoxyphene(DB00647)													---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29609220	29609220	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29609220C>T	uc001bru.2	+	12	2011	c.1901C>T	c.(1900-1902)GCG>GTG	p.A634V	PTPRU_uc001brv.2_Missense_Mutation_p.A634V|PTPRU_uc001brw.2_Missense_Mutation_p.A634V|PTPRU_uc009vtq.2_Missense_Mutation_p.A634V|PTPRU_uc009vtr.2_Missense_Mutation_p.A634V	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	634	Extracellular (Potential).|Fibronectin type-III 4.				canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)														---	---	---	---
HCRTR1	3061	broad.mit.edu	37	1	32084902	32084902	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32084902C>T	uc009vtx.2	+	3	494	c.109C>T	c.(109-111)CGC>TGC	p.R37C	HCRTR1_uc001btb.2_Intron|HCRTR1_uc001btc.3_Silent_p.G10G|HCRTR1_uc001btd.2_Missense_Mutation_p.R37C|HCRTR1_uc010ogl.1_Missense_Mutation_p.R37C	NM_001525	NP_001516	O43613	OX1R_HUMAN	orexin receptor 1	37	Extracellular (Potential).				feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)														---	---	---	---
DCDC2B	149069	broad.mit.edu	37	1	32678403	32678403	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32678403C>T	uc001bun.2	+							NM_001099434	NP_001092904			doublecortin domain containing 2B						intracellular signal transduction						0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33764565	33764565	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33764565C>T	uc001bxc.1	+	9	1351	c.1181C>T	c.(1180-1182)ACG>ATG	p.T394M		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	394					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)														OREG0013343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	33777725	33777725	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33777725T>C	uc001bxd.1	-	4	263	c.263A>G	c.(262-264)GAC>GGC	p.D88G		NM_001080438	NP_001073907			RecName: Full=Alpha 1,3-galactosyltransferase 2;          Short=A3galt2;          EC=2.4.1.87; AltName: Full=Isoglobotriaosylceramide synthase; AltName: Full=iGb3 synthase;          Short=iGb3S; Flags: Precursor;																														---	---	---	---
PHC2	1912	broad.mit.edu	37	1	33837981	33837981	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33837981G>A	uc001bxg.1	-	2	296	c.242C>T	c.(241-243)GCC>GTC	p.A81V	PHC2_uc001bxh.1_Missense_Mutation_p.A81V|PHC2_uc009vuh.1_Missense_Mutation_p.A81V|PHC2_uc001bxi.1_Missense_Mutation_p.A81V	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a	81	Gln-rich.				multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34209009	34209009	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34209009G>A	uc001bxn.1	-	14	1954	c.1925C>T	c.(1924-1926)GCG>GTG	p.A642V	CSMD2_uc001bxm.1_Missense_Mutation_p.A682V	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	642	Extracellular (Potential).|CUB 4.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
KIAA0319L	79932	broad.mit.edu	37	1	35919961	35919961	+	Splice_Site	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35919961A>C	uc001byx.2	-	11	2038	c.1780_splice	c.e11+1	p.E594_splice	KIAA0319L_uc001byw.2_Splice_Site_p.E31_splice|KIAA0319L_uc010ohv.1_Splice_Site_p.E236_splice	NM_024874	NP_079150			dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
NCDN	23154	broad.mit.edu	37	1	36028933	36028933	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36028933G>A	uc001bza.2	+	6	1643	c.1516G>A	c.(1516-1518)GAC>AAC	p.D506N	NCDN_uc001bzb.2_Missense_Mutation_p.D506N|NCDN_uc001bzc.2_Missense_Mutation_p.D489N	NM_001014839	NP_001014839	Q9UBB6	NCDN_HUMAN	neurochondrin isoform 1	506					neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
RSPO1	284654	broad.mit.edu	37	1	38078495	38078495	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38078495G>A	uc001cbl.1	-	8	1512	c.724C>T	c.(724-726)CGC>TGC	p.R242C	RSPO1_uc001cbm.1_Missense_Mutation_p.R242C|RSPO1_uc009vvf.1_Missense_Mutation_p.R215C|RSPO1_uc009vvg.1_Missense_Mutation_p.R179C	NM_001038633	NP_001033722	Q2MKA7	RSPO1_HUMAN	R-spondin1 precursor	242					positive regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization		heparin binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39924141	39924141	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39924141G>T	uc010oiu.1	+	55	16635	c.16504G>T	c.(16504-16506)GAG>TAG	p.E5502*	MACF1_uc010ois.1_Nonsense_Mutation_p.E5000*	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	6958					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
CAP1	10487	broad.mit.edu	37	1	40530044	40530044	+	Splice_Site	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40530044T>C	uc001cfa.3	+	5	667	c.438_splice	c.e5+2	p.M146_splice	CAP1_uc001cey.3_Splice_Site_p.M146_splice|CAP1_uc001cez.3_Splice_Site_p.M146_splice|CAP1_uc009vvz.2_Splice_Site_p.M146_splice|CAP1_uc010oje.1_Splice_Site_p.M63_splice	NM_006367	NP_006358			adenylyl cyclase-associated protein						activation of adenylate cyclase activity|axon guidance|establishment or maintenance of cell polarity|platelet activation|platelet degranulation|signal transduction	plasma membrane	actin binding			ovary(1)	1	Lung NSC(20;5.03e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;4.63e-18)|Epithelial(16;1.27e-16)|all cancers(16;2.3e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
CTPS	1503	broad.mit.edu	37	1	41461742	41461742	+	Splice_Site	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41461742T>G	uc001cgk.3	+	8	1380	c.872_splice	c.e8+2	p.R291_splice	CTPS_uc010ojo.1_Splice_Site_p.R60_splice|CTPS_uc010ojp.1_Missense_Mutation_p.F299V|CTPS_uc001cgl.3_Splice_Site_p.R291_splice|CTPS_uc010ojq.1_Splice_Site_p.R135_splice|CTPS_uc009vwe.2_Splice_Site_p.R11_splice	NM_001905	NP_001896			CTP synthase						CTP biosynthetic process|glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|response to drug	cytosol	ATP binding|CTP synthase activity|protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)			L-Glutamine(DB00130)													---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	41979312	41979312	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41979312G>A	uc001cgz.3	-	8	6793	c.5580C>T	c.(5578-5580)GAC>GAT	p.D1860D	HIVEP3_uc001cha.3_Silent_p.D1860D|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1860	Acidic 3.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42045819	42045819	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42045819G>A	uc001cgz.3	-	4	5863	c.4650C>T	c.(4648-4650)AGC>AGT	p.S1550S	HIVEP3_uc001cha.3_Silent_p.S1550S|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1550					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
PPIH	10465	broad.mit.edu	37	1	43131707	43131707	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43131707C>A	uc001chq.2	+	7	463	c.393C>A	c.(391-393)TGC>TGA	p.C131*	PPIH_uc009vwl.2_Nonsense_Mutation_p.C88*	NM_006347	NP_006338	O43447	PPIH_HUMAN	peptidylprolyl isomerase H	131	PPIase cyclophilin-type.				protein complex assembly|protein folding	cytoplasm|nuclear speck|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity|protein binding|ribonucleoprotein binding				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)			L-Proline(DB00172)													---	---	---	---
KDM4A	9682	broad.mit.edu	37	1	44137383	44137383	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44137383A>T	uc001cjx.2	+	11	1737	c.1571A>T	c.(1570-1572)GAT>GTT	p.D524V	KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	524					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
KLF17	128209	broad.mit.edu	37	1	44595524	44595524	+	Missense_Mutation	SNP	C	T	T	rs138244178	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44595524C>T	uc001clp.2	+	2	639	c.581C>T	c.(580-582)CCG>CTG	p.P194L	KLF17_uc009vxf.1_Missense_Mutation_p.P157L	NM_173484	NP_775755	Q5JT82	KLF17_HUMAN	zinc finger protein 393	194					regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
STIL	6491	broad.mit.edu	37	1	47759161	47759161	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47759161G>A	uc001crc.1	-	8	996	c.841C>T	c.(841-843)CGA>TGA	p.R281*	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Nonsense_Mutation_p.R234*|STIL_uc010omo.1_Nonsense_Mutation_p.R281*|STIL_uc001crd.1_Nonsense_Mutation_p.R281*|STIL_uc001cre.1_Nonsense_Mutation_p.R281*|STIL_uc001crg.1_Nonsense_Mutation_p.R234*	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2	281					cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
ORC1L	4998	broad.mit.edu	37	1	52863445	52863445	+	Missense_Mutation	SNP	C	T	T	rs143141689	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52863445C>T	uc001ctt.2	-	4	533	c.314G>A	c.(313-315)CGG>CAG	p.R105Q	ORC1L_uc010oni.1_Missense_Mutation_p.R105Q|ORC1L_uc001ctu.2_Missense_Mutation_p.R105Q|ORC1L_uc009vzd.2_5'UTR	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	105	BAH.		R -> Q (in MGORS1).		cell cycle checkpoint|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
ORC1L	4998	broad.mit.edu	37	1	52863460	52863460	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52863460C>T	uc001ctt.2	-	4	518	c.299G>A	c.(298-300)CGG>CAG	p.R100Q	ORC1L_uc010oni.1_Missense_Mutation_p.R100Q|ORC1L_uc001ctu.2_Missense_Mutation_p.R100Q|ORC1L_uc009vzd.2_5'UTR	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	100	BAH.				cell cycle checkpoint|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52912011	52912011	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52912011A>G	uc001ctx.2	-	22	3851	c.3617T>C	c.(3616-3618)GTA>GCA	p.V1206A	ZCCHC11_uc001cty.2_Missense_Mutation_p.V1206A|ZCCHC11_uc001ctz.2_Missense_Mutation_p.V1206A|ZCCHC11_uc009vze.1_Missense_Mutation_p.V1206A|ZCCHC11_uc009vzf.1_Missense_Mutation_p.V927A|ZCCHC11_uc001cua.1_Missense_Mutation_p.V123A	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	1206	PAP-associated 2.				miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52991866	52991866	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52991866T>C	uc001ctx.2	-	2	321	c.87A>G	c.(85-87)ATA>ATG	p.I29M	ZCCHC11_uc001cty.2_Missense_Mutation_p.I29M|ZCCHC11_uc001ctz.2_Missense_Mutation_p.I29M|ZCCHC11_uc009vze.1_Missense_Mutation_p.I29M|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Missense_Mutation_p.I29M|ZCCHC11_uc001cuc.2_RNA|ZCCHC11_uc001cud.2_Missense_Mutation_p.I29M	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	29					miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
YIPF1	54432	broad.mit.edu	37	1	54325832	54325832	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54325832G>T	uc001cvu.2	-						YIPF1_uc001cvv.2_Intron|YIPF1_uc001cvw.2_Intron|YIPF1_uc001cvx.2_Intron|YIPF1_uc001cvy.2_Intron	NM_018982	NP_061855			Yip1 domain family, member 1							integral to membrane|transport vesicle				large_intestine(1)|ovary(1)	2																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57756683	57756683	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57756683A>C	uc001cys.1	-	4	694	c.20T>G	c.(19-21)CTT>CGT	p.L7R	DAB1_uc001cyt.1_Missense_Mutation_p.L7R|DAB1_uc001cyq.1_Missense_Mutation_p.L7R|DAB1_uc001cyr.1_Missense_Mutation_p.L7R|DAB1_uc009vzw.1_Missense_Mutation_p.L7R|DAB1_uc009vzx.1_Missense_Mutation_p.L7R	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	7					cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	63084513	63084513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63084513C>T	uc001daq.2	-	14	1580	c.1546G>A	c.(1546-1548)GCA>ACA	p.A516T	DOCK7_uc001dan.2_Missense_Mutation_p.A408T|DOCK7_uc001dao.2_Missense_Mutation_p.A408T|DOCK7_uc001dap.2_Missense_Mutation_p.A516T|DOCK7_uc009wah.1_Missense_Mutation_p.A516T	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	516					activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66723334	66723334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66723334G>A	uc001dcn.2	+	5	672	c.481G>A	c.(481-483)GGC>AGC	p.G161S	PDE4B_uc009war.2_Missense_Mutation_p.G69S|PDE4B_uc001dco.2_Missense_Mutation_p.G161S|PDE4B_uc001dcp.2_Missense_Mutation_p.G146S	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1	161					signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)													---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67147886	67147886	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67147886C>T	uc001dcr.2	+	15	1366	c.1149C>T	c.(1147-1149)GTC>GTT	p.V383V	SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Silent_p.V150V	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	383	Pro-rich.				positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
ANKRD13C	81573	broad.mit.edu	37	1	70742515	70742515	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70742515G>A	uc001dex.3	-	10	1554	c.1228C>T	c.(1228-1230)CAG>TAG	p.Q410*	ANKRD13C_uc009wbk.2_Nonsense_Mutation_p.Q375*	NM_030816	NP_110443	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	410					protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0																		---	---	---	---
ZRANB2	9406	broad.mit.edu	37	1	71532579	71532579	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71532579C>T	uc001dft.2	-	9	876	c.809G>A	c.(808-810)CGA>CAA	p.R270Q	uc001dfr.2_RNA|ZRANB2_uc001dfs.2_Missense_Mutation_p.R270Q	NM_203350	NP_976225	O95218	ZRAB2_HUMAN	zinc finger protein 265 isoform 1	270	Required for nuclear targeting.				mRNA processing|RNA splicing	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
GIPC2	54810	broad.mit.edu	37	1	78560730	78560730	+	Missense_Mutation	SNP	G	A	A	rs143579527		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78560730G>A	uc001dik.2	+	3	711	c.521G>A	c.(520-522)CGT>CAT	p.R174H		NM_017655	NP_060125	Q8TF65	GIPC2_HUMAN	PDZ domain protein GIPC2	174	PDZ.					cytoplasm				ovary(1)	1																		---	---	---	---
IFI44	10561	broad.mit.edu	37	1	79120849	79120849	+	Silent	SNP	G	A	A	rs114352124	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79120849G>A	uc001dip.3	+	4	769	c.645G>A	c.(643-645)ACG>ACA	p.T215T	IFI44_uc010orr.1_Silent_p.T215T|IFI44_uc010ors.1_5'UTR	NM_006417	NP_006408	Q8TCB0	IFI44_HUMAN	interferon-induced, hepatitis C-associated	215					response to virus	cytoplasm				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
BCL10	8915	broad.mit.edu	37	1	85733317	85733317	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85733317C>T	uc001dkz.2	-	4	1400	c.695G>A	c.(694-696)CGA>CAA	p.R232Q		NM_003921	NP_003912	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	232					apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway	CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding			lung(2)	2				all cancers(265;0.0114)|Epithelial(280;0.0311)				T	IGH@	MALT 								---	---	---	---
CLCA2	9635	broad.mit.edu	37	1	86904636	86904636	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86904636C>T	uc001dlr.3	+	7	1212	c.1050C>T	c.(1048-1050)GGC>GGT	p.G350G		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	350	VWFA.|Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)														---	---	---	---
CLCA2	9635	broad.mit.edu	37	1	86909662	86909662	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86909662A>G	uc001dlr.3	+	10	1843	c.1681A>G	c.(1681-1683)ACA>GCA	p.T561A		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	561	Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)														---	---	---	---
CLCA4	22802	broad.mit.edu	37	1	87029448	87029448	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87029448A>G	uc009wcs.2	+	4	597	c.553A>G	c.(553-555)ACA>GCA	p.T185A	CLCA4_uc009wct.2_Intron|CLCA4_uc009wcu.2_Intron	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	185						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)														---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89273443	89273443	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89273443G>T	uc001dmn.2	+	15	2429	c.2087G>T	c.(2086-2088)CGA>CTA	p.R696L	PKN2_uc010osp.1_Missense_Mutation_p.R680L|PKN2_uc010osq.1_Missense_Mutation_p.R539L|PKN2_uc009wcv.2_Missense_Mutation_p.R648L|PKN2_uc010osr.1_Missense_Mutation_p.R361L	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2	696	Protein kinase.				signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)														---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91406878	91406878	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91406878A>G	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron|ZNF644_uc001dny.1_Intron	NM_201269	NP_958357			zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
STXBP3	6814	broad.mit.edu	37	1	109302599	109302599	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109302599C>T	uc001dvy.2	+						STXBP3_uc001dvz.2_Intron	NM_007269	NP_009200			syntaxin binding protein 3						negative regulation of calcium ion-dependent exocytosis|neutrophil degranulation|platelet aggregation|protein transport|vesicle docking involved in exocytosis	cytosol|nucleus|platelet alpha granule|specific granule|tertiary granule	syntaxin-2 binding			ovary(3)|central_nervous_system(1)	4		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)														---	---	---	---
SARS	6301	broad.mit.edu	37	1	109779902	109779902	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109779902G>A	uc001dwu.1	+	10	1369	c.1294G>A	c.(1294-1296)GCC>ACC	p.A432T	SARS_uc001dwv.1_Missense_Mutation_p.A457T|SARS_uc001dww.1_Missense_Mutation_p.A365T|SARS_uc001dwx.1_Missense_Mutation_p.A384T|SARS_uc009wfa.1_Intron|SARS_uc001dwy.1_Missense_Mutation_p.A257T|SARS_uc001dwz.1_Missense_Mutation_p.A257T	NM_006513	NP_006504	P49591	SYSC_HUMAN	seryl-tRNA synthetase	432					seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)													---	---	---	---
AMIGO1	57463	broad.mit.edu	37	1	110050530	110050530	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110050530G>A	uc001dxx.3	-	2	1387	c.1005C>T	c.(1003-1005)GAC>GAT	p.D335D		NM_020703	NP_065754	Q86WK6	AMGO1_HUMAN	AMIGO protein precursor	335	Ig-like C2-type.|Extracellular (Potential).				axonal fasciculation|heterophilic cell-cell adhesion|homophilic cell adhesion|myelination|positive regulation of axonogenesis	axon|integral to membrane				ovary(1)|breast(1)	2		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0182)|Epithelial(280;0.046)|all cancers(265;0.0492)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)														---	---	---	---
EPS8L3	79574	broad.mit.edu	37	1	110295773	110295773	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110295773G>A	uc001dyr.1	-	13	1311	c.1166C>T	c.(1165-1167)TCA>TTA	p.S389L	EPS8L3_uc001dys.1_Missense_Mutation_p.S389L|EPS8L3_uc001dyq.1_Missense_Mutation_p.S390L|EPS8L3_uc009wfm.1_Missense_Mutation_p.S356L|EPS8L3_uc009wfn.1_Missense_Mutation_p.S364L|EPS8L3_uc009wfo.1_Missense_Mutation_p.S336L	NM_133181	NP_573444	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway	389						cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
SLC6A17	388662	broad.mit.edu	37	1	110716613	110716613	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110716613C>A	uc009wfq.2	+	4	924	c.463C>A	c.(463-465)CTG>ATG	p.L155M		NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN	solute carrier family 6, member 17	155	Helical; Name=3; (Potential).				alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)														---	---	---	---
SLC16A4	9122	broad.mit.edu	37	1	110921785	110921785	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110921785A>G	uc001dzo.1	-	6	902	c.720T>C	c.(718-720)AGT>AGC	p.S240S	SLC16A4_uc009wfs.1_Silent_p.S192S|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Silent_p.S178S|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Silent_p.S130S	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4	240	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)													---	---	---	---
WNT2B	7482	broad.mit.edu	37	1	113059734	113059734	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113059734C>A	uc001ecb.2	+						WNT2B_uc001eca.2_Intron|WNT2B_uc009wgg.2_Intron	NM_024494	NP_078613			wingless-type MMTV integration site family,						chondrocyte differentiation|cornea development in camera-type eye|dorsal/ventral axis specification|forebrain regionalization|hemopoietic stem cell proliferation|iris morphogenesis|lens development in camera-type eye|lung induction|male gonad development|neuron differentiation|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding|signal transducer activity			ovary(2)|breast(2)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
HIPK1	204851	broad.mit.edu	37	1	114506081	114506081	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114506081C>T	uc001eem.2	+	10	2337	c.2176C>T	c.(2176-2178)CCC>TCC	p.P726S	HIPK1_uc001eel.2_Missense_Mutation_p.P726S|HIPK1_uc001een.2_Missense_Mutation_p.P726S|HIPK1_uc001eeo.2_Missense_Mutation_p.P352S|HIPK1_uc001eep.2_Missense_Mutation_p.P332S|HIPK1_uc001eeq.2_Missense_Mutation_p.P19S	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	726					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
DENND2C	163259	broad.mit.edu	37	1	115168553	115168553	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115168553C>T	uc001efd.1	-	4	755	c.53G>A	c.(52-54)TGC>TAC	p.C18Y	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Missense_Mutation_p.C18Y	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	18										skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
VANGL1	81839	broad.mit.edu	37	1	116202294	116202294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116202294G>A	uc001efv.1	+	3	375	c.104G>A	c.(103-105)CGG>CAG	p.R35Q	VANGL1_uc009wgy.1_Missense_Mutation_p.R35Q|VANGL1_uc001efw.1_Missense_Mutation_p.R35Q	NM_138959	NP_620409	Q8TAA9	VANG1_HUMAN	vang-like 1	35	Cytoplasmic (Potential).				multicellular organismal development	integral to membrane	protein binding			central_nervous_system(1)	1	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
C1orf161	126868	broad.mit.edu	37	1	116675980	116675980	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116675980G>A	uc001egc.1	+	7	1348	c.1083G>A	c.(1081-1083)CCG>CCA	p.P361P		NM_152367	NP_689580	Q8N8X9	MB213_HUMAN	hypothetical protein LOC126868	361											0	Lung SC(450;0.184)	all_cancers(81;0.00142)|all_lung(203;0.000139)|all_epithelial(167;0.000401)|Lung NSC(69;0.000705)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
CD101	9398	broad.mit.edu	37	1	117552625	117552625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117552625C>T	uc010oxb.1	+	2	255	c.197C>T	c.(196-198)CCG>CTG	p.P66L	CD101_uc009whd.2_Missense_Mutation_p.P66L|CD101_uc010oxc.1_Missense_Mutation_p.P66L|CD101_uc010oxd.1_Missense_Mutation_p.P66L	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	66	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
WDR3	10885	broad.mit.edu	37	1	118482161	118482161	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118482161A>G	uc010oxe.1	+	6	707	c.641A>G	c.(640-642)GAA>GGA	p.E214G	WDR3_uc001ehi.2_Intron|WDR3_uc001ehh.2_Missense_Mutation_p.E43G	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	214	WD 5.					nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)														---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118642336	118642336	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118642336C>T	uc001ehk.2	-	6	790	c.722G>A	c.(721-723)GGC>GAC	p.G241D		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	241						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)														---	---	---	---
NBPF7	343505	broad.mit.edu	37	1	120378827	120378827	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120378827G>T	uc010oxk.1	-	7	1540	c.919C>A	c.(919-921)CTG>ATG	p.L307M		NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505	307	NBPF 2.					cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)														---	---	---	---
GJA8	2703	broad.mit.edu	37	1	147380436	147380436	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147380436G>A	uc001epu.1	+	2	417	c.354G>A	c.(352-354)GCG>GCA	p.A118A		NM_005267	NP_005258	P48165	CXA8_HUMAN	connexin 50	118	Cytoplasmic (Potential).				cell communication|visual perception	connexon complex|integral to plasma membrane	channel activity			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.0276)																	---	---	---	---
OTUD7B	56957	broad.mit.edu	37	1	149916399	149916399	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149916399C>T	uc001etn.2	-	12	2245	c.1889G>A	c.(1888-1890)CGC>CAC	p.R630H		NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne	630					negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150933052	150933052	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150933052A>G	uc001evu.2	+	16	2704	c.2514A>G	c.(2512-2514)ACA>ACG	p.T838T	SETDB1_uc001evv.2_Silent_p.T838T|SETDB1_uc009wmg.1_Silent_p.T838T	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	838	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
VPS72	6944	broad.mit.edu	37	1	151149217	151149217	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151149217G>A	uc001exe.1	-	6	1041	c.998C>T	c.(997-999)CCG>CTG	p.P333L	TMOD4_uc001exd.2_5'Flank|TMOD4_uc001exc.3_5'Flank|TMOD4_uc010pct.1_5'Flank	NM_005997	NP_005988	Q15906	VPS72_HUMAN	transcription factor-like 1	333	Pro-rich.				chromatin modification|negative regulation of transcription from RNA polymerase II promoter	nucleus|protein complex	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|pancreas(1)	2	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PI4KB	5298	broad.mit.edu	37	1	151276075	151276075	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151276075C>T	uc001ext.2	-	6	1877	c.1462G>A	c.(1462-1464)GAC>AAC	p.D488N	PI4KB_uc001exr.2_Missense_Mutation_p.D500N|PI4KB_uc001exs.2_Missense_Mutation_p.D473N|PI4KB_uc001exu.2_Missense_Mutation_p.D473N|PI4KB_uc010pcw.1_Missense_Mutation_p.D156N	NM_002651	NP_002642	Q9UBF8	PI4KB_HUMAN	catalytic phosphatidylinositol 4-kinase beta	488					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis	endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			ovary(2)|skin(2)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151384177	151384177	+	Missense_Mutation	SNP	C	T	T	rs72996036	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151384177C>T	uc001eyd.1	-	12	2156	c.1850G>A	c.(1849-1851)CGG>CAG	p.R617Q	POGZ_uc001eye.1_Missense_Mutation_p.R564Q|POGZ_uc010pdb.1_Missense_Mutation_p.R608Q|POGZ_uc001eyf.1_Missense_Mutation_p.R573Q|POGZ_uc010pdc.1_Missense_Mutation_p.R555Q|POGZ_uc009wmv.1_Missense_Mutation_p.R522Q|POGZ_uc010pdd.1_Missense_Mutation_p.R108Q	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	617					cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TUFT1	7286	broad.mit.edu	37	1	151553437	151553437	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151553437G>A	uc001eyl.2	+	12	1090	c.1028G>A	c.(1027-1029)CGG>CAG	p.R343Q	TUFT1_uc001eym.2_Missense_Mutation_p.R318Q|TUFT1_uc010pdf.1_Missense_Mutation_p.R362Q|TUFT1_uc010pdg.1_Missense_Mutation_p.R291Q	NM_020127	NP_064512	Q9NNX1	TUFT1_HUMAN	tuftelin 1 isoform 1	343	Potential.				bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TCHHL1	126637	broad.mit.edu	37	1	152058263	152058263	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152058263T>C	uc001ezo.1	-	3	1960	c.1895A>G	c.(1894-1896)GAA>GGA	p.E632G		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	632							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)															---	---	---	---
LCE1D	353134	broad.mit.edu	37	1	152770474	152770474	+	Silent	SNP	T	A	A	rs145076405		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152770474T>A	uc009wnp.2	+	2	247	c.204T>A	c.(202-204)GGT>GGA	p.G68G		NM_178352	NP_848129	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	68	Cys-rich.				cellular response to calcium ion|keratinization	cornified envelope|perinuclear region of cytoplasm					0	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
LCE1A	353131	broad.mit.edu	37	1	152800070	152800070	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152800070C>A	uc010pdw.1	+	1	122	c.122C>A	c.(121-123)TCT>TAT	p.S41Y		NM_178348	NP_848125	Q5T7P2	LCE1A_HUMAN	late cornified envelope 1A	41	Cys-rich.				keratinization					ovary(1)|skin(1)	2	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153782652	153782652	+	3'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153782652G>A	uc001fdb.3	-	11						NM_020699	NP_065750			GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
CRTC2	200186	broad.mit.edu	37	1	153924526	153924526	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153924526C>T	uc010ped.1	-	10	1035	c.965G>A	c.(964-966)GGC>GAC	p.G322D	CRTC2_uc001fde.3_RNA|CRTC2_uc001fdf.3_5'UTR	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	322					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
DCST1	149095	broad.mit.edu	37	1	155006942	155006942	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155006942A>G	uc001fgn.1	+	3	189	c.93A>G	c.(91-93)CCA>CCG	p.P31P	DCST2_uc001fgm.2_5'Flank|DCST2_uc009wpb.2_5'Flank|DCST1_uc010per.1_Silent_p.P56P|DCST1_uc010pes.1_Silent_p.P31P	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1	31	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)|skin(1)	2	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)															---	---	---	---
HCN3	57657	broad.mit.edu	37	1	155257083	155257083	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155257083C>T	uc001fjz.1	+	7	1605	c.1597C>T	c.(1597-1599)CGC>TGC	p.R533C	RAG1AP1_uc010pey.1_Intron|HCN3_uc010pfz.1_Missense_Mutation_p.R228C	NM_020897	NP_065948	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic	533	Cytoplasmic (Potential).|cAMP.					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)|breast(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
SYT11	23208	broad.mit.edu	37	1	155851289	155851289	+	Missense_Mutation	SNP	G	A	A	rs141914865		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155851289G>A	uc001fmg.2	+	4	1549	c.1286G>A	c.(1285-1287)AGC>AAC	p.S429N	SYT11_uc010pgq.1_Missense_Mutation_p.S122N	NM_152280	NP_689493	Q9BT88	SYT11_HUMAN	synaptotagmin XI	429	Cytoplasmic (Potential).					cell junction|synaptic vesicle membrane	protein binding|transporter activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)															---	---	---	---
ARHGEF2	9181	broad.mit.edu	37	1	155936216	155936216	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155936216G>A	uc001fmt.2	-	4	449	c.331C>T	c.(331-333)CGA>TGA	p.R111*	ARHGEF2_uc001fmr.2_Nonsense_Mutation_p.R84*|ARHGEF2_uc001fms.2_Nonsense_Mutation_p.R111*|ARHGEF2_uc001fmu.2_Nonsense_Mutation_p.R156*|ARHGEF2_uc010pgt.1_Nonsense_Mutation_p.R84*|ARHGEF2_uc010pgu.1_Nonsense_Mutation_p.R156*	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2	111					actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
MEF2D	4209	broad.mit.edu	37	1	156437847	156437847	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156437847G>A	uc001fpc.2	-	11	1882	c.1492C>T	c.(1492-1494)CGC>TGC	p.R498C	MEF2D_uc001fpb.2_Missense_Mutation_p.R491C|MEF2D_uc001fpd.2_Missense_Mutation_p.R491C|MEF2D_uc001fpe.1_Missense_Mutation_p.R498C|MEF2D_uc009wsa.2_RNA	NM_005920	NP_005911	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	498					apoptosis|muscle organ development|nervous system development|positive regulation of transcription from RNA polymerase II promoter	nucleus	activating transcription factor binding|histone deacetylase binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158064116	158064116	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158064116A>G	uc001frn.3	+	14	2137	c.1733A>G	c.(1732-1734)GAT>GGT	p.D578G	KIRREL_uc010pib.1_Missense_Mutation_p.D478G|KIRREL_uc009wsq.2_Missense_Mutation_p.D414G|KIRREL_uc001fro.3_Missense_Mutation_p.D392G|uc001frp.2_5'Flank	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	578	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158064758	158064758	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158064758T>C	uc001frn.3	+	15	2526	c.2122T>C	c.(2122-2124)TAC>CAC	p.Y708H	KIRREL_uc010pib.1_Missense_Mutation_p.Y608H|KIRREL_uc009wsq.2_Missense_Mutation_p.Y544H|KIRREL_uc001fro.3_Missense_Mutation_p.Y522H|uc001frp.2_5'Flank	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	708	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
B4GALT3	8703	broad.mit.edu	37	1	161145641	161145641	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161145641A>G	uc001fyq.1	-	3	472	c.210T>C	c.(208-210)GCT>GCC	p.A70A	PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron|B4GALT3_uc001fyo.1_5'Flank|B4GALT3_uc001fyp.1_5'Flank|B4GALT3_uc001fyr.1_Silent_p.A70A|B4GALT3_uc001fys.1_Silent_p.A70A|B4GALT3_uc009wud.1_Silent_p.A70A	NM_003779	NP_003770	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	70	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|metal ion binding|N-acetyllactosamine synthase activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
TOMM40L	84134	broad.mit.edu	37	1	161197675	161197675	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161197675C>T	uc001fzd.2	+	6	609	c.380C>T	c.(379-381)ACG>ATG	p.T127M	TOMM40L_uc010pkk.1_RNA|TOMM40L_uc010pkl.1_Missense_Mutation_p.T93M|TOMM40L_uc009wue.2_Missense_Mutation_p.T9M|TOMM40L_uc009wuf.1_RNA|TOMM40L_uc001fze.2_Missense_Mutation_p.T127M	NM_032174	NP_115550	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40	127					protein transport	mitochondrial outer membrane|pore complex	porin activity|voltage-gated anion channel activity			large_intestine(1)	1	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)													OREG0013943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GPR161	23432	broad.mit.edu	37	1	168065774	168065774	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168065774C>T	uc001gfc.2	-	5	1385	c.1071G>A	c.(1069-1071)AGG>AGA	p.R357R	GPR161_uc001gfb.2_Silent_p.R225R|GPR161_uc010pll.1_Silent_p.R267R|GPR161_uc010plm.1_Silent_p.R243R|GPR161_uc009wvo.2_Silent_p.R374R|GPR161_uc001gfd.2_Silent_p.R357R|GPR161_uc010pln.1_Silent_p.R377R|GPR161_uc001gfe.1_Silent_p.R357R	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2	357	Cytoplasmic (Potential).				multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)																	---	---	---	---
PRRX1	5396	broad.mit.edu	37	1	170705330	170705330	+	3'UTR	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170705330A>G	uc001ghf.2	+	4					PRRX1_uc001ghe.2_3'UTR	NM_022716	NP_073207			paired mesoderm homeobox 1 isoform pmx-1b							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
MYOC	4653	broad.mit.edu	37	1	171605492	171605492	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171605492G>T	uc001ghu.2	-	3	1110	c.1088C>A	c.(1087-1089)GCT>GAT	p.A363D	MYOC_uc010pmk.1_Missense_Mutation_p.A305D	NM_000261	NP_000252	Q99972	MYOC_HUMAN	myocilin precursor	363	Olfactomedin-like.		A -> T (in GLC1A).		anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
C1orf220	400798	broad.mit.edu	37	1	178514795	178514795	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178514795C>T	uc001glx.1	+	2	538	c.181C>T	c.(181-183)CGA>TGA	p.R61*	C1orf49_uc001glv.1_Intron	NM_207467	NP_997350			hypothetical protein LOC400798												0																		---	---	---	---
DHX9	1660	broad.mit.edu	37	1	182812424	182812424	+	Intron	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182812424T>A	uc001gpr.2	+						DHX9_uc001gps.2_Intron	NM_001357	NP_001348			DEAH (Asp-Glu-Ala-His) box polypeptide 9						CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2																		---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183192390	183192390	+	Missense_Mutation	SNP	G	A	A	rs141901570	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183192390G>A	uc001gqa.2	+	7	1198	c.884G>A	c.(883-885)CGG>CAG	p.R295Q	LAMC2_uc001gpz.3_Missense_Mutation_p.R295Q|LAMC2_uc010poa.1_5'UTR	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	295	Laminin IV type A.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185970760	185970760	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185970760A>G	uc001grq.1	+	28	4464	c.4235A>G	c.(4234-4236)AAT>AGT	p.N1412S		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1412	Ig-like C2-type 11.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186010138	186010138	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186010138T>C	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186056372	186056372	+	Missense_Mutation	SNP	C	T	T	rs138982761		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186056372C>T	uc001grq.1	+	59	9299	c.9070C>T	c.(9070-9072)CGG>TGG	p.R3024W		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	3024	Ig-like C2-type 28.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186060044	186060044	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186060044A>G	uc001grq.1	+	64	10111	c.9882A>G	c.(9880-9882)AGA>AGG	p.R3294R		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	3294	Ig-like C2-type 31.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197160961	197160961	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197160961G>A	uc001gtx.1	-	2	1258	c.1189C>T	c.(1189-1191)CGC>TGC	p.R397C	ZBTB41_uc009wyz.1_RNA	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	397	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197298006	197298006	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197298006C>A	uc001gtz.2	+	2	660	c.525C>A	c.(523-525)GTC>GTA	p.V175V	CRB1_uc010poz.1_Silent_p.V106V|CRB1_uc001gty.1_Silent_p.V175V|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Silent_p.V175V|CRB1_uc010ppb.1_Silent_p.V175V	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	175	Extracellular (Potential).|EGF-like 4; calcium-binding (Potential).				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198608457	198608457	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198608457A>T	uc001gur.1	+	2	233	c.53A>T	c.(52-54)GAA>GTA	p.E18V	PTPRC_uc001gus.1_Missense_Mutation_p.E18V|PTPRC_uc001gut.1_Missense_Mutation_p.E18V|PTPRC_uc001guq.2_Missense_Mutation_p.E18V|PTPRC_uc009wze.1_Missense_Mutation_p.E20V|PTPRC_uc009wzf.1_Missense_Mutation_p.E20V|PTPRC_uc010ppg.1_Missense_Mutation_p.E20V|PTPRC_uc001guu.1_Missense_Mutation_p.E20V|PTPRC_uc001guv.1_RNA|PTPRC_uc001guw.1_RNA	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	18					axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12																		---	---	---	---
ZNF281	23528	broad.mit.edu	37	1	200377574	200377574	+	Silent	SNP	G	A	A	rs149361792		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200377574G>A	uc001gve.2	-	2	1367	c.1260C>T	c.(1258-1260)ACC>ACT	p.T420T	ZNF281_uc001gvf.1_Silent_p.T420T|ZNF281_uc001gvg.1_Silent_p.T384T	NM_012482	NP_036614	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	420					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201755629	201755629	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201755629C>T	uc001gwu.2	+	9	3266	c.2919C>T	c.(2917-2919)TCC>TCT	p.S973S	NAV1_uc001gwv.1_Silent_p.S481S|NAV1_uc001gww.1_Silent_p.S582S|NAV1_uc001gwx.2_Silent_p.S582S|NAV1_uc001gwy.1_Silent_p.S354S	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	973					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201824979	201824979	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201824979A>G	uc001gwz.2	+	10	1089	c.1039A>G	c.(1039-1041)AGC>GGC	p.S347G		NM_018085	NP_060555	Q96P70	IPO9_HUMAN	importin 9	347					protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
KDM5B	10765	broad.mit.edu	37	1	202699134	202699134	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202699134G>A	uc001gyf.2	-	26	4314	c.4198C>T	c.(4198-4200)CGA>TGA	p.R1400*	KDM5B_uc009xag.2_Nonsense_Mutation_p.R1436*|KDM5B_uc001gyg.1_Nonsense_Mutation_p.R1242*	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	1400					negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5																		---	---	---	---
KDM5B	10765	broad.mit.edu	37	1	202727521	202727521	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202727521G>T	uc001gyf.2	-	9	1311	c.1195C>A	c.(1195-1197)CAT>AAT	p.H399N	KDM5B_uc009xag.2_Missense_Mutation_p.H435N|KDM5B_uc001gyg.1_Missense_Mutation_p.H241N	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	399					negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5																		---	---	---	---
TMEM183A	92703	broad.mit.edu	37	1	202992009	202992009	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202992009G>A	uc001gyu.1	+	8	1030	c.972G>A	c.(970-972)ATG>ATA	p.M324I	TMEM183A_uc001gyv.1_RNA|TMEM183A_uc001gyw.1_Missense_Mutation_p.M323I|TMEM183A_uc001gyx.1_Missense_Mutation_p.A321T|TMEM183A_uc001gyy.2_5'Flank	NM_001079809	NP_001073277	Q8IXX5	T183A_HUMAN	transmembrane protein 183B	324						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)															---	---	---	---
PLEKHA6	22874	broad.mit.edu	37	1	204234123	204234123	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204234123G>A	uc001hau.2	-	6	645	c.328C>T	c.(328-330)CGG>TGG	p.R110W		NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3	110	PH.									ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204394731	204394731	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204394731C>T	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron	NM_002646	NP_002637			phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
CTSE	1510	broad.mit.edu	37	1	206331156	206331156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206331156C>T	uc001hdu.2	+	9	1280	c.1162C>T	c.(1162-1164)CGT>TGT	p.R388C	CTSE_uc001hdv.2_Silent_p.T340T|CTSE_uc010prs.1_Silent_p.T265T	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein	393					antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
FCAMR	83953	broad.mit.edu	37	1	207140453	207140453	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207140453G>A	uc001hfa.3	-	3	613	c.113C>T	c.(112-114)ACC>ATC	p.T38I	FCAMR_uc001hfb.2_Missense_Mutation_p.T38I|FCAMR_uc009xca.1_Missense_Mutation_p.T38I|FCAMR_uc001hfc.2_Intron	NM_001122980	NP_001116452	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity isoform 2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane|plasma membrane	receptor activity			ovary(1)	1																		---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208390081	208390081	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208390081G>A	uc001hgz.2	-	2	1945	c.1187C>T	c.(1186-1188)GCG>GTG	p.A396V	PLXNA2_uc001hha.3_Missense_Mutation_p.A450V	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	396	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210977463	210977463	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210977463T>C	uc001hib.2	-	8	1678	c.1508A>G	c.(1507-1509)CAA>CGA	p.Q503R	KCNH1_uc001hic.2_Missense_Mutation_p.Q476R	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	503	Cytoplasmic (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
KCNK2	3776	broad.mit.edu	37	1	215259715	215259715	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215259715G>A	uc001hkq.2	+	2	220	c.51G>A	c.(49-51)GCG>GCA	p.A17A	KCNK2_uc001hko.2_Silent_p.A13A|KCNK2_uc009xdm.2_RNA|KCNK2_uc001hkp.2_RNA|KCNK2_uc010pua.1_RNA|KCNK2_uc001hkr.3_Silent_p.A2A	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform	17	Cytoplasmic (Potential).						outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)													---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215848155	215848155	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215848155G>A	uc001hku.1	-	63	13485	c.13098C>T	c.(13096-13098)GCC>GCT	p.A4366A		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4366	Extracellular (Potential).|Fibronectin type-III 29.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215848894	215848894	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215848894C>T	uc001hku.1	-	63	12746	c.12359G>A	c.(12358-12360)CGC>CAC	p.R4120H		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4120	Fibronectin type-III 26.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216243491	216243491	+	Missense_Mutation	SNP	G	T	T	rs141539554	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216243491G>T	uc001hku.1	-	30	6388	c.6001C>A	c.(6001-6003)CGC>AGC	p.R2001S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2001	Extracellular (Potential).|Fibronectin type-III 6.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216251421	216251421	+	Intron	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216251421T>G	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
IARS2	55699	broad.mit.edu	37	1	220269438	220269438	+	Intron	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220269438T>A	uc001hmc.2	+							NM_018060	NP_060530			mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)													---	---	---	---
IARS2	55699	broad.mit.edu	37	1	220279375	220279375	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220279375T>C	uc001hmc.2	+	9	1313	c.1209T>C	c.(1207-1209)GGT>GGC	p.G403G		NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase	403					isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)													---	---	---	---
DISP1	84976	broad.mit.edu	37	1	223116220	223116220	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223116220G>A	uc001hnu.1	+	2	202	c.55G>A	c.(55-57)GCA>ACA	p.A19T		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	19					diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)														---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223947087	223947087	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223947087C>T	uc001hob.3	+	12	1657	c.1433C>T	c.(1432-1434)CCG>CTG	p.P478L	CAPN2_uc010puy.1_Missense_Mutation_p.P400L|CAPN2_uc001hoc.2_Missense_Mutation_p.P59L	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1	478	Domain III.				proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)														---	---	---	---
EPHX1	2052	broad.mit.edu	37	1	226016565	226016565	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226016565C>T	uc001hpk.2	+	2	215	c.135C>T	c.(133-135)GAC>GAT	p.D45D	EPHX1_uc001hpl.2_Silent_p.D45D	NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1	45					aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)																	---	---	---	---
CABC1	56997	broad.mit.edu	37	1	227174293	227174293	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227174293T>A	uc001hqm.1	+	20	5218	c.1799T>A	c.(1798-1800)GTC>GAC	p.V600D	CABC1_uc001hqn.1_Missense_Mutation_p.V600D|CABC1_uc009xeq.1_Missense_Mutation_p.V548D|CABC1_uc010pvq.1_Missense_Mutation_p.V321D|CABC1_uc010pvr.1_Missense_Mutation_p.V274D|CABC1_uc001hqo.1_Missense_Mutation_p.V321D|CABC1_uc009xer.1_Missense_Mutation_p.V116D	NM_020247	NP_064632	Q8NI60	ADCK3_HUMAN	chaperone, ABC1 activity of bc1 complex like	600					cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)																---	---	---	---
WNT9A	7483	broad.mit.edu	37	1	228112035	228112035	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228112035G>A	uc001hri.2	-	3	507	c.419C>T	c.(418-420)GCG>GTG	p.A140V		NM_003395	NP_003386	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family,	140					anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|cornea development in camera-type eye|embryonic arm morphogenesis|embryonic skeletal joint morphogenesis|endoderm development|iris morphogenesis|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|neuron differentiation|positive regulation of smoothened signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding|signal transducer activity			central_nervous_system(1)|pancreas(1)	2		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228459636	228459636	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228459636G>A	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
RAB4A	5867	broad.mit.edu	37	1	229438649	229438649	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229438649C>T	uc001hth.2	+	7	790	c.582C>T	c.(580-582)TAC>TAT	p.Y194Y	RAB4A_uc001hti.2_RNA|RAB4A_uc001htj.2_RNA|SPHAR_uc001htk.3_5'Flank	NM_004578	NP_004569	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	189							GDP binding|GTP binding|GTPase activity			ovary(1)	1	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)																---	---	---	---
URB2	9816	broad.mit.edu	37	1	229781684	229781684	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229781684C>T	uc001hts.1	+	6	4010	c.3874C>T	c.(3874-3876)CGT>TGT	p.R1292C	URB2_uc009xfd.1_Missense_Mutation_p.R1292C	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	1292						nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
AGT	183	broad.mit.edu	37	1	230846391	230846391	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230846391G>T	uc001hty.3	-	2	714	c.206C>A	c.(205-207)CCT>CAT	p.P69H	AGT_uc009xfe.2_Missense_Mutation_p.P69H|AGT_uc009xff.2_Intron	NM_000029	NP_000020	P01019	ANGT_HUMAN	angiotensinogen preproprotein	69					activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|blood vessel remodeling|cell-cell signaling|cellular lipid metabolic process|G-protein signaling, coupled to cGMP nucleotide second messenger|kidney development|low-density lipoprotein particle remodeling|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of activation of JAK2 kinase activity|positive regulation of apoptosis|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of cardiac muscle hypertrophy|positive regulation of cholesterol esterification|positive regulation of cytokine production|positive regulation of endothelial cell migration|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of NAD(P)H oxidase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein tyrosine kinase activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription, DNA-dependent|regulation of proteolysis|regulation of renal output by angiotensin|regulation of renal sodium excretion|regulation of vasoconstriction|renin-angiotensin regulation of aldosterone production|response to muscle activity involved in regulation of muscle adaptation	extracellular space|soluble fraction	acetyltransferase activator activity|growth factor activity|hormone activity|serine-type endopeptidase inhibitor activity|type 1 angiotensin receptor binding|type 2 angiotensin receptor binding				0	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	Aliskiren(DB01258)|Atorvastatin(DB01076)|Cilazapril(DB01340)|Irbesartan(DB01029)|Lisinopril(DB00722)|Ouabain(DB01092)|Simvastatin(DB00641)													---	---	---	---
SIPA1L2	57568	broad.mit.edu	37	1	232579385	232579385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232579385C>T	uc001hvg.2	-	10	3558	c.3400G>A	c.(3400-3402)GGG>AGG	p.G1134R	SIPA1L2_uc001hvf.2_Missense_Mutation_p.G208R	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1134					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)																---	---	---	---
KIAA1383	54627	broad.mit.edu	37	1	232941911	232941911	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232941911T>A	uc001hvh.2	+	1	1274	c.1142T>A	c.(1141-1143)ATC>AAC	p.I381N		NM_019090	NP_061963	Q9P2G4	K1383_HUMAN	hypothetical protein LOC54627	239										ovary(1)	1		all_cancers(173;0.00528)|Prostate(94;0.122)|all_epithelial(177;0.169)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233136181	233136181	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233136181G>A	uc001hvl.2	-	30	5433	c.5198C>T	c.(5197-5199)CCG>CTG	p.P1733L	PCNXL2_uc001hvk.1_Missense_Mutation_p.P385L|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1733						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234367435	234367435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234367435G>A	uc001hwa.1	+	2	577	c.349G>A	c.(349-351)GTG>ATG	p.V117M	SLC35F3_uc001hvy.1_Missense_Mutation_p.V186M	NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	117	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236925902	236925902	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236925902G>T	uc001hyf.2	+	21	2872	c.2668G>T	c.(2668-2670)GGG>TGG	p.G890W	ACTN2_uc001hyg.2_Missense_Mutation_p.G682W|ACTN2_uc009xgi.1_Missense_Mutation_p.G890W|ACTN2_uc010pxu.1_Missense_Mutation_p.G579W|ACTN2_uc001hyh.2_Missense_Mutation_p.G578W	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	890					focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237675042	237675042	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237675042C>T	uc001hyl.1	+	24	2893	c.2773C>T	c.(2773-2775)CCT>TCT	p.P925S		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	925	Cytoplasmic (By similarity).|1.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237729897	237729897	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237729897G>A	uc001hyl.1	+	28	3365	c.3245G>A	c.(3244-3246)GGG>GAG	p.G1082E		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1082	Cytoplasmic (By similarity).|4 X approximate repeats.|B30.2/SPRY 2.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
HNRNPU	3192	broad.mit.edu	37	1	245027233	245027233	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245027233G>T	uc001iaz.1	-	1	595	c.377C>A	c.(376-378)GCC>GAC	p.A126D	HNRNPU_uc001iay.1_5'Flank|HNRNPU_uc001iba.1_Missense_Mutation_p.A126D|HNRNPU_uc001ibb.1_Intron	NM_031844	NP_114032	Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U	126	Asp/Glu-rich (acidic).				CRD-mediated mRNA stabilization	catalytic step 2 spliceosome|cell surface|CRD-mediated mRNA stability complex|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	ATP binding|DNA binding|protein binding|RNA binding				0	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)															---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246091299	246091299	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246091299A>G	uc001ibl.2	-	7	731	c.636T>C	c.(634-636)TGT>TGC	p.C212C	SMYD3_uc001ibk.2_Silent_p.C153C|SMYD3_uc001ibi.2_Silent_p.C23C|SMYD3_uc001ibj.2_Silent_p.C23C	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	212	SET.					cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
NLRP3	114548	broad.mit.edu	37	1	247587999	247587999	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247587999G>A	uc001icr.2	+	5	1392	c.1254G>A	c.(1252-1254)GTG>GTA	p.V418V	NLRP3_uc001ics.2_Silent_p.V418V|NLRP3_uc001icu.2_Silent_p.V418V|NLRP3_uc001icw.2_Silent_p.V418V|NLRP3_uc001icv.2_Silent_p.V418V|NLRP3_uc010pyw.1_Silent_p.V416V|NLRP3_uc001ict.1_Silent_p.V416V	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	418	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)															---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1667419	1667419	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1667419C>T	uc002qxa.2	-	12	1589	c.1525G>A	c.(1525-1527)GGC>AGC	p.G509S	PXDN_uc002qxb.1_Missense_Mutation_p.G509S	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	509	Ig-like C2-type 3.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1795783	1795783	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1795783C>T	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewk.2_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10729287	10729287	+	Missense_Mutation	SNP	G	A	A	rs149749353	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10729287G>A	uc002raq.2	-	19	1851	c.1726C>T	c.(1726-1728)CGG>TGG	p.R576W	NOL10_uc010yje.1_Missense_Mutation_p.R550W|NOL10_uc010yjf.1_Missense_Mutation_p.R526W|NOL10_uc002rap.2_Missense_Mutation_p.R526W	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	576	Potential.					nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17897525	17897525	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17897525T>C	uc002rco.2	-	15	1649	c.1353A>G	c.(1351-1353)GAA>GAG	p.E451E	SMC6_uc010exo.2_Silent_p.E451E|SMC6_uc002rcn.2_Silent_p.E451E|SMC6_uc002rcp.1_Silent_p.E477E|SMC6_uc002rcq.2_Silent_p.E477E	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	451	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SF3B14	51639	broad.mit.edu	37	2	24291311	24291311	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24291311A>G	uc002rev.2	-	3	383	c.168T>C	c.(166-168)ACT>ACC	p.T56T	SF3B14_uc010eyb.2_RNA	NM_016047	NP_057131	Q9Y3B4	PM14_HUMAN	splicing factor 3B, 14 kDa subunit	56	RRM.				nuclear mRNA splicing, via spliceosome	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf79	391356	broad.mit.edu	37	2	25016209	25016209	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25016209C>A	uc002rfm.2	-	1	43	c.38G>T	c.(37-39)AGG>ATG	p.R13M	CENPO_uc002rfn.2_5'Flank|CENPO_uc002rfo.1_5'Flank|CENPO_uc002rfp.1_5'Flank|CENPO_uc002rfq.1_5'Flank	NM_001013663	NP_001013685	Q6GMV3	PTRD1_HUMAN	hypothetical protein LOC391356	13					translation		aminoacyl-tRNA hydrolase activity|protein tyrosine phosphatase activity				0																		---	---	---	---
HADHA	3030	broad.mit.edu	37	2	26414342	26414342	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26414342C>T	uc002rgy.2	-						HADHA_uc010yks.1_Intron	NM_000182	NP_000173			mitochondrial trifunctional protein, alpha						fatty acid beta-oxidation	fatty acid beta-oxidation multienzyme complex|mitochondrial nucleoid|nucleolus	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acetyltransferase activity|coenzyme binding|enoyl-CoA hydratase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				NADH(DB00157)													---	---	---	---
CAD	790	broad.mit.edu	37	2	27458142	27458142	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27458142G>A	uc002rji.2	+	24	3978	c.3816G>A	c.(3814-3816)GCG>GCA	p.A1272A	CAD_uc010eyw.2_Silent_p.A1209A	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1272	CPSase B.|CPSase (Carbamoyl-phosphate synthase).				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)													---	---	---	---
IFT172	26160	broad.mit.edu	37	2	27676994	27676994	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27676994C>T	uc002rku.2	-	33	3617	c.3566G>A	c.(3565-3567)CGT>CAT	p.R1189H	IFT172_uc010ezb.2_RNA	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	1189					cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
C2orf16	84226	broad.mit.edu	37	2	27804523	27804523	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27804523G>A	uc002rkz.3	+	1	5135	c.5084G>A	c.(5083-5085)CGC>CAC	p.R1695H	ZNF512_uc010ylv.1_5'Flank|ZNF512_uc010ylw.1_5'Flank|ZNF512_uc002rlb.2_5'Flank|ZNF512_uc010ylx.1_5'Flank|ZNF512_uc002rlc.2_5'Flank|ZNF512_uc002rla.2_5'Flank|ZNF512_uc010yly.1_5'Flank|ZNF512_uc010ylz.1_5'Flank	NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	1695	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.|8.									large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31155040	31155040	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31155040T>A	uc002rnr.2	-	10	1571	c.952A>T	c.(952-954)ATG>TTG	p.M318L	GALNT14_uc002rnq.2_Missense_Mutation_p.M298L|GALNT14_uc002rns.2_Missense_Mutation_p.M323L|GALNT14_uc010ymr.1_Missense_Mutation_p.M283L|GALNT14_uc010ezo.1_Missense_Mutation_p.M285L|GALNT14_uc010ezp.1_Silent_p.G196G	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	318	Lumenal (Potential).|Catalytic subdomain B.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
XDH	7498	broad.mit.edu	37	2	31605867	31605867	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31605867C>T	uc002rnv.1	-	11	1117	c.1038G>A	c.(1036-1038)GCG>GCA	p.A346A		NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase	346	FAD-binding PCMH-type.				purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)													---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32693517	32693517	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32693517T>C	uc010ezu.2	+	29	5927	c.5793T>C	c.(5791-5793)GCT>GCC	p.A1931A		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	1931					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33590470	33590470	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33590470C>T	uc002ros.2	+	31	4614	c.4614C>T	c.(4612-4614)AGC>AGT	p.S1538S	LTBP1_uc002rot.2_Silent_p.S1212S|LTBP1_uc002rou.2_Silent_p.S1211S|LTBP1_uc002rov.2_Silent_p.S1158S|LTBP1_uc010ymz.1_Silent_p.S1169S|LTBP1_uc010yna.1_Silent_p.S1116S|LTBP1_uc010ynb.1_Silent_p.S435S	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1537	TB 4.				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37259861	37259861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37259861C>T	uc002rpp.1	-	22	3368	c.3272G>A	c.(3271-3273)CGG>CAG	p.R1091Q		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1091	HEAT 2.						binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
ATL2	64225	broad.mit.edu	37	2	38570418	38570418	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38570418A>G	uc002rqq.2	-	2	385	c.355T>C	c.(355-357)TAT>CAT	p.Y119H	ATL2_uc010ynm.1_Missense_Mutation_p.Y101H|ATL2_uc010ynn.1_Missense_Mutation_p.Y101H|ATL2_uc010yno.1_Intron|ATL2_uc002rqs.2_Missense_Mutation_p.Y119H|ATL2_uc002rqr.2_Intron	NM_001135673	NP_001129145	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2 isoform 2	119	Cytoplasmic.				endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
LRPPRC	10128	broad.mit.edu	37	2	44176742	44176742	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44176742C>A	uc002rtr.2	-	16	1792	c.1734G>T	c.(1732-1734)ACG>ACT	p.T578T	LRPPRC_uc010yob.1_Silent_p.T478T	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein	578					mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
SLC3A1	6519	broad.mit.edu	37	2	44507877	44507877	+	Silent	SNP	C	T	T	rs112369341		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44507877C>T	uc002ruc.3	+	2	531	c.453C>T	c.(451-453)TAC>TAT	p.Y151Y	SLC3A1_uc002rty.2_Silent_p.Y151Y|SLC3A1_uc002rtz.2_Silent_p.Y151Y|SLC3A1_uc002rua.2_Silent_p.Y151Y|SLC3A1_uc002rub.2_Silent_p.Y151Y	NM_000341	NP_000332	Q07837	SLC31_HUMAN	solute carrier family 3, member 1	151	Extracellular (Potential).		Y -> C (in CSNU1).		carbohydrate metabolic process|cellular amino acid metabolic process|ion transport	integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)													---	---	---	---
EPAS1	2034	broad.mit.edu	37	2	46588013	46588013	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46588013G>A	uc002ruv.2	+							NM_001430	NP_001421			endothelial PAS domain protein 1						angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50724812	50724812	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50724812G>A	uc010fbq.2	-	14	4135	c.2658C>T	c.(2656-2658)AAC>AAT	p.N886N	NRXN1_uc002rxb.3_Silent_p.N518N|NRXN1_uc002rxe.3_Silent_p.N846N|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	212	Extracellular (Potential).|Laminin G-like.				angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	51149818	51149818	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51149818C>T	uc010fbq.2	-	5	2374	c.897G>A	c.(895-897)GCG>GCA	p.A299A	NRXN1_uc002rxe.3_Silent_p.A266A|NRXN1_uc002rxd.1_Silent_p.A265A	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:Variant_position_missing_in_P58400_after_alignment					angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
ASB3	51130	broad.mit.edu	37	2	53897785	53897785	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53897785C>T	uc002rxg.1	-	10	1547	c.1412G>A	c.(1411-1413)CGG>CAG	p.R471Q	ASB3_uc002rxh.1_Missense_Mutation_p.R398Q|ASB3_uc002rxi.3_Missense_Mutation_p.R509Q|ASB3_uc002rxf.1_RNA	NM_016115	NP_057199	Q9Y575	ASB3_HUMAN	ankyrin repeat and SOCS box-containing protein 3	471	SOCS box.				intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54839412	54839412	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54839412G>A	uc002rxu.2	+	4	664	c.415G>A	c.(415-417)GTG>ATG	p.V139M	SPTBN1_uc002rxv.1_Missense_Mutation_p.V139M|SPTBN1_uc002rxx.2_Missense_Mutation_p.V126M	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	139	CH 1.|Actin-binding.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
FANCL	55120	broad.mit.edu	37	2	58392869	58392869	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58392869T>C	uc002rzw.3	-	8	748	c.681A>G	c.(679-681)AGA>AGG	p.R227R	FANCL_uc002rzx.3_Silent_p.R232R|FANCL_uc010fce.2_Silent_p.R227R|FANCL_uc010fcf.1_Silent_p.R168R	NM_018062	NP_060532	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L isoform	227					DNA repair	cytoplasm|nucleoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2													Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
PUS10	150962	broad.mit.edu	37	2	61172212	61172212	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61172212C>T	uc010fci.2	-	17	1543	c.1483G>A	c.(1483-1485)GGG>AGG	p.G495R	PUS10_uc002sao.2_Missense_Mutation_p.G495R|PUS10_uc010ypk.1_Missense_Mutation_p.G272R	NM_144709	NP_653310	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	495					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)															---	---	---	---
PUS10	150962	broad.mit.edu	37	2	61198693	61198693	+	Splice_Site	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61198693C>T	uc010fci.2	-	5	529	c.469_splice	c.e5-1	p.H157_splice	PUS10_uc002sao.2_Splice_Site_p.H157_splice|PUS10_uc010ypk.1_Splice_Site	NM_144709	NP_653310			pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61575043	61575043	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61575043A>G	uc002sbe.2	-	15	2269	c.2247T>C	c.(2245-2247)CAT>CAC	p.H749H		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	749					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63609089	63609089	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63609089C>T	uc002sch.2	-	11	2022	c.1576G>A	c.(1576-1578)GCC>ACC	p.A526T	C2orf86_uc002sce.2_RNA|C2orf86_uc002scf.2_Missense_Mutation_p.A367T|C2orf86_uc010ypu.1_RNA|C2orf86_uc002scg.2_Missense_Mutation_p.A334T|C2orf86_uc002sci.1_Missense_Mutation_p.A502T	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	526					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
CEP68	23177	broad.mit.edu	37	2	65299431	65299431	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65299431C>A	uc002sdl.3	+	3	1415	c.1201C>A	c.(1201-1203)CCC>ACC	p.P401T	CEP68_uc002sdj.2_Missense_Mutation_p.P401T|CEP68_uc010yqb.1_Missense_Mutation_p.P401T|CEP68_uc002sdk.3_Missense_Mutation_p.P401T|CEP68_uc010yqc.1_Missense_Mutation_p.P401T|CEP68_uc010yqd.1_Missense_Mutation_p.P401T	NM_015147	NP_055962	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	401					centrosome organization	centrosome				skin(1)	1																		---	---	---	---
SPRED2	200734	broad.mit.edu	37	2	65540716	65540716	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65540716G>T	uc002sdr.3	-	6	1711	c.1176C>A	c.(1174-1176)TGC>TGA	p.C392*	SPRED2_uc010fcw.2_Nonsense_Mutation_p.C389*	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2	392	SPR.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
GMCL1	64395	broad.mit.edu	37	2	70098930	70098930	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70098930C>G	uc002sfu.2	+	13	1625	c.1418C>G	c.(1417-1419)ACT>AGT	p.T473S		NM_178439	NP_848526	Q96IK5	GMCL1_HUMAN	germ cell-less	473					cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3																		---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70396800	70396800	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70396800A>G	uc002sgh.2	-							NM_017880	NP_060350			hypothetical protein LOC54980												0																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71755432	71755432	+	Silent	SNP	C	T	T	rs147244033		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71755432C>T	uc002sie.2	+	13	1561	c.1185C>T	c.(1183-1185)GAC>GAT	p.D395D	DYSF_uc010feg.2_Silent_p.D426D|DYSF_uc010feh.2_Silent_p.D395D|DYSF_uc002sig.3_Silent_p.D395D|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Silent_p.D395D|DYSF_uc010fef.2_Silent_p.D426D|DYSF_uc010fei.2_Silent_p.D426D|DYSF_uc010fek.2_Silent_p.D427D|DYSF_uc010fej.2_Silent_p.D396D|DYSF_uc010fel.2_Silent_p.D396D|DYSF_uc010feo.2_Silent_p.D427D|DYSF_uc010fem.2_Silent_p.D396D|DYSF_uc010fen.2_Silent_p.D427D|DYSF_uc002sif.2_Silent_p.D396D	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	395	Cytoplasmic (Potential).|C2 3.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71838454	71838454	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71838454C>T	uc002sie.2	+	37	4359	c.3983C>T	c.(3982-3984)GCG>GTG	p.A1328V	DYSF_uc010feg.2_Missense_Mutation_p.A1359V|DYSF_uc010feh.2_Missense_Mutation_p.A1314V|DYSF_uc002sig.3_Missense_Mutation_p.A1314V|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Missense_Mutation_p.A1328V|DYSF_uc010fef.2_Missense_Mutation_p.A1345V|DYSF_uc010fei.2_Missense_Mutation_p.A1345V|DYSF_uc010fek.2_Missense_Mutation_p.A1346V|DYSF_uc010fej.2_Missense_Mutation_p.A1315V|DYSF_uc010fel.2_Missense_Mutation_p.A1315V|DYSF_uc010feo.2_Missense_Mutation_p.A1360V|DYSF_uc010fem.2_Missense_Mutation_p.A1329V|DYSF_uc010fen.2_Missense_Mutation_p.A1346V|DYSF_uc002sif.2_Missense_Mutation_p.A1329V|DYSF_uc010yqy.1_Missense_Mutation_p.A209V|DYSF_uc010yqz.1_Missense_Mutation_p.A68V	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1328	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
RAB11FIP5	26056	broad.mit.edu	37	2	73302664	73302664	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73302664C>A	uc002siu.3	-	5	2188	c.1947G>T	c.(1945-1947)CCG>CCT	p.P649P	RAB11FIP5_uc002sis.3_Missense_Mutation_p.R28L|RAB11FIP5_uc002sit.3_Silent_p.P571P	NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	649					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0																		---	---	---	---
DCTN1	1639	broad.mit.edu	37	2	74595935	74595935	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74595935T>C	uc002skx.2	-	16	2085	c.1774A>G	c.(1774-1776)ATG>GTG	p.M592V	DCTN1_uc002skv.2_Missense_Mutation_p.M458V|DCTN1_uc002sku.2_Missense_Mutation_p.M458V|DCTN1_uc002skw.1_Missense_Mutation_p.M568V|DCTN1_uc010ffd.2_Missense_Mutation_p.M572V|DCTN1_uc002sky.2_Missense_Mutation_p.M555V	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	592					cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5																		---	---	---	---
AUP1	550	broad.mit.edu	37	2	74754120	74754120	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74754120G>A	uc010yrx.1	-	10	1441	c.1315C>T	c.(1315-1317)CGG>TGG	p.R439W	DQX1_uc010yrw.1_5'Flank|AUP1_uc002sme.2_Missense_Mutation_p.R115W|AUP1_uc002smf.2_Missense_Mutation_p.R382W|AUP1_uc002smg.2_RNA|AUP1_uc002smh.2_Missense_Mutation_p.R291W|HTRA2_uc002smi.1_5'Flank|HTRA2_uc002smj.1_5'Flank|HTRA2_uc002smk.1_5'Flank|HTRA2_uc002sml.1_5'Flank|HTRA2_uc002smm.1_5'Flank|HTRA2_uc002smn.1_5'Flank			Q9Y679	AUP1_HUMAN	SubName: Full=cDNA FLJ57204, highly similar to Homo sapiens ancient ubiquitous protein 1 (AUP1), transcript variant 2, mRNA;	448	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nucleus	protein binding				0																		---	---	---	---
HTRA2	27429	broad.mit.edu	37	2	74758994	74758994	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74758994G>A	uc002smi.1	+	6	1659	c.1057G>A	c.(1057-1059)GGA>AGA	p.G353R	AUP1_uc002smf.2_5'Flank|AUP1_uc002smg.2_5'Flank|AUP1_uc002smh.2_5'Flank|AUP1_uc010yrx.1_5'Flank|AUP1_uc010yry.1_5'Flank|HTRA2_uc002smj.1_Missense_Mutation_p.G288R|HTRA2_uc002smk.1_Missense_Mutation_p.G363R|HTRA2_uc002sml.1_Missense_Mutation_p.G353R|HTRA2_uc002smm.1_Missense_Mutation_p.G94R|HTRA2_uc002smn.1_Missense_Mutation_p.G94R|HTRA2_uc010ffl.2_3'UTR	NM_013247	NP_037379	O43464	HTRA2_HUMAN	HtrA serine peptidase 2 isoform 1 preproprotein	353					apoptosis|proteolysis|response to stress	CD40 receptor complex|endoplasmic reticulum membrane|internal side of plasma membrane|mitochondrial intermembrane space|mitochondrial membrane|nucleus	serine-type endopeptidase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
LRRTM1	347730	broad.mit.edu	37	2	80529429	80529429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80529429C>T	uc002sok.1	-	2	1786	c.1516G>A	c.(1516-1518)GAG>AAG	p.E506K	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	506	Cytoplasmic (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5															HNSCC(69;0.2)			---	---	---	---
LRRTM1	347730	broad.mit.edu	37	2	80529548	80529548	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80529548G>A	uc002sok.1	-	2	1667	c.1397C>T	c.(1396-1398)ACG>ATG	p.T466M	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	466	Cytoplasmic (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5															HNSCC(69;0.2)			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80646567	80646567	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80646567A>G	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80801379	80801379	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80801379T>A	uc010ysh.1	+	12	1838	c.1833T>A	c.(1831-1833)GAT>GAA	p.D611E	CTNNA2_uc010yse.1_Missense_Mutation_p.D611E|CTNNA2_uc010ysf.1_Missense_Mutation_p.D611E|CTNNA2_uc010ysg.1_Missense_Mutation_p.D611E|CTNNA2_uc010ysi.1_Missense_Mutation_p.D243E	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	611					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84777113	84777113	+	Nonsense_Mutation	SNP	C	T	T	rs143013494		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84777113C>T	uc010fgb.2	+	9	1554	c.1417C>T	c.(1417-1419)CGA>TGA	p.R473*	DNAH6_uc002soo.2_Nonsense_Mutation_p.R52*|DNAH6_uc002sop.2_Nonsense_Mutation_p.R52*	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	473	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
SMYD1	150572	broad.mit.edu	37	2	88390608	88390608	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88390608C>T	uc002ssr.2	+	4	608	c.606C>T	c.(604-606)GGC>GGT	p.G202G	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_5'UTR	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	202	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
THNSL2	55258	broad.mit.edu	37	2	88482534	88482534	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88482534T>C	uc002ssz.3	+	7	1172	c.1019T>C	c.(1018-1020)CTC>CCC	p.L340P	THNSL2_uc002ssv.2_RNA|THNSL2_uc002ssw.3_Missense_Mutation_p.L340P|THNSL2_uc002ssx.3_Intron|THNSL2_uc002sta.3_Missense_Mutation_p.L182P|THNSL2_uc002ssy.3_Missense_Mutation_p.L340P|THNSL2_uc010fhe.2_Missense_Mutation_p.L182P	NM_018271	NP_060741	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2	340					threonine biosynthetic process		threonine synthase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89160095	89160095	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89160095G>A	uc010ytr.1	-	239		c.9695C>T			uc002sti.1_RNA|uc002stj.1_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89265996	89265996	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89265996G>A	uc010ytr.1	-	95		c.7570C>T			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
TEKT4	150483	broad.mit.edu	37	2	95537510	95537510	+	Silent	SNP	G	A	A	rs111349391		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95537510G>A	uc002stw.1	+	1	279	c.186G>A	c.(184-186)TCG>TCA	p.S62S	uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4	62					cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ASTL	431705	broad.mit.edu	37	2	96801091	96801091	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96801091G>A	uc010yui.1	-	3	242	c.242C>T	c.(241-243)CCG>CTG	p.P81L		NM_001002036	NP_001002036	Q6HA08	ASTL_HUMAN	astacin-like metalloendopeptidase precursor	81					proteolysis		metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98429195	98429195	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98429195G>T	uc002syh.3	-	16	1864	c.1635C>A	c.(1633-1635)CCC>CCA	p.P545P		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	545						integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99681506	99681506	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99681506A>T	uc002szg.3	-	14	1928	c.1300T>A	c.(1300-1302)TCA>ACA	p.S434T	TSGA10_uc002szh.3_Missense_Mutation_p.S434T|TSGA10_uc002szi.3_Missense_Mutation_p.S434T|TSGA10_uc010fin.1_Missense_Mutation_p.S434T	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10	434					spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	100015841	100015841	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100015841T>C	uc002tab.2	+	24	3811	c.3627T>C	c.(3625-3627)CTT>CTC	p.L1209L	EIF5B_uc010yvq.1_Silent_p.L191L	NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	1209					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101594198	101594198	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101594198C>T	uc002tap.1	+	15	1705	c.1419C>T	c.(1417-1419)TGC>TGT	p.C473C	NPAS2_uc010yvt.1_Silent_p.C538C|NPAS2_uc010fit.1_Silent_p.C51C	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	473					central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109086698	109086698	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109086698G>A	uc002tec.2	+	6	1067	c.913G>A	c.(913-915)GCC>ACC	p.A305T	GCC2_uc002ted.2_Missense_Mutation_p.A204T	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	305	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109098263	109098263	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109098263G>A	uc002tec.2	+	10	3325	c.3171G>A	c.(3169-3171)TCG>TCA	p.S1057S	GCC2_uc002ted.2_Silent_p.S956S	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1057	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109109204	109109204	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109109204G>A	uc002tec.2	+	19	4559	c.4405G>A	c.(4405-4407)GAA>AAA	p.E1469K	GCC2_uc002ted.2_Missense_Mutation_p.E1368K	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1469	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	110259141	110259141	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110259141G>A	uc010ywt.1	+	10	2542	c.2542G>A	c.(2542-2544)GAC>AAC	p.D848N		NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	848	SH3 4.						zinc ion binding			ovary(1)	1																		---	---	---	---
CBWD2	150472	broad.mit.edu	37	2	114212335	114212335	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114212335G>A	uc002tju.2	+	6	686	c.508G>A	c.(508-510)GAT>AAT	p.D170N	CBWD2_uc010yxw.1_Missense_Mutation_p.D134N|CBWD2_uc002tjv.2_Missense_Mutation_p.D134N|CBWD2_uc010fkv.2_RNA	NM_172003	NP_742000	Q8IUF1	CBWD2_HUMAN	COBW domain-containing protein 2	170							ATP binding|protein binding				0																		---	---	---	---
FOXD4L1	200350	broad.mit.edu	37	2	114257672	114257672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114257672C>T	uc002tjw.3	+	1	1012	c.839C>T	c.(838-840)GCA>GTA	p.A280V		NM_012184	NP_036316	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	280	Pro-rich.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116447467	116447467	+	Silent	SNP	C	T	T	rs151071213	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116447467C>T	uc002tla.1	+	7	1003	c.546C>T	c.(544-546)TAC>TAT	p.Y182Y	DPP10_uc002tlb.1_Silent_p.Y132Y|DPP10_uc002tlc.1_Silent_p.Y178Y|DPP10_uc002tle.2_Silent_p.Y186Y|DPP10_uc002tlf.1_Silent_p.Y175Y	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	182	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
RALB	5899	broad.mit.edu	37	2	121047169	121047169	+	Missense_Mutation	SNP	C	T	T	rs1804270		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121047169C>T	uc002tmk.2	+	4	527	c.337C>T	c.(337-339)CGT>TGT	p.R113C	RALB_uc010yys.1_Missense_Mutation_p.R135C|RALB_uc002tml.2_Missense_Mutation_p.R134C|RALB_uc002tmm.2_RNA|RALB_uc010yyt.1_RNA	NM_002881	NP_002872	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	113					apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding			lung(3)	3		Prostate(154;0.122)																---	---	---	---
TSN	7247	broad.mit.edu	37	2	122514891	122514891	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122514891G>A	uc002tnl.2	+	2	377	c.142G>A	c.(142-144)GGT>AGT	p.G48S	TSN_uc002tnm.2_5'UTR|TSN_uc010yze.1_Missense_Mutation_p.G48S|TSN_uc010flt.2_Intron	NM_004622	NP_004613	Q15631	TSN_HUMAN	translin	48					DNA recombination	cytoplasm|nucleus	sequence-specific DNA binding			breast(2)|large_intestine(1)	3		Ovarian(717;0.0563)|Prostate(154;0.116)																---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125204470	125204470	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125204470T>G	uc002tno.2	+	6	1238	c.874T>G	c.(874-876)TTC>GTC	p.F292V	CNTNAP5_uc010flu.2_Missense_Mutation_p.F292V	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	292	Laminin G-like 1.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
HS6ST1	9394	broad.mit.edu	37	2	129026328	129026328	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129026328G>A	uc002tpt.3	-	2	678	c.644C>T	c.(643-645)ACG>ATG	p.T215M		NM_004807	NP_004798	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	215	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
CCDC115	84317	broad.mit.edu	37	2	131098608	131098608	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131098608C>T	uc002tqy.1	-	4	527	c.303G>A	c.(301-303)CTG>CTA	p.L101L	CCDC115_uc002tqw.1_Silent_p.L93L|CCDC115_uc010zaf.1_Silent_p.L96L|CCDC115_uc002tqx.2_Silent_p.L96L|CCDC115_uc002tqz.1_Silent_p.L101L|IMP4_uc002tra.1_5'Flank	NM_032357	NP_115733	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	101						endosome|lysosome					0	Colorectal(110;0.1)																	---	---	---	---
FAM123C	205147	broad.mit.edu	37	2	131520996	131520996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131520996C>T	uc002trw.2	+	2	1541	c.1351C>T	c.(1351-1353)CCG>TCG	p.P451S	FAM123C_uc010fmv.2_Missense_Mutation_p.P451S|FAM123C_uc010fms.1_Missense_Mutation_p.P451S|FAM123C_uc010fmt.1_Missense_Mutation_p.P451S|FAM123C_uc010fmu.1_Missense_Mutation_p.P451S	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	451										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)														---	---	---	---
ARHGEF4	50649	broad.mit.edu	37	2	131704220	131704220	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131704220G>A	uc002tsa.1	+						ARHGEF4_uc010fmw.1_Intron|ARHGEF4_uc002tsb.1_Intron|ARHGEF4_uc010fmx.1_Intron|ARHGEF4_uc002trz.1_Missense_Mutation_p.A793T	NM_015320	NP_056135			Rho guanine nucleotide exchange factor 4 isoform						apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)														---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133542842	133542842	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133542842C>T	uc002ttp.2	-	14	1916	c.1542G>A	c.(1540-1542)TGG>TGA	p.W514*	NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	514							protein binding				0																		---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136473169	136473169	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136473169C>T	uc002tuo.2	+	23	3051	c.2681C>T	c.(2680-2682)GCA>GTA	p.A894V	R3HDM1_uc010fni.2_Missense_Mutation_p.A893V|R3HDM1_uc002tup.2_Missense_Mutation_p.A839V|R3HDM1_uc010zbh.1_Missense_Mutation_p.A642V	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	894							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
UBXN4	23190	broad.mit.edu	37	2	136505832	136505832	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136505832T>C	uc002tur.2	+							NM_014607	NP_055422			UBX domain containing 2						response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2																		---	---	---	---
MCM6	4175	broad.mit.edu	37	2	136626426	136626426	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136626426G>A	uc002tuw.2	-	4	446	c.370C>T	c.(370-372)CGA>TGA	p.R124*		NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	124					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)													---	---	---	---
DARS	1615	broad.mit.edu	37	2	136700974	136700974	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136700974G>A	uc002tux.1	-	5	581	c.397C>T	c.(397-399)CAA>TAA	p.Q133*	DARS_uc010fnj.1_Nonsense_Mutation_p.Q33*	NM_001349	NP_001340	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	133					aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)													---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141528559	141528559	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141528559T>G	uc002tvj.1	-	34	6489	c.5517A>C	c.(5515-5517)CAA>CAC	p.Q1839H		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1839	Extracellular (Potential).|EGF-like 4.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152318979	152318979	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152318979C>T	uc002txm.2	+	29	3492	c.3362C>T	c.(3361-3363)ACG>ATG	p.T1121M	RIF1_uc002txl.2_Missense_Mutation_p.T1121M|RIF1_uc002txn.2_Missense_Mutation_p.T1121M|RIF1_uc002txo.2_Missense_Mutation_p.T1121M|RIF1_uc002txp.2_5'Flank	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	1121					cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152476054	152476054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152476054C>T	uc010fnx.2	-	69	10245	c.10054G>A	c.(10054-10056)GAC>AAC	p.D3352N		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3352	Nebulin 91.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	155306995	155306995	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155306995A>G	uc002tyr.3	+	13	2170	c.1603A>G	c.(1603-1605)ACA>GCA	p.T535A	GALNT13_uc002tyt.3_3'UTR|GALNT13_uc010fod.2_3'UTR|uc002tyu.1_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	535	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159533309	159533309	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159533309C>T	uc002tzv.2	+	20	3446	c.3186C>T	c.(3184-3186)TAC>TAT	p.Y1062Y	PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Silent_p.Y719Y|PKP4_uc002uaa.2_Intron|uc002uab.1_Intron|PKP4_uc002uac.2_Silent_p.Y243Y|PKP4_uc002uad.2_RNA|PKP4_uc002uae.1_Silent_p.Y149Y	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	1062					cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7															HNSCC(62;0.18)			---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160303460	160303460	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160303460T>C	uc002uao.2	-	6	881	c.529A>G	c.(529-531)AAT>GAT	p.N177D	BAZ2B_uc002uap.2_Missense_Mutation_p.N175D|BAZ2B_uc002uas.1_Missense_Mutation_p.N114D|BAZ2B_uc002uau.1_Missense_Mutation_p.N175D|BAZ2B_uc002uaq.1_Missense_Mutation_p.N105D|BAZ2B_uc002uat.3_Missense_Mutation_p.N114D|BAZ2B_uc010fop.1_Missense_Mutation_p.N175D	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	177	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
PLA2R1	22925	broad.mit.edu	37	2	160898578	160898578	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160898578G>A	uc002ube.1	-	3	832	c.625C>T	c.(625-627)CGT>TGT	p.R209C	PLA2R1_uc010zcp.1_Missense_Mutation_p.R209C|PLA2R1_uc002ubf.2_Missense_Mutation_p.R209C	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	209	Extracellular (Potential).|Fibronectin type-II.				endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3																		---	---	---	---
FAP	2191	broad.mit.edu	37	2	163083093	163083093	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163083093G>A	uc002ucd.2	-	3	338	c.130C>T	c.(130-132)CTG>TTG	p.L44L	FAP_uc010zct.1_Silent_p.L44L|FAP_uc010fpd.2_Intron|FAP_uc010fpe.1_Intron	NM_004460	NP_004451	Q12884	SEPR_HUMAN	fibroblast activation protein, alpha subunit	44	Extracellular (Potential).				endothelial cell migration|negative regulation of extracellular matrix disassembly|proteolysis	cell junction|integral to membrane|invadopodium membrane|lamellipodium membrane	dipeptidyl-peptidase activity|metalloendopeptidase activity|protein homodimerization activity|serine-type endopeptidase activity			ovary(3)	3																		---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	166020903	166020903	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166020903C>T	uc002ucx.2	-	6	1093	c.601G>A	c.(601-603)GCA>ACA	p.A201T	SCN3A_uc002ucy.2_Missense_Mutation_p.A201T|SCN3A_uc002ucz.2_Missense_Mutation_p.A201T|SCN3A_uc002uda.1_Missense_Mutation_p.A70T|SCN3A_uc002udb.1_Missense_Mutation_p.A70T	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	201	Helical; Name=S3 of repeat I; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166533101	166533101	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166533101G>A	uc002udf.2	+	6	1064	c.688G>A	c.(688-690)GCT>ACT	p.A230T	CSRNP3_uc002udg.2_Missense_Mutation_p.A230T	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	230	Cys-rich.				apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5																		---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167134794	167134794	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167134794C>A	uc010fpl.2	-	15	2681	c.2340G>T	c.(2338-2340)ATG>ATT	p.M780I	uc002udp.2_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	791	II.|Helical; Name=S2 of repeat II; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)													---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167137024	167137024	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167137024T>C	uc010fpl.2	-	14	2494	c.2153A>G	c.(2152-2154)TAT>TGT	p.Y718C	uc002udp.2_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	729						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)													---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168096389	168096389	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168096389G>T	uc002udx.2	+	5	901	c.883G>T	c.(883-885)GGC>TGC	p.G295C	XIRP2_uc010fpn.2_Missense_Mutation_p.G328C|XIRP2_uc010fpo.2_Missense_Mutation_p.G295C|XIRP2_uc010fpp.2_Missense_Mutation_p.G295C|XIRP2_uc002udy.2_Missense_Mutation_p.G120C|XIRP2_uc010fpq.2_Missense_Mutation_p.G73C|XIRP2_uc010fpr.2_Missense_Mutation_p.G73C	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	120					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168102878	168102878	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168102878T>C	uc002udx.2	+	8	4994	c.4976T>C	c.(4975-4977)GTA>GCA	p.V1659A	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.V1484A|XIRP2_uc010fpq.2_Missense_Mutation_p.V1437A|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1484					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
ABCB11	8647	broad.mit.edu	37	2	169787257	169787257	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169787257G>A	uc002ueo.1	-	25	3455	c.3329C>T	c.(3328-3330)GCG>GTG	p.A1110V	ABCB11_uc010zda.1_Missense_Mutation_p.A552V|ABCB11_uc010zdb.1_Missense_Mutation_p.A586V	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1110	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)													---	---	---	---
PPIG	9360	broad.mit.edu	37	2	170492638	170492638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170492638C>T	uc002uez.2	+	13	1274	c.1054C>T	c.(1054-1056)CGT>TGT	p.R352C	PPIG_uc010fpx.2_Missense_Mutation_p.R337C|PPIG_uc010fpy.2_Missense_Mutation_p.R345C|PPIG_uc002ufb.2_Missense_Mutation_p.R352C|PPIG_uc002ufd.2_Missense_Mutation_p.R349C	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	352					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)													---	---	---	---
SP5	389058	broad.mit.edu	37	2	171573778	171573778	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171573778A>C	uc002uge.2	+	2	1227	c.1061A>C	c.(1060-1062)AAG>ACG	p.K354T		NM_001003845	NP_001003845	Q6BEB4	SP5_HUMAN	Sp5 transcription factor	354					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171850439	171850439	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171850439G>A	uc002ugn.2	-	21	2624	c.2152C>T	c.(2152-2154)CGA>TGA	p.R718*	TLK1_uc002ugo.2_Nonsense_Mutation_p.R739*|TLK1_uc002ugp.2_Nonsense_Mutation_p.R670*|TLK1_uc010zdn.1_Nonsense_Mutation_p.R622*	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1	718	Protein kinase.				cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
TTN	7273	broad.mit.edu	37	2	179485535	179485535	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179485535C>A	uc010zfg.1	-	196	38322	c.38098G>T	c.(38098-38100)GAT>TAT	p.D12700Y	TTN_uc010zfh.1_Missense_Mutation_p.D6395Y|TTN_uc010zfi.1_Missense_Mutation_p.D6328Y|TTN_uc010zfj.1_Missense_Mutation_p.D6203Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13627							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179585181	179585181	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179585181C>T	uc010zfg.1	-	77	19800	c.19576G>A	c.(19576-19578)GGG>AGG	p.G6526R	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.G3187R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7453							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179610848	179610848	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179610848A>T	uc002unb.2	-	46	16503	c.16279T>A	c.(16279-16281)TAC>AAC	p.Y5427N	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	8934							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
ITGA4	3676	broad.mit.edu	37	2	182323017	182323017	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182323017G>T	uc002unu.2	+	2	1055	c.292G>T	c.(292-294)GGC>TGC	p.G98C	ITGA4_uc002unt.2_Missense_Mutation_p.G98C|ITGA4_uc010zfl.1_Missense_Mutation_p.G98C	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	98	FG-GAP 1.|Extracellular (Potential).				blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)													---	---	---	---
DNAJC10	54431	broad.mit.edu	37	2	183621194	183621194	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183621194C>T	uc002uow.1	+	18	2222	c.1807C>T	c.(1807-1809)CGG>TGG	p.R603W	DNAJC10_uc002uox.1_RNA|DNAJC10_uc002uoy.1_RNA|DNAJC10_uc002uoz.1_Missense_Mutation_p.R557W|DNAJC10_uc010fro.1_RNA	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	603	Thioredoxin 3.				apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189864304	189864304	+	Splice_Site	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189864304G>A	uc002uqj.1	+	31	2346	c.2229_splice	c.e31+1	p.K743_splice		NM_000090	NP_000081			collagen type III alpha 1 preproprotein						axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)													---	---	---	---
TRAK2	66008	broad.mit.edu	37	2	202248895	202248895	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202248895T>A	uc002uyb.3	-	15	2454	c.2008A>T	c.(2008-2010)ACA>TCA	p.T670S		NM_015049	NP_055864	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	670				Missing (in Ref. 2).		early endosome|plasma membrane	GABA receptor binding				0																		---	---	---	---
IDH1	3417	broad.mit.edu	37	2	209106865	209106865	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209106865A>T	uc002vcs.2	-	7	949	c.703T>A	c.(703-705)TAC>AAC	p.Y235N	IDH1_uc002vct.2_Missense_Mutation_p.Y235N|IDH1_uc002vcu.2_Missense_Mutation_p.Y235N	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	235					2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity			central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)				Mis		gliobastoma 								---	---	---	---
RPE	6120	broad.mit.edu	37	2	210880970	210880970	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210880970G>T	uc002vdn.2	+						RPE_uc002vdm.2_Intron|RPE_uc002vdo.2_Missense_Mutation_p.G61C|RPE_uc010zjf.1_Intron|RPE_uc002vdp.2_Missense_Mutation_p.G58C|RPE_uc010fup.2_Intron|RPE_uc002vdq.2_Missense_Mutation_p.G61C|RPE_uc002vdr.2_Missense_Mutation_p.G61C	NM_199229	NP_954699			ribulose-5-phosphate-3-epimerase isoform 1						pentose-phosphate shunt	cytosol	metal ion binding|protein homodimerization activity|ribulose-phosphate 3-epimerase activity				0				Epithelial(149;0.00241)|Lung(261;0.041)|all cancers(144;0.0429)|LUSC - Lung squamous cell carcinoma(261;0.0431)														---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213921619	213921619	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213921619T>C	uc002vem.2	-	4	513	c.344A>G	c.(343-345)GAC>GGC	p.D115G	IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Missense_Mutation_p.D62G|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Intron|IKZF2_uc002vel.2_Intron|IKZF2_uc010fuw.2_5'UTR|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Intron|IKZF2_uc002ven.2_Intron	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	115	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)														---	---	---	---
ATIC	471	broad.mit.edu	37	2	216211661	216211661	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216211661C>T	uc002vex.3	+	14	1674	c.1500C>T	c.(1498-1500)GGC>GGT	p.G500G	ATIC_uc010zjo.1_Silent_p.G441G|ATIC_uc002vey.3_Silent_p.G499G	NM_004044	NP_004035	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide	500					IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)			T	ALK	ALCL								---	---	---	---
ABCB6	10058	broad.mit.edu	37	2	220079169	220079169	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220079169T>G	uc002vkc.1	-	7	1605	c.1328A>C	c.(1327-1329)AAC>ACC	p.N443T	ABCB6_uc010fwe.1_Missense_Mutation_p.N397T|ABCB6_uc010zku.1_RNA	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6	443	ABC transmembrane type-1.				cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220309443	220309443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220309443G>A	uc010fwg.2	+	2	457	c.457G>A	c.(457-459)GGG>AGG	p.G153R	SPEG_uc002vlm.2_RNA|SPEG_uc010fwh.1_5'UTR|SPEG_uc002vln.1_5'UTR	NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	153					muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
STK11IP	114790	broad.mit.edu	37	2	220479233	220479233	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220479233G>A	uc002vml.2	+	23	2910	c.2867G>A	c.(2866-2868)CGC>CAC	p.R956H		NM_052902	NP_443134	Q8N1F8	S11IP_HUMAN	LKB1 interacting protein	956					protein localization	cytoplasm	protein kinase binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
KCNE4	23704	broad.mit.edu	37	2	223917584	223917584	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223917584C>T	uc002vnl.3	+	2	190	c.36C>T	c.(34-36)CCC>CCT	p.P12P		NM_080671	NP_542402	Q8WWG9	KCNE4_HUMAN	potassium voltage-gated channel, Isk-related	12						integral to membrane	voltage-gated potassium channel activity			ovary(1)	1		Renal(207;0.0183)|Lung NSC(271;0.137)|all_lung(227;0.175)		Epithelial(121;4.48e-11)|all cancers(144;2.88e-08)|Lung(261;0.00688)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230683149	230683149	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230683149A>T	uc002vpw.1	-	8	1495	c.1386T>A	c.(1384-1386)TGT>TGA	p.C462*	TRIP12_uc002vpx.1_Nonsense_Mutation_p.C510*|TRIP12_uc002vpy.1_Nonsense_Mutation_p.C165*|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Nonsense_Mutation_p.C468*	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	462					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
SLC16A14	151473	broad.mit.edu	37	2	230923997	230923997	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230923997G>A	uc002vqd.1	-	2	435	c.72C>T	c.(70-72)CCC>CCT	p.P24P	FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Silent_p.P24P|SLC16A14_uc002vqf.2_Silent_p.P24P	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid	24	Extracellular (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
B3GNT7	93010	broad.mit.edu	37	2	232263382	232263382	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232263382G>A	uc002vrs.2	+	2	1132	c.952G>A	c.(952-954)GAC>AAC	p.D318N		NM_145236	NP_660279	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal	318	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity				0		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)														---	---	---	---
NCL	4691	broad.mit.edu	37	2	232326383	232326383	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232326383C>T	uc002vru.2	-	3	622	c.481G>A	c.(481-483)GAG>AAG	p.E161K	SNORD82_uc010fxw.1_5'Flank	NM_005381	NP_005372	P19338	NUCL_HUMAN	nucleolin	161	Asp/Glu-rich (acidic).				angiogenesis	cell cortex|nucleolus|ribonucleoprotein complex	nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding			ovary(2)|pancreas(1)	3		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)														---	---	---	---
ALPP	250	broad.mit.edu	37	2	233245422	233245422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233245422C>T	uc002vsq.2	+	8	1120	c.955C>T	c.(955-957)CGC>TGC	p.R319C	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	319						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)														---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233599941	233599941	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233599941C>T	uc002vti.3	+	5	371	c.34C>T	c.(34-36)CCT>TCT	p.P12S	GIGYF2_uc002vte.2_RNA|GIGYF2_uc002vtf.2_RNA|GIGYF2_uc010zmj.1_Missense_Mutation_p.P12S|GIGYF2_uc002vtg.2_Missense_Mutation_p.P12S|GIGYF2_uc002vtj.3_Missense_Mutation_p.P12S|GIGYF2_uc002vtk.3_Missense_Mutation_p.P12S|GIGYF2_uc002vth.3_Missense_Mutation_p.P12S|GIGYF2_uc002vtl.2_RNA|GIGYF2_uc010zmk.1_RNA	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b	12					cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
KCNJ13	3769	broad.mit.edu	37	2	233633259	233633259	+	Missense_Mutation	SNP	G	A	A	rs142849460		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233633259G>A	uc002vto.2	-	2	768	c.725C>T	c.(724-726)ACG>ATG	p.T242M	GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vti.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtn.2_3'UTR|KCNJ13_uc002vtp.2_Missense_Mutation_p.T242M	NM_002242	NP_002233	O60928	IRK13_HUMAN	potassium inwardly-rectifying channel J13	242	Cytoplasmic (By similarity).					voltage-gated potassium channel complex	inward rectifier potassium channel activity				0		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)														---	---	---	---
DGKD	8527	broad.mit.edu	37	2	234357926	234357926	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234357926G>A	uc002vui.1	+	15	1804	c.1792G>A	c.(1792-1794)GCC>ACC	p.A598T	DGKD_uc002vuj.1_Missense_Mutation_p.A554T|DGKD_uc010fyh.1_Missense_Mutation_p.A465T|DGKD_uc010fyi.1_RNA	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	598					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)											OREG0015296	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPP2	6694	broad.mit.edu	37	2	234959420	234959420	+	5'UTR	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234959420C>T	uc002vvk.1	+	1					SPP2_uc010fyl.1_5'UTR	NM_006944	NP_008875			secreted phosphoprotein 2, 24kDa precursor						bone remodeling|skeletal system development	extracellular region	endopeptidase inhibitor activity				0		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)														---	---	---	---
CXCR7	57007	broad.mit.edu	37	2	237489368	237489368	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237489368C>T	uc010fyq.2	+	3	490	c.260C>T	c.(259-261)GCC>GTC	p.A87V	CXCR7_uc002vwd.2_Missense_Mutation_p.A87V	NM_020311	NP_064707	P25106	CXCR7_HUMAN	chemokine orphan receptor 1	87	Helical; Name=2; (Potential).				interspecies interaction between organisms	integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3		Breast(86;0.000182)|Renal(207;0.00339)|all_hematologic(139;0.0048)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|all_lung(227;0.147)|all_neural(83;0.223)		Epithelial(121;8.35e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.09e-11)|Kidney(56;1.11e-07)|KIRC - Kidney renal clear cell carcinoma(57;3.03e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000176)|Lung(119;0.00468)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.118)														---	---	---	---
OR6B2	389090	broad.mit.edu	37	2	240969550	240969550	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240969550C>T	uc002vyr.2	-	2	343	c.297G>A	c.(295-297)ACG>ACA	p.T99T	OR6B2_uc010zoc.1_Silent_p.T99T	NM_001005853	NP_001005853	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B,	99	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)														---	---	---	---
GPC1	2817	broad.mit.edu	37	2	241404983	241404983	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241404983G>A	uc002vyw.3	+	8	1583	c.1362G>A	c.(1360-1362)CGG>CGA	p.R454R		NM_002081	NP_002072	P35052	GPC1_HUMAN	glypican 1 precursor	454					axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)														---	---	---	---
GPR35	2859	broad.mit.edu	37	2	241570285	241570285	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241570285G>A	uc002vzs.1	+	1	1491	c.916G>A	c.(916-918)GTG>ATG	p.V306M	GPR35_uc010fzh.1_Missense_Mutation_p.V337M|GPR35_uc010fzi.1_Missense_Mutation_p.V337M	NM_005301	NP_005292	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	306	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			skin(2)|pancreas(1)	3		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)														---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242431092	242431092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242431092G>A	uc002wbi.1	+	24	2902	c.2785G>A	c.(2785-2787)GAG>AAG	p.E929K		NM_014808	NP_055623	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	929	PH 2.				axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)														---	---	---	---
LRRN1	57633	broad.mit.edu	37	3	3887815	3887815	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3887815A>T	uc003bpt.3	+	2	2251	c.1490A>T	c.(1489-1491)TAC>TTC	p.Y497F	SUMF1_uc003bps.1_Intron	NM_020873	NP_065924	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1 precursor	497	Ig-like C2-type.|Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7188166	7188166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7188166G>A	uc003bqm.2	+	2	821	c.547G>A	c.(547-549)GCA>ACA	p.A183T	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.A183T|GRM7_uc003bql.2_Missense_Mutation_p.A183T	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	183	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7456729	7456729	+	Silent	SNP	G	A	A	rs150722276		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7456729G>A	uc003bqm.2	+	5	1327	c.1053G>A	c.(1051-1053)ACG>ACA	p.T351T	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Silent_p.T351T|GRM7_uc003bql.2_Silent_p.T351T|GRM7_uc003bqn.1_5'UTR	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	351	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
TADA3	10474	broad.mit.edu	37	3	9822154	9822154	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9822154G>A	uc003bsx.1	-	9	1734	c.1186C>T	c.(1186-1188)CGC>TGC	p.R396C	TADA3_uc010hcn.1_Missense_Mutation_p.R396C|TADA3_uc003bsw.1_Missense_Mutation_p.R225C	NM_006354	NP_006345	O75528	TADA3_HUMAN	transcriptional adaptor 3 isoform a	396	Potential.				estrogen receptor signaling pathway|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	ligand-dependent nuclear receptor binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12626094	12626094	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12626094C>A	uc003bxf.3	-	17	2281	c.1866G>T	c.(1864-1866)GAG>GAT	p.E622D	RAF1_uc011aut.1_Missense_Mutation_p.E407D|RAF1_uc011auu.1_Missense_Mutation_p.E540D	NM_002880	NP_002871	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog	622					activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13383337	13383337	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13383337G>A	uc003bxv.1	-	23	3222	c.3139C>T	c.(3139-3141)CGC>TGC	p.R1047C		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	1047	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
SLC6A6	6533	broad.mit.edu	37	3	14508053	14508053	+	Silent	SNP	C	T	T	rs139561700		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14508053C>T	uc010heg.2	+	14	1053	c.762C>T	c.(760-762)TTC>TTT	p.F254F	SLC6A6_uc003byq.2_Silent_p.F254F|SLC6A6_uc003byr.2_RNA	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter	254	Helical; Name=5; (Potential).				cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1																		---	---	---	---
BTD	686	broad.mit.edu	37	3	15686525	15686525	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15686525G>A	uc003cah.2	+	4	1265	c.1162G>A	c.(1162-1164)GTG>ATG	p.V388M	BTD_uc011avv.1_Missense_Mutation_p.V390M|BTD_uc011avw.1_Missense_Mutation_p.V390M|BTD_uc011avx.1_Missense_Mutation_p.V368M	NM_000060	NP_000051	P43251	BTD_HUMAN	biotinidase precursor	388					central nervous system development|epidermis development|nitrogen compound metabolic process	extracellular space	biotin carboxylase activity|biotinidase activity				0																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17052239	17052239	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17052239C>T	uc011awc.1	+	5	1482	c.1377C>T	c.(1375-1377)TGC>TGT	p.C459C	PLCL2_uc010het.1_Intron|PLCL2_uc011awd.1_Silent_p.C341C	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	467	PI-PLC X-box.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
GLB1	2720	broad.mit.edu	37	3	33110438	33110438	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33110438C>T	uc003cfi.1	-	3	387	c.270G>A	c.(268-270)GAG>GAA	p.E90E	GLB1_uc003cfh.1_Silent_p.E60E|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Silent_p.E138E	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein	90					carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)																---	---	---	---
DCLK3	85443	broad.mit.edu	37	3	36778692	36778692	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36778692G>T	uc003cgi.2	-							NM_033403	NP_208382			doublecortin-like kinase 3							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1)	9																		---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37107788	37107788	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37107788G>T	uc003cgp.2	-	23	1916	c.1493C>A	c.(1492-1494)GCC>GAC	p.A498D	LRRFIP2_uc011ayf.1_Intron|LRRFIP2_uc003cgr.2_Intron|LRRFIP2_uc003cgs.3_Intron|LRRFIP2_uc003cgt.3_Intron	NM_006309	NP_006300	Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting	498	Potential.				Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
CX3CR1	1524	broad.mit.edu	37	3	39307682	39307682	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39307682C>T	uc003cjl.2	-	2	411	c.319G>A	c.(319-321)GCC>ACC	p.A107T		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	107	Helical; Name=3; (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)														---	---	---	---
ZNF619	285267	broad.mit.edu	37	3	40529519	40529519	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40529519C>A	uc011azb.1	+	6	1916	c.1638C>A	c.(1636-1638)CCC>CCA	p.P546P	ZNF619_uc010hhz.2_Silent_p.P497P|ZNF619_uc003ckj.2_Silent_p.P490P|ZNF619_uc011azc.1_Silent_p.P506P|ZNF619_uc011azd.1_Silent_p.P462P|ZNF619_uc011aza.1_Silent_p.P448P	NM_001145082	NP_001138554	E9PCD9	E9PCD9_HUMAN	zinc finger protein 619 isoform 1	546					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)														---	---	---	---
SEC22C	9117	broad.mit.edu	37	3	42605031	42605031	+	Silent	SNP	G	A	A	rs146161491		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42605031G>A	uc003clj.2	-	3	448	c.330C>T	c.(328-330)TAC>TAT	p.Y110Y	SEC22C_uc003clh.2_Silent_p.Y110Y|SEC22C_uc011azo.1_Silent_p.Y40Y|SEC22C_uc010hic.2_Silent_p.Y110Y|SEC22C_uc003cli.2_Silent_p.Y110Y	NM_032970	NP_116752	Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C	110	Longin.|Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.222)														---	---	---	---
ZNF197	10168	broad.mit.edu	37	3	44670770	44670770	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44670770C>A	uc003cnm.2	+	2	330	c.124C>A	c.(124-126)CAC>AAC	p.H42N	ZNF197_uc003cnn.2_Missense_Mutation_p.H42N|ZNF197_uc003cno.2_RNA|ZNF197_uc003cnp.2_Missense_Mutation_p.H42N	NM_006991	NP_008922	O14709	ZN197_HUMAN	zinc finger protein 197 isoform 1	42	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|skin(1)	4				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)														---	---	---	---
FYCO1	79443	broad.mit.edu	37	3	46008065	46008065	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46008065G>A	uc003cpb.3	-	8	2967	c.2761C>T	c.(2761-2763)CGA>TGA	p.R921*	FYCO1_uc011bal.1_Nonsense_Mutation_p.R921*	NM_024513	NP_078789	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	921	Potential.				transport	integral to membrane	metal ion binding|protein binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)														---	---	---	---
ALS2CL	259173	broad.mit.edu	37	3	46722765	46722765	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46722765G>A	uc003cqa.1	-	13	1597	c.1407C>T	c.(1405-1407)AGC>AGT	p.S469S	ALS2CL_uc003cpz.1_5'UTR|ALS2CL_uc003cqb.1_Silent_p.S469S|ALS2CL_uc003cqc.1_RNA	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1	469	MORN 5.				endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)														---	---	---	---
ALS2CL	259173	broad.mit.edu	37	3	46722820	46722820	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46722820G>A	uc003cqa.1	-	13	1542	c.1352C>T	c.(1351-1353)CCG>CTG	p.P451L	ALS2CL_uc003cpz.1_5'UTR|ALS2CL_uc003cqb.1_Missense_Mutation_p.P451L|ALS2CL_uc003cqc.1_RNA	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1	451	MORN 4.				endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)														---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47039180	47039180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47039180G>A	uc003cqp.2	+	20	3133	c.2954G>A	c.(2953-2955)CGA>CAA	p.R985Q	NBEAL2_uc010hjm.1_Missense_Mutation_p.R546Q	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	985							binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)														---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47277058	47277058	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47277058G>A	uc010hjp.2	-	21	2871	c.2267C>T	c.(2266-2268)CCT>CTT	p.P756L	KIF9_uc003cqx.2_Missense_Mutation_p.P756L|KIF9_uc003cqy.2_Missense_Mutation_p.P691L|KIF9_uc011bat.1_RNA|uc003cqw.1_Intron	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	756					blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)														---	---	---	---
SCAP	22937	broad.mit.edu	37	3	47460959	47460959	+	Missense_Mutation	SNP	C	T	T	rs150799323		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47460959C>T	uc003crh.1	-	13	2054	c.1799G>A	c.(1798-1800)CGT>CAT	p.R600H	SCAP_uc011baz.1_Missense_Mutation_p.R345H|SCAP_uc003crg.2_Missense_Mutation_p.R208H	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein	600	Lumenal (By similarity).				cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)														---	---	---	---
SHISA5	51246	broad.mit.edu	37	3	48510574	48510574	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48510574C>T	uc003ctp.1	-	6	789	c.655G>A	c.(655-657)GCG>ACG	p.A219T	SHISA5_uc003ctn.1_Missense_Mutation_p.R87H|SHISA5_uc003ctm.1_Missense_Mutation_p.A116T|SHISA5_uc011bbk.1_Missense_Mutation_p.R127H|SHISA5_uc003cto.1_Missense_Mutation_p.A188T|SHISA5_uc003ctq.1_Missense_Mutation_p.A212T|SHISA5_uc003ctr.1_Missense_Mutation_p.A188T|SHISA5_uc003cts.1_Missense_Mutation_p.A188T|SHISA5_uc003ctt.2_3'UTR|SHISA5_uc003ctu.1_RNA|SHISA5_uc011bbl.1_Missense_Mutation_p.A117T	NM_016479	NP_057563	Q8N114	SHSA5_HUMAN	scotin precursor	219	Cytoplasmic (Potential).|Pro-rich.				apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|integral to membrane|nuclear membrane	signal transducer activity|WW domain binding				0																		---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48616652	48616652	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48616652G>A	uc003ctz.2	-	61	5367	c.5366C>T	c.(5365-5367)GCC>GTC	p.A1789V	MIR711_hsa-mir-711|MI0012488_5'Flank	NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1789	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48622168	48622168	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48622168G>A	uc003ctz.2	-	34	4047	c.4046C>T	c.(4045-4047)CCG>CTG	p.P1349L		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1349	Triple-helical region.|Interrupted collagenous region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48630076	48630076	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48630076G>A	uc003ctz.2	-	7	904	c.903C>T	c.(901-903)ACC>ACT	p.T301T		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	301	Nonhelical region (NC1).|Fibronectin type-III 1.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	48965066	48965066	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48965066A>G	uc003cvb.2	+	3	387	c.75A>G	c.(73-75)GAA>GAG	p.E25E	ARIH2_uc003cvc.2_Silent_p.E25E|ARIH2_uc003cvf.2_5'UTR|ARIH2_uc010hkl.2_Silent_p.E25E|ARIH2_uc003cvd.1_Silent_p.E25E|ARIH2_uc003cve.1_Silent_p.E25E	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2	25	Asp/Glu-rich (acidic).|Poly-Glu.				developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)														---	---	---	---
DALRD3	55152	broad.mit.edu	37	3	49055142	49055142	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49055142G>A	uc003cvk.1	-	3	642	c.622C>T	c.(622-624)CTG>TTG	p.L208L	DALRD3_uc003cvl.1_Silent_p.L208L|DALRD3_uc003cvm.1_Silent_p.L41L|DALRD3_uc010hko.1_Silent_p.L41L|DALRD3_uc011bca.1_Silent_p.L208L|NDUFAF3_uc003cvn.2_5'Flank	NM_001009996	NP_001009996	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	208					arginyl-tRNA aminoacylation	cytoplasm	arginine-tRNA ligase activity|ATP binding				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
QARS	5859	broad.mit.edu	37	3	49137410	49137410	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49137410G>A	uc003cvx.2	-	14	1284	c.1279C>T	c.(1279-1281)CGC>TGC	p.R427C	QARS_uc011bcc.1_5'Flank|QARS_uc011bcd.1_Missense_Mutation_p.R282C|QARS_uc003cvy.2_Missense_Mutation_p.R282C|QARS_uc011bce.1_Missense_Mutation_p.R416C	NM_005051	NP_005042	P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	427					glutaminyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|glutamine-tRNA ligase activity|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)													---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49569284	49569284	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49569284G>A	uc003cxc.3	+	3	1758	c.1340G>A	c.(1339-1341)CGC>CAC	p.R447H		NM_004393	NP_004384	Q14118	DAG1_HUMAN	dystroglycan 1 preproprotein	447	Thr-rich.|Mucin-like domain.				cytoskeletal anchoring at plasma membrane|interspecies interaction between organisms|microtubule anchoring|negative regulation of cell migration|negative regulation of MAPKKK cascade|negative regulation of protein kinase B signaling cascade	basement membrane|contractile ring|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|extracellular space|filopodium|integral to membrane|integral to membrane of membrane fraction|lamellipodium|nucleoplasm	actin binding|alpha-actinin binding|calcium ion binding|laminin-1 binding|receptor activity|structural constituent of muscle|tubulin binding|vinculin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50211657	50211657	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50211657G>A	uc003cyj.2	+						SEMA3F_uc003cyk.2_Intron	NM_004186	NP_004177			semaphorin 3F precursor						axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
GNAT1	2779	broad.mit.edu	37	3	50229224	50229224	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50229224C>T	uc003cym.2	+	1	182	c.66C>T	c.(64-66)GAC>GAT	p.D22D	GNAT1_uc003cyl.2_Silent_p.D22D	NM_144499	NP_653082	P11488	GNAT1_HUMAN	rod-type transducin alpha subunit	22					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|negative regulation of cyclic-nucleotide phosphodiesterase activity|rhodopsin mediated phototransduction|sensory perception of umami taste	heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment membrane	acyl binding|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GDP binding|GTP binding|GTPase activity|protein kinase binding|signal transducer activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)														---	---	---	---
HYAL2	8692	broad.mit.edu	37	3	50357443	50357443	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50357443C>T	uc003czu.2	-	2	698	c.478G>A	c.(478-480)GCC>ACC	p.A160T	HYAL2_uc003czx.2_Missense_Mutation_p.A160T|HYAL2_uc003czv.2_Missense_Mutation_p.A160T|HYAL2_uc003czw.2_Missense_Mutation_p.A160T|HYAL2_uc010hlj.2_Missense_Mutation_p.A160T	NM_033158	NP_149348	Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2 precursor	160						anchored to membrane|lysosome|plasma membrane	hyalurononglucosaminidase activity|receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)	Hyaluronidase(DB00070)													---	---	---	---
HYAL2	8692	broad.mit.edu	37	3	50357676	50357676	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50357676C>T	uc003czu.2	-	2	465	c.245G>A	c.(244-246)CGT>CAT	p.R82H	HYAL2_uc003czx.2_Missense_Mutation_p.R82H|HYAL2_uc003czv.2_Missense_Mutation_p.R82H|HYAL2_uc003czw.2_Missense_Mutation_p.R82H|HYAL2_uc010hlj.2_Missense_Mutation_p.R82H	NM_033158	NP_149348	Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2 precursor	82						anchored to membrane|lysosome|plasma membrane	hyalurononglucosaminidase activity|receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)	Hyaluronidase(DB00070)													---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51411901	51411901	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51411901C>T	uc011bds.1	+	50	5318	c.5295C>T	c.(5293-5295)GGC>GGT	p.G1765G		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1765	Ser-rich.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51743292	51743292	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51743292C>T	uc010hlv.2	+	2	532	c.293C>T	c.(292-294)GCG>GTG	p.A98V	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	98	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
PARP3	10039	broad.mit.edu	37	3	51979617	51979617	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51979617A>G	uc003dby.2	+	7	1339	c.968A>G	c.(967-969)AAG>AGG	p.K323R	PARP3_uc003dbz.2_Missense_Mutation_p.K330R	NM_005485	NP_005476	Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	323	PARP catalytic.				DNA repair|protein ADP-ribosylation	centriole|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52387595	52387595	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52387595C>T	uc011bef.1	+	20	3687	c.3426C>T	c.(3424-3426)ATC>ATT	p.I1142I	DNAH1_uc003ddt.1_Silent_p.I1142I	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1142	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52387624	52387624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52387624C>T	uc011bef.1	+	20	3716	c.3455C>T	c.(3454-3456)GCT>GTT	p.A1152V	DNAH1_uc003ddt.1_Missense_Mutation_p.A1152V	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1152	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
NT5DC2	64943	broad.mit.edu	37	3	52562086	52562086	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52562086C>T	uc003deo.2	-	7	1088	c.664G>A	c.(664-666)GCC>ACC	p.A222T	NT5DC2_uc003dem.2_Missense_Mutation_p.A92T|NT5DC2_uc003den.2_Missense_Mutation_p.A259T|NT5DC2_uc010hmi.2_Missense_Mutation_p.A234T|NT5DC2_uc010hmj.2_Missense_Mutation_p.A38T	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2	222							hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)														---	---	---	---
ITIH3	3699	broad.mit.edu	37	3	52841838	52841838	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52841838C>A	uc003dfv.2	+	20	2373	c.2337C>A	c.(2335-2337)CAC>CAA	p.H779Q	ITIH3_uc011bek.1_Missense_Mutation_p.H587Q	NM_002217	NP_002208	Q06033	ITIH3_HUMAN	inter-alpha (globulin) inhibitor H3	779					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53756426	53756426	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53756426G>A	uc003dgv.3	+	12	1754	c.1591G>A	c.(1591-1593)GTC>ATC	p.V531I	CACNA1D_uc003dgu.3_Missense_Mutation_p.V551I|CACNA1D_uc003dgy.3_Missense_Mutation_p.V531I|CACNA1D_uc003dgw.3_Missense_Mutation_p.V198I	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	531	Helical; Name=S1 of repeat II; (Potential).|II.				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
IL17RD	54756	broad.mit.edu	37	3	57131882	57131882	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57131882C>T	uc003dil.2	-	12	1938	c.1849G>A	c.(1849-1851)GAC>AAC	p.D617N	IL17RD_uc003dik.2_Missense_Mutation_p.D593N|IL17RD_uc010hna.2_Missense_Mutation_p.D473N|IL17RD_uc011bex.1_Missense_Mutation_p.D473N	NM_017563	NP_060033	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D precursor	617	Cytoplasmic (Potential).					Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)														---	---	---	---
APPL1	26060	broad.mit.edu	37	3	57291362	57291362	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57291362C>A	uc003dio.2	+	15	1483	c.1336C>A	c.(1336-1338)CTT>ATT	p.L446I	APPL1_uc010hnb.2_Missense_Mutation_p.L446I|APPL1_uc011bey.1_Missense_Mutation_p.L429I	NM_012096	NP_036228	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH	446					apoptosis|cell cycle|cell proliferation|insulin receptor signaling pathway|regulation of apoptosis|regulation of establishment of protein localization in plasma membrane|regulation of glucose import	cytosol|early endosome membrane|microsome|nucleus|vesicle membrane	protein kinase B binding			breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)														---	---	---	---
ASB14	142686	broad.mit.edu	37	3	57310617	57310617	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57310617G>A	uc003diq.2	-	10	1821	c.1233C>T	c.(1231-1233)TAC>TAT	p.Y411Y	ASB14_uc003dip.1_Silent_p.Y290Y	NM_001142733	NP_001136205	A6NK59	ASB14_HUMAN	ankyrin repeat and SOCS box-containing 14	575	SOCS box.				intracellular signal transduction						0				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58083699	58083699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58083699C>T	uc003djj.2	+	7	1307	c.1142C>T	c.(1141-1143)ACG>ATG	p.T381M	FLNB_uc010hne.2_Missense_Mutation_p.T381M|FLNB_uc003djk.2_Missense_Mutation_p.T381M|FLNB_uc010hnf.2_Missense_Mutation_p.T381M|FLNB_uc003djl.2_Missense_Mutation_p.T212M|FLNB_uc003djm.2_Missense_Mutation_p.T212M	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	381	Filamin 2.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60522614	60522614	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60522614T>C	uc003dkx.3	-	5	453	c.82A>G	c.(82-84)AGG>GGG	p.R28G	FHIT_uc003dky.2_Missense_Mutation_p.R28G|FHIT_uc010hnn.1_Missense_Mutation_p.R28G	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene	28	HIT.				nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62535693	62535693	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62535693C>T	uc003dll.2	-	11	2211	c.1851G>A	c.(1849-1851)CAG>CAA	p.Q617Q	CADPS_uc003dlk.1_Silent_p.Q121Q|CADPS_uc003dlm.2_Silent_p.Q617Q|CADPS_uc003dln.2_Silent_p.Q617Q	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	617	PH.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66434530	66434530	+	Silent	SNP	C	A	A	rs141524760	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66434530C>A	uc003dmx.2	-	14	1970	c.1956G>T	c.(1954-1956)CCG>CCT	p.P652P	SLC25A26_uc011bft.1_Intron|LRIG1_uc011bfu.1_Silent_p.P272P|LRIG1_uc003dmw.2_Silent_p.P318P|LRIG1_uc010hnz.2_Silent_p.P368P|LRIG1_uc010hoa.2_Intron	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	652	Extracellular (Potential).|Ig-like C2-type 2.					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)														---	---	---	---
TMF1	7110	broad.mit.edu	37	3	69087803	69087803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69087803C>T	uc003dnn.2	-	8	2310	c.2063G>A	c.(2062-2064)CGT>CAT	p.R688H	TMF1_uc011bfx.1_Missense_Mutation_p.R691H	NM_007114	NP_009045	P82094	TMF1_HUMAN	TATA element modulatory factor 1	688	Potential.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi membrane|nucleus	DNA binding|protein binding|transcription cofactor activity				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)														---	---	---	---
PROS1	5627	broad.mit.edu	37	3	93598107	93598107	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93598107C>T	uc003drb.3	-	13	1885	c.1544G>A	c.(1543-1545)CGT>CAT	p.R515H	PROS1_uc010hoo.2_Missense_Mutation_p.R384H|PROS1_uc003dqz.3_Missense_Mutation_p.R384H	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	515	Laminin G-like 2.		R -> P (in PROS1D).|R -> C (in PROS1D; secretion of the mutant markedly decreased compared with that of the wild-type; intracellular degradation and impaired secretion of the mutant).	R->K: No change in secretion of the mutant.|R->A,E: Markedly reduced secretion of the mutant.	leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)													---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108107843	108107843	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108107843G>A	uc003dxa.1	-	39	5626	c.5569C>T	c.(5569-5571)CGA>TGA	p.R1857*		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1857	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108214654	108214654	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108214654G>T	uc003dxa.1	-	8	801	c.744C>A	c.(742-744)ACC>ACA	p.T248T		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	248	Myosin head-like.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111769576	111769576	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111769576C>T	uc010hqb.2	+	7	941	c.771C>T	c.(769-771)AGC>AGT	p.S257S	TMPRSS7_uc011bhr.1_Silent_p.S112S	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	383	Extracellular (Potential).|CUB 2.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113152416	113152416	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113152416T>C	uc003eae.1	-	2	142	c.96A>G	c.(94-96)TCA>TCG	p.S32S		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	32										central_nervous_system(1)	1																		---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121386917	121386917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121386917G>A	uc003eei.3	-	19	9521	c.9395C>T	c.(9394-9396)CCG>CTG	p.P3132L	GOLGB1_uc010hrc.2_Missense_Mutation_p.P3142L|GOLGB1_uc003eej.3_Missense_Mutation_p.P3098L	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	3132	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
SLC15A2	6565	broad.mit.edu	37	3	121641671	121641671	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121641671G>A	uc003eep.2	+	9	983	c.830G>A	c.(829-831)CGA>CAA	p.R277Q	SLC15A2_uc011bjn.1_Missense_Mutation_p.R246Q	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	277					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)													---	---	---	---
ILDR1	286676	broad.mit.edu	37	3	121725902	121725902	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121725902G>A	uc003ees.2	-	2	271	c.165C>T	c.(163-165)GAC>GAT	p.D55D	ILDR1_uc003eeq.2_Silent_p.D67D|ILDR1_uc003eer.2_Silent_p.D55D|ILDR1_uc010hrg.2_Silent_p.D55D	NM_175924	NP_787120	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor	55	Extracellular (Potential).|Ig-like V-type.					cytosol|integral to membrane|plasma membrane	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.156)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	123987826	123987826	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123987826A>G	uc003ehg.2	+	5	814	c.687A>G	c.(685-687)GAA>GAG	p.E229E	KALRN_uc010hrv.1_Silent_p.E229E|KALRN_uc003ehf.1_Silent_p.E229E|KALRN_uc011bjy.1_Silent_p.E229E	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	229	Spectrin 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124438313	124438313	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124438313C>T	uc003ehg.2	+	60	9084	c.8957C>T	c.(8956-8958)ACG>ATG	p.T2986M	KALRN_uc003ehk.2_Missense_Mutation_p.T1289M	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	2985					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125873470	125873470	+	Missense_Mutation	SNP	G	A	A	rs150865017	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125873470G>A	uc003eim.1	-	6	837	c.647C>T	c.(646-648)CCG>CTG	p.P216L	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc003eio.2_5'UTR|ALDH1L1_uc010hsf.1_Missense_Mutation_p.P242L|ALDH1L1_uc003eip.1_Missense_Mutation_p.P123L|ALDH1L1_uc011bkj.1_Missense_Mutation_p.P41L	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	216					10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)													---	---	---	---
ABTB1	80325	broad.mit.edu	37	3	127395194	127395194	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127395194G>A	uc003ejt.2	+	5	488	c.400G>A	c.(400-402)GGT>AGT	p.G134S	ABTB1_uc003ejr.2_5'UTR|ABTB1_uc003ejs.2_Missense_Mutation_p.G109S|ABTB1_uc003eju.2_5'UTR|ABTB1_uc010hsm.2_5'Flank	NM_172027	NP_742024	Q969K4	ABTB1_HUMAN	ankyrin repeat and BTB (POZ) domain containing 1	134	BTB 1.					cytoplasm|nucleolus|plasma membrane	translation elongation factor activity				0																		---	---	---	---
CCRL1	51554	broad.mit.edu	37	3	132319300	132319300	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132319300G>A	uc003eow.2	+	2	142	c.59G>A	c.(58-60)GGC>GAC	p.G20D	ACAD11_uc003eov.3_Intron|ACAD11_uc011blr.1_Intron|CCRL1_uc003eox.2_Missense_Mutation_p.G20D	NM_016557	NP_057641	Q9NPB9	CCRL1_HUMAN	chemokine (C-C motif) receptor-like 1	20	Extracellular (Potential).				chemotaxis|immune response	integral to plasma membrane	C-C chemokine receptor activity				0																		---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133169162	133169162	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133169162C>T	uc003epn.1	+	4	883	c.745C>T	c.(745-747)CAC>TAC	p.H249Y	uc003epo.2_Intron	NM_003571	NP_003562	Q13515	BFSP2_HUMAN	phakinin	249	Rod.|Potential.				response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
PCCB	5096	broad.mit.edu	37	3	136046547	136046547	+	Silent	SNP	C	T	T	rs140630332		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136046547C>T	uc003eqy.1	+	13	1422	c.1371C>T	c.(1369-1371)ACC>ACT	p.T457T	PCCB_uc003eqz.1_Silent_p.T457T|PCCB_uc011bmc.1_Silent_p.T477T	NM_000532	NP_000523	P05166	PCCB_HUMAN	propionyl Coenzyme A carboxylase, beta	457	Carboxyltransferase.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|propionyl-CoA carboxylase activity				0					Biotin(DB00121)|L-Valine(DB00161)													---	---	---	---
ESYT3	83850	broad.mit.edu	37	3	138183273	138183273	+	Silent	SNP	C	T	T	rs138220144		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138183273C>T	uc003esk.2	+	9	1228	c.1002C>T	c.(1000-1002)TAC>TAT	p.Y334Y	ESYT3_uc010hug.2_RNA	NM_031913	NP_114119	A0FGR9	ESYT3_HUMAN	family with sequence similarity 62 (C2 domain	334	C2 1.					integral to membrane|plasma membrane					0																		---	---	---	---
COPB2	9276	broad.mit.edu	37	3	139098223	139098223	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139098223G>A	uc003etf.3	-	3	357	c.227C>T	c.(226-228)GCG>GTG	p.A76V	COPB2_uc011bmv.1_Missense_Mutation_p.A47V|COPB2_uc010hui.2_Missense_Mutation_p.A47V|COPB2_uc011bmw.1_Missense_Mutation_p.A76V	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta	76	WD 2.				COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141291993	141291993	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141291993G>A	uc003etz.1	+	13	1289	c.1289G>A	c.(1288-1290)TGT>TAT	p.C430Y	RASA2_uc010huq.1_Missense_Mutation_p.C430Y|RASA2_uc003eua.1_Missense_Mutation_p.C430Y|RASA2_uc011bnc.1_Missense_Mutation_p.C22Y	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	430	Ras-GAP.				intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6																		---	---	---	---
CPB1	1360	broad.mit.edu	37	3	148545855	148545855	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148545855C>T	uc003ewl.2	+	2	161	c.138C>T	c.(136-138)AGC>AGT	p.S46S		NM_001871	NP_001862	P15086	CBPB1_HUMAN	pancreatic carboxypeptidase B1 preproprotein	46					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)															---	---	---	---
HPS3	84343	broad.mit.edu	37	3	148868446	148868446	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148868446G>A	uc003ewu.1	+	6	1364	c.1224G>A	c.(1222-1224)CCG>CCA	p.P408P	HPS3_uc003ewt.1_Silent_p.P408P|HPS3_uc011bnq.1_Silent_p.P243P	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein	408						cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											Hermansky-Pudlak_syndrome				---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150903217	150903217	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150903217T>C	uc003eyp.2	+	11	1633	c.1595T>C	c.(1594-1596)CTG>CCG	p.L532P	MED12L_uc011bnz.1_Missense_Mutation_p.L392P|MED12L_uc003eyn.2_Missense_Mutation_p.L532P|MED12L_uc003eyo.2_Missense_Mutation_p.L532P	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	532					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151072917	151072917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151072917G>A	uc003eyp.2	+	16	2340	c.2302G>A	c.(2302-2304)GAA>AAA	p.E768K	MED12L_uc011bnz.1_Missense_Mutation_p.E628K|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_5'Flank	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	768					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	159998531	159998531	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159998531T>A	uc011boy.1	-	15	2021	c.1588A>T	c.(1588-1590)ATA>TTA	p.I530L	IFT80_uc003fda.2_RNA|IFT80_uc003fdb.1_Missense_Mutation_p.I393L|IFT80_uc003fdd.1_Missense_Mutation_p.I213L|IFT80_uc003fde.1_Missense_Mutation_p.I393L	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56	530	WD 7.					cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167023706	167023706	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167023706C>T	uc003fep.2	-	17	1773	c.1450G>A	c.(1450-1452)GTG>ATG	p.V484M	ZBBX_uc011bpc.1_Missense_Mutation_p.V484M|ZBBX_uc003feq.2_Missense_Mutation_p.V455M	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	484						intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
LRRIQ4	344657	broad.mit.edu	37	3	169540471	169540471	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169540471C>T	uc003fgb.2	+	1	762	c.762C>T	c.(760-762)GCC>GCT	p.A254A		NM_001080460	NP_001073929	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	254	LRR 10.										0																		---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169981187	169981187	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169981187C>T	uc003fgs.2	+	4	572	c.334C>T	c.(334-336)CGT>TGT	p.R112C		NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota	112	Regulatory domain.				anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
GNB4	59345	broad.mit.edu	37	3	179138685	179138685	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179138685G>T	uc003fjv.3	-	3	368	c.88C>A	c.(88-90)CTT>ATT	p.L30I		NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4	30					cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)															---	---	---	---
FXR1	8087	broad.mit.edu	37	3	180693950	180693950	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180693950C>T	uc003fkq.2	+	17	1758	c.1736C>T	c.(1735-1737)GCA>GTA	p.A579V	FXR1_uc003fkp.2_Missense_Mutation_p.A494V|FXR1_uc003fkr.2_3'UTR|FXR1_uc011bqj.1_3'UTR|FXR1_uc003fks.2_Missense_Mutation_p.A522V|FXR1_uc011bqk.1_3'UTR|FXR1_uc011bql.1_Missense_Mutation_p.A566V	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	579					apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)															---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	183056658	183056658	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183056658C>A	uc003fli.1	-	5	506	c.416G>T	c.(415-417)CGC>CTC	p.R139L	MCF2L2_uc003flj.1_Missense_Mutation_p.R139L|MCF2L2_uc003flp.1_Missense_Mutation_p.R174L	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	139	CRAL-TRIO.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
KLHL24	54800	broad.mit.edu	37	3	183381293	183381293	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183381293G>A	uc003flv.2	+	4	1263	c.968G>A	c.(967-969)CGA>CAA	p.R323Q	KLHL24_uc003flw.2_Missense_Mutation_p.R323Q|KLHL24_uc003flx.2_Missense_Mutation_p.R323Q	NM_017644	NP_060114	Q6TFL4	KLH24_HUMAN	DRE1 protein	323	Kelch 1.					axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184043061	184043061	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184043061G>A	uc003fnp.2	+	19	3059	c.2861G>A	c.(2860-2862)CGA>CAA	p.R954Q	EIF4G1_uc003fno.1_Missense_Mutation_p.R895Q|EIF4G1_uc010hxw.1_Missense_Mutation_p.R790Q|EIF4G1_uc003fnt.2_Missense_Mutation_p.R665Q|EIF4G1_uc003fnq.2_Missense_Mutation_p.R867Q|EIF4G1_uc003fnr.2_Missense_Mutation_p.R790Q|EIF4G1_uc010hxx.2_Missense_Mutation_p.R961Q|EIF4G1_uc003fns.2_Missense_Mutation_p.R914Q|EIF4G1_uc010hxy.2_Missense_Mutation_p.R961Q|EIF4G1_uc003fnv.3_Missense_Mutation_p.R955Q|EIF4G1_uc003fnu.3_Missense_Mutation_p.R954Q|EIF4G1_uc003fnw.2_Missense_Mutation_p.R961Q|EIF4G1_uc003fnx.2_Missense_Mutation_p.R759Q|EIF4G1_uc003fny.3_Missense_Mutation_p.R758Q|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	954	eIF3/EIF4A-binding.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
MAP3K13	9175	broad.mit.edu	37	3	185198261	185198261	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185198261C>T	uc010hyf.2	+	14	3009	c.2743C>T	c.(2743-2745)CGT>TGT	p.R915C	MAP3K13_uc011brt.1_Missense_Mutation_p.R708C|MAP3K13_uc011bru.1_Missense_Mutation_p.R771C|MAP3K13_uc003fpi.2_Missense_Mutation_p.R915C|MAP3K13_uc010hyg.2_Missense_Mutation_p.R605C	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase	915					activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)															---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195495991	195495991	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195495991G>A	uc011bto.1	-	8	13507	c.13047C>T	c.(13045-13047)GAC>GAT	p.D4349D	MUC4_uc003fuz.2_Missense_Mutation_p.T105M|MUC4_uc003fva.2_Translation_Start_Site|MUC4_uc003fvb.2_Missense_Mutation_p.T23M|MUC4_uc003fvc.2_RNA|MUC4_uc003fvd.2_RNA|MUC4_uc003fve.2_Missense_Mutation_p.T23M|MUC4_uc010hzr.2_RNA|MUC4_uc011btf.1_Translation_Start_Site|MUC4_uc011btg.1_RNA|MUC4_uc011bth.1_Silent_p.D41D|MUC4_uc011bti.1_Silent_p.D41D|MUC4_uc011btj.1_Silent_p.D218D|MUC4_uc011btk.1_Translation_Start_Site|MUC4_uc011btl.1_Translation_Start_Site|MUC4_uc011btm.1_Silent_p.D166D|MUC4_uc011btn.1_Translation_Start_Site|MUC4_uc003fvo.2_Silent_p.D241D|MUC4_uc003fvp.2_Silent_p.D190D|MUC4_uc010hzu.1_Silent_p.D1089D	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1234	NIDO.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)														---	---	---	---
RNF168	165918	broad.mit.edu	37	3	196198985	196198985	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196198985T>C	uc003fwq.2	-	6	1959	c.1421A>G	c.(1420-1422)TAT>TGT	p.Y474C	RNF168_uc010iah.2_Missense_Mutation_p.Y307C|uc010iag.1_5'Flank	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	474					double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)														---	---	---	---
RNF168	165918	broad.mit.edu	37	3	196199175	196199175	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196199175A>G	uc003fwq.2	-	6	1769	c.1231T>C	c.(1231-1233)TCC>CCC	p.S411P	RNF168_uc010iah.2_Missense_Mutation_p.S244P|uc010iag.1_5'Flank	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	411					double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)														---	---	---	---
SENP5	205564	broad.mit.edu	37	3	196613556	196613556	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196613556T>A	uc003fwz.3	+	2	1753	c.1504T>A	c.(1504-1506)TGT>AGT	p.C502S	SENP5_uc011bty.1_Missense_Mutation_p.C502S	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	502					cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196803463	196803463	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196803463C>T	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Missense_Mutation_p.A700T|DLG1_uc011bue.1_Missense_Mutation_p.A666T|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_RNA	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
MFSD7	84179	broad.mit.edu	37	4	680325	680325	+	Missense_Mutation	SNP	G	A	A	rs139449222		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:680325G>A	uc003gay.2	-	2	347	c.290C>T	c.(289-291)GCG>GTG	p.A97V	MFSD7_uc003gaw.2_5'Flank|MFSD7_uc003gax.2_Missense_Mutation_p.A97V|MFSD7_uc003gaz.2_Missense_Mutation_p.A75V|MFSD7_uc003gba.2_Missense_Mutation_p.A97V|MFSD7_uc003gbb.1_Missense_Mutation_p.A33V	NM_032219	NP_115595	Q6UXD7	MFSD7_HUMAN	major facilitator superfamily domain containing	97					transmembrane transport	integral to membrane					0																		---	---	---	---
KIAA1530	57654	broad.mit.edu	37	4	1374753	1374753	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1374753A>G	uc003gde.3	+	12	2285	c.1838A>G	c.(1837-1839)CAG>CGG	p.Q613R	KIAA1530_uc010ibv.2_Missense_Mutation_p.Q164R	NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654	613											0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
ADD1	118	broad.mit.edu	37	4	2930073	2930073	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2930073C>T	uc003gfr.2	+	15	2225	c.2037C>T	c.(2035-2037)CCC>CCT	p.P679P	ADD1_uc003gfn.2_RNA|ADD1_uc003gfo.2_3'UTR|ADD1_uc003gfp.2_3'UTR|ADD1_uc003gfq.2_Silent_p.P710P|ADD1_uc003gfs.2_3'UTR	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	679					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
HTT	3064	broad.mit.edu	37	4	3225825	3225825	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3225825G>A	uc011bvq.1	+	57	7883	c.7738G>A	c.(7738-7740)GAT>AAT	p.D2580N		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	2578					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3419262	3419262	+	Missense_Mutation	SNP	G	A	A	rs138449809		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3419262G>A	uc003ggw.2	+	9	3659	c.2755G>A	c.(2755-2757)GCA>ACA	p.A919T	RGS12_uc010ics.1_Missense_Mutation_p.A118T|RGS12_uc003ggv.2_Missense_Mutation_p.A919T|RGS12_uc003ggy.1_Missense_Mutation_p.A317T|RGS12_uc010ict.1_Missense_Mutation_p.A271T|RGS12_uc003ggz.2_Missense_Mutation_p.A271T|RGS12_uc010icu.1_Missense_Mutation_p.A118T|RGS12_uc011bvs.1_Missense_Mutation_p.A261T|RGS12_uc003gha.2_Missense_Mutation_p.A261T|RGS12_uc010icv.2_Missense_Mutation_p.A118T|RGS12_uc003ghb.2_Missense_Mutation_p.A118T	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	919						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
EVC	2121	broad.mit.edu	37	4	5754733	5754733	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5754733G>A	uc003gil.1	+	9	1453	c.1269G>A	c.(1267-1269)ACG>ACA	p.T423T	EVC_uc003gim.1_RNA|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	423					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5862854	5862854	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5862854T>A	uc003gip.2	-	4	313	c.212A>T	c.(211-213)GAT>GTT	p.D71V	CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Missense_Mutation_p.D71V|CRMP1_uc003gir.2_Missense_Mutation_p.D66V|CRMP1_uc003gis.2_Missense_Mutation_p.D185V	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2	71					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
CPZ	8532	broad.mit.edu	37	4	8620243	8620243	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8620243G>A	uc003glm.2	+	10	1717	c.1591G>A	c.(1591-1593)GAC>AAC	p.D531N	CPZ_uc003gll.2_RNA|CPZ_uc003gln.2_Missense_Mutation_p.D394N|CPZ_uc003glo.2_Missense_Mutation_p.D520N|CPZ_uc003glp.2_RNA	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	531					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13605148	13605148	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13605148G>T	uc003gmz.1	-	10	3493	c.3376C>A	c.(3376-3378)CCA>ACA	p.P1126T	BOD1L_uc010idr.1_Missense_Mutation_p.P463T	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1126							DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13606438	13606438	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13606438T>G	uc003gmz.1	-	10	2203	c.2086A>C	c.(2086-2088)ACA>CCA	p.T696P	BOD1L_uc010idr.1_Missense_Mutation_p.T33P	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	696	Lys-rich.						DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
QDPR	5860	broad.mit.edu	37	4	17493871	17493871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17493871C>T	uc003gpd.2	-	5	709	c.529G>A	c.(529-531)GCC>ACC	p.A177T	QDPR_uc003gpe.2_Missense_Mutation_p.A146T|QDPR_uc003gpf.2_Intron	NM_000320	NP_000311	P09417	DHPR_HUMAN	quinoid dihydropteridine reductase	177					dihydrobiopterin metabolic process|L-phenylalanine catabolic process|tetrahydrobiopterin biosynthetic process	cytosol	6,7-dihydropteridine reductase activity|binding|electron carrier activity			ovary(1)	1					NADH(DB00157)													---	---	---	---
NCAPG	64151	broad.mit.edu	37	4	17839403	17839403	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17839403C>A	uc003gpp.2	+	16	2621	c.2445C>A	c.(2443-2445)GCC>GCA	p.A815A	NCAPG_uc011bxj.1_Silent_p.A324A	NM_022346	NP_071741	Q9BPX3	CND3_HUMAN	chromosome condensation protein G	815					cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)														---	---	---	---
PPARGC1A	10891	broad.mit.edu	37	4	23815951	23815951	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23815951G>C	uc003gqs.2	-	8	1275	c.1155C>G	c.(1153-1155)GAC>GAG	p.D385E	PPARGC1A_uc003gqt.2_RNA|PPARGC1A_uc011bxp.1_RNA|PPARGC1A_uc010ier.1_RNA	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor	385					androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)																---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25382072	25382072	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25382072C>T	uc003gro.2	+	3	335	c.206C>T	c.(205-207)ACG>ATG	p.T69M	ANAPC4_uc003grp.2_5'Flank	NM_013367	NP_037499	Q9UJX5	APC4_HUMAN	anaphase-promoting complex subunit 4	69					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	38117394	38117394	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38117394A>G	uc003gtb.2	+	16	2964	c.2621A>G	c.(2620-2622)TAC>TGC	p.Y874C	TBC1D1_uc011byd.1_Missense_Mutation_p.Y968C|TBC1D1_uc010ifd.2_Missense_Mutation_p.Y661C	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,	874	Rab-GAP TBC.					nucleus	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	55139789	55139789	+	Missense_Mutation	SNP	G	A	A	rs149031291	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55139789G>A	uc003han.3	+	10	1781	c.1450G>A	c.(1450-1452)GTG>ATG	p.V484M	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Missense_Mutation_p.V378M|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	484	Ig-like C2-type 5.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			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)			---	---	---	---
KDR	3791	broad.mit.edu	37	4	55974003	55974003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55974003C>T	uc003has.2	-	10	1615	c.1313G>A	c.(1312-1314)GGC>GAC	p.G438D	KDR_uc003hat.1_Missense_Mutation_p.G438D|KDR_uc011bzx.1_Missense_Mutation_p.G438D	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	438	Ig-like C2-type 5.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62813808	62813808	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62813808T>C	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68566816	68566816	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68566816C>T	uc003hdg.3	-	1	74	c.22G>A	c.(22-24)GCC>ACC	p.A8T	UBA6_uc003hdi.2_Missense_Mutation_p.A8T|UBA6_uc003hdj.2_Missense_Mutation_p.A8T|LOC550112_uc003hdl.3_5'Flank|LOC550112_uc003hdk.2_5'Flank	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2	8					protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0																OREG0016213	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69179917	69179917	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69179917C>T	uc003hdx.2	-	17	2437	c.2084G>A	c.(2083-2085)CGA>CAA	p.R695Q	YTHDC1_uc003hdy.2_Missense_Mutation_p.R677Q	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	695	Arg-rich.									upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69343176	69343176	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69343176A>G	uc003hdz.3	+	8	861	c.797A>G	c.(796-798)CAT>CGT	p.H266R		NM_014058	NP_054777			transmembrane protease, serine 11E																														---	---	---	---
UGT2B28	54490	broad.mit.edu	37	4	70152481	70152481	+	Silent	SNP	A	G	G	rs141618560		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70152481A>G	uc003hej.2	+	3	884	c.882A>G	c.(880-882)GAA>GAG	p.E294E	UGT2B28_uc010ihr.2_Silent_p.E294E	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	294					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)													---	---	---	---
SMR3A	26952	broad.mit.edu	37	4	71232663	71232663	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71232663C>T	uc003hfg.1	+	3	438	c.357C>T	c.(355-357)TTC>TTT	p.F119F	SMR3B_uc011cas.1_Intron	NM_012390	NP_036522	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3	119	Pro-rich.					extracellular region					0		all_hematologic(202;0.196)																---	---	---	---
NPFFR2	10886	broad.mit.edu	37	4	73013380	73013380	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73013380C>T	uc003hgg.2	+	4	1518	c.1420C>T	c.(1420-1422)CTC>TTC	p.L474F	NPFFR2_uc010iig.1_Missense_Mutation_p.L256F|NPFFR2_uc003hgi.2_Missense_Mutation_p.L375F|NPFFR2_uc003hgh.2_Missense_Mutation_p.L372F|NPFFR2_uc003hgj.2_RNA	NM_004885	NP_004876	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	474	Cytoplasmic (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)															---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73164158	73164158	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73164158A>T	uc003hgk.1	-	18	2463	c.2426T>A	c.(2425-2427)ATT>AAT	p.I809N	ADAMTS3_uc003hgl.2_Missense_Mutation_p.I150N	NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	809	Spacer.				collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
CDKL2	8999	broad.mit.edu	37	4	76522214	76522214	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76522214G>A	uc003hiq.2	-	9	1752	c.1227C>T	c.(1225-1227)AGC>AGT	p.S409S	CDKL2_uc011cbp.1_Silent_p.S409S	NM_003948	NP_003939	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2	409					sex differentiation|signal transduction	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(2)|stomach(2)|breast(2)|skin(1)	7			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
CCDC158	339965	broad.mit.edu	37	4	77244550	77244550	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77244550G>A	uc003hkb.3	-	23	3323	c.3170C>T	c.(3169-3171)CCG>CTG	p.P1057L		NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	1057										skin(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
CCDC158	339965	broad.mit.edu	37	4	77300522	77300522	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77300522C>T	uc003hkb.3	-	8	1103	c.950G>A	c.(949-951)CGT>CAT	p.R317H	CCDC158_uc003hkd.2_Missense_Mutation_p.R317H	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	317	Potential.									skin(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77661450	77661450	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77661450C>T	uc011cbx.1	+	5	3077	c.2124C>T	c.(2122-2124)GCC>GCT	p.A708A	SHROOM3_uc011cbz.1_Silent_p.A532A|SHROOM3_uc003hkf.1_Silent_p.A583A|SHROOM3_uc003hkg.2_Silent_p.A486A	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein	708					apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)															---	---	---	---
SEPT11	55752	broad.mit.edu	37	4	77951964	77951964	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77951964G>A	uc003hkj.2	+	9	1277	c.1115G>A	c.(1114-1116)CGG>CAG	p.R372Q	SEPT11_uc010ijh.1_Missense_Mutation_p.R364Q|SEPT11_uc011cca.1_Missense_Mutation_p.R382Q	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11	372	Potential.				cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0																		---	---	---	---
ANXA3	306	broad.mit.edu	37	4	79522683	79522683	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79522683G>A	uc003hld.2	+	11	1060	c.750G>A	c.(748-750)ACG>ACA	p.T250T	ANXA3_uc003hle.2_Silent_p.T211T|ANXA3_uc010ijk.2_Silent_p.T211T	NM_005139	NP_005130	P12429	ANXA3_HUMAN	annexin A3	250					defense response to bacterium|neutrophil degranulation|phagocytosis|positive regulation of angiogenesis|positive regulation of endothelial cell migration|positive regulation of sequence-specific DNA binding transcription factor activity	phagocytic vesicle membrane|plasma membrane|specific granule	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity				0																		---	---	---	---
BMP2K	55589	broad.mit.edu	37	4	79832300	79832300	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79832300C>T	uc003hlk.2	+	16	2765	c.2599C>T	c.(2599-2601)CGT>TGT	p.R867C	PAQR3_uc003hlm.2_Intron|PAQR3_uc003hln.2_Intron|uc010ijm.1_5'Flank	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	867						nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1																		---	---	---	---
AGPAT9	84803	broad.mit.edu	37	4	84516016	84516016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84516016G>A	uc003how.2	+	8	975	c.757G>A	c.(757-759)GGC>AGC	p.G253S	AGPAT9_uc003hox.2_Missense_Mutation_p.G253S|AGPAT9_uc003hoy.2_Missense_Mutation_p.G253S	NM_032717	NP_116106	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	253					phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)																---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85654553	85654553	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85654553C>T	uc003hpd.2	-	44	7611	c.7203G>A	c.(7201-7203)GAG>GAA	p.E2401E	WDFY3_uc003hpe.1_Silent_p.E29E	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2401						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87703387	87703387	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87703387C>T	uc003hpz.2	+	37	6476	c.5996C>T	c.(5995-5997)GCC>GTC	p.A1999V	PTPN13_uc003hpy.2_Missense_Mutation_p.A2004V|PTPN13_uc003hqa.2_Missense_Mutation_p.A1980V|PTPN13_uc003hqb.2_Missense_Mutation_p.A1808V|PTPN13_uc003hqc.1_Missense_Mutation_p.A365V	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1999						cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
PKD2	5311	broad.mit.edu	37	4	88996790	88996790	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88996790T>A	uc003hre.2	+	15	2917	c.2851T>A	c.(2851-2853)TCT>ACT	p.S951T	PKD2_uc011cdf.1_Missense_Mutation_p.S369T|PKD2_uc011cdg.1_Missense_Mutation_p.S277T|PKD2_uc011cdh.1_Missense_Mutation_p.S174T	NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	951	C-terminal coiled coil domain.|Cytoplasmic (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity			skin(1)	1		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96104149	96104149	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96104149C>A	uc003htp.1	-	14	2504	c.2350G>T	c.(2350-2352)GAA>TAA	p.E784*		NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor	784	Cytoplasmic (Potential).				apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109546305	109546305	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109546305C>A	uc003hyz.2	+	5	335	c.291C>A	c.(289-291)ATC>ATA	p.I97I	RPL34_uc003hza.2_Silent_p.I97I	NM_000995	NP_000986	P49207	RL34_HUMAN	ribosomal protein L34	97					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109782136	109782136	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109782136G>A	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
NEUROG2	63973	broad.mit.edu	37	4	113436274	113436274	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113436274G>A	uc003ias.2	-	2	685	c.358C>T	c.(358-360)CGC>TGC	p.R120C		NM_024019	NP_076924	Q9H2A3	NGN2_HUMAN	neurogenin 2	120	Helix-loop-helix motif.				positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nucleus	E-box binding			skin(2)|central_nervous_system(1)	3		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114204012	114204012	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114204012T>A	uc003ibe.3	+	18	2163	c.2063T>A	c.(2062-2064)ATC>AAC	p.I688N	ANK2_uc003ibd.3_Missense_Mutation_p.I667N|ANK2_uc003ibf.3_Missense_Mutation_p.I688N|ANK2_uc003ibc.2_Missense_Mutation_p.I664N|ANK2_uc011cgb.1_Missense_Mutation_p.I703N	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	688	ANK 20.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114278302	114278302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114278302G>A	uc003ibe.3	+	38	8628	c.8528G>A	c.(8527-8529)AGC>AAC	p.S2843N	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Missense_Mutation_p.S145N|ANK2_uc011cgb.1_Missense_Mutation_p.S2858N	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	2810					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
EXOSC9	5393	broad.mit.edu	37	4	122734401	122734401	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122734401A>G	uc003iea.2	+	9	948	c.840A>G	c.(838-840)GGA>GGG	p.G280G	EXOSC9_uc003idz.2_Silent_p.G280G|EXOSC9_uc003ieb.2_Silent_p.G264G|EXOSC9_uc010inp.1_Intron	NM_005033	NP_005024	Q06265	EXOS9_HUMAN	exosome component 9 isoform 2	280					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|immune response|nuclear mRNA surveillance|nuclear polyadenylation-dependent rRNA catabolic process|positive regulation of cell growth|rRNA processing	cytosol|nuclear exosome (RNase complex)|nucleolus|nucleolus|nucleus	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0																		---	---	---	---
TRPC3	7222	broad.mit.edu	37	4	122853733	122853733	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122853733C>T	uc003ieg.2	-	2	754	c.680G>A	c.(679-681)GGC>GAC	p.G227D	TRPC3_uc010inr.2_Missense_Mutation_p.G154D|TRPC3_uc003ief.2_Missense_Mutation_p.G154D|TRPC3_uc011cgl.1_5'UTR	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	142	Cytoplasmic (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126239097	126239097	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126239097C>T	uc003ifj.3	+	1	1531	c.1531C>T	c.(1531-1533)CGT>TGT	p.R511C		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	511	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ABCE1	6059	broad.mit.edu	37	4	146044515	146044515	+	Intron	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146044515T>A	uc003ijx.2	+						ABCE1_uc003ijy.2_Intron|ABCE1_uc010iot.2_Intron	NM_001040876	NP_001035809			ATP-binding cassette, sub-family E, member 1						interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)																	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146767114	146767114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146767114G>A	uc003ikn.2	-	7	2321	c.2273C>T	c.(2272-2274)ACG>ATG	p.T758M	ZNF827_uc003ikm.2_Missense_Mutation_p.T758M|ZNF827_uc010iox.2_Missense_Mutation_p.T408M	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	758					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
SLC10A7	84068	broad.mit.edu	37	4	147363889	147363889	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147363889A>G	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron|SLC10A7_uc003ikt.2_3'UTR	NM_001029998	NP_001025169			solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)																	---	---	---	---
MAB21L2	10586	broad.mit.edu	37	4	151504472	151504472	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151504472C>T	uc003ilw.2	+	1	1396	c.291C>T	c.(289-291)TGC>TGT	p.C97C	LRBA_uc003ils.3_5'Flank|LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron|LRBA_uc010ipj.2_Intron	NM_006439	NP_006430	Q9Y586	MB212_HUMAN	mab-21-like protein 2	97					nervous system development	nucleus				ovary(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)														---	---	---	---
PET112L	5188	broad.mit.edu	37	4	152629194	152629194	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152629194C>T	uc003iml.2	-	6	835	c.823G>A	c.(823-825)GTT>ATT	p.V275I	PET112L_uc003imm.3_Missense_Mutation_p.V275I	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like precursor	275						mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
FHDC1	85462	broad.mit.edu	37	4	153896089	153896089	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153896089G>A	uc003inf.2	+	11	1721	c.1646G>A	c.(1645-1647)CGG>CAG	p.R549Q		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	549					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)																	---	---	---	---
FHDC1	85462	broad.mit.edu	37	4	153896754	153896754	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153896754T>C	uc003inf.2	+	11	2386	c.2311T>C	c.(2311-2313)TTC>CTC	p.F771L		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	771					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)																	---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154641355	154641355	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154641355T>C	uc003int.2	-	6	984	c.611A>G	c.(610-612)TAC>TGC	p.Y204C	RNF175_uc003inu.1_Missense_Mutation_p.Y76C	NM_173662	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	204						integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
FGA	2243	broad.mit.edu	37	4	155507743	155507743	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155507743C>T	uc003iod.1	-	5	896	c.838G>A	c.(838-840)GGA>AGA	p.G280R	FGA_uc003ioe.1_Missense_Mutation_p.G280R|FGA_uc003iof.1_Intron	NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	280	By similarity.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)													---	---	---	---
GUCY1B3	2983	broad.mit.edu	37	4	156716546	156716546	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156716546T>A	uc003ipc.2	+	7	947	c.780T>A	c.(778-780)CAT>CAA	p.H260Q	GUCY1B3_uc011cio.1_Missense_Mutation_p.H282Q|GUCY1B3_uc011cip.1_Missense_Mutation_p.H240Q|GUCY1B3_uc003ipd.2_Missense_Mutation_p.H188Q|GUCY1B3_uc010iqf.2_Missense_Mutation_p.H260Q|GUCY1B3_uc010iqg.2_Missense_Mutation_p.H188Q|GUCY1B3_uc011ciq.1_Missense_Mutation_p.H188Q	NM_000857	NP_000848	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	260					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble|intracellular membrane-bounded organelle	GTP binding|guanylate cyclase activity|receptor activity				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)														---	---	---	---
FNIP2	57600	broad.mit.edu	37	4	159825650	159825650	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159825650C>T	uc003iqe.3	+	17	3482	c.3299C>T	c.(3298-3300)GCT>GTT	p.A1100V	C4orf45_uc003iqf.1_Intron|C4orf45_uc010iqt.1_Intron	NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	1100					DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)														---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160277233	160277233	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160277233C>A	uc003iqg.3	+	23	4707	c.4397C>A	c.(4396-4398)CCT>CAT	p.P1466H		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1466					cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
C4orf43	55319	broad.mit.edu	37	4	164436538	164436538	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164436538C>T	uc003iqq.3	+	5	594	c.313C>T	c.(313-315)CGG>TGG	p.R105W		NM_018352	NP_060822	Q96EY4	CD043_HUMAN	hypothetical protein LOC55319	105											0																		---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183664402	183664402	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183664402G>A	uc003ivd.1	+	18	3496	c.3459G>A	c.(3457-3459)GGG>GGA	p.G1153G	ODZ3_uc003ive.1_Silent_p.G559G	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	1153	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
RWDD4A	201965	broad.mit.edu	37	4	184572139	184572139	+	Missense_Mutation	SNP	C	T	T	rs140946722		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184572139C>T	uc003ivt.1	-	4	587	c.361G>A	c.(361-363)GCA>ACA	p.A121T	RWDD4A_uc003ivu.1_RNA|RWDD4A_uc003ivv.1_Missense_Mutation_p.A58T|RWDD4A_uc011ckl.1_RNA	NM_152682	NP_689895	Q6NW29	RWDD4_HUMAN	RWD domain containing 4A	121											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;7.35e-27)|Epithelial(43;1.49e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.76e-10)|GBM - Glioblastoma multiforme(59;5.54e-06)|Colorectal(24;7.92e-06)|STAD - Stomach adenocarcinoma(60;2.35e-05)|COAD - Colon adenocarcinoma(29;6.26e-05)|LUSC - Lung squamous cell carcinoma(40;0.00935)|READ - Rectum adenocarcinoma(43;0.166)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186545136	186545136	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186545136G>A	uc003iyl.2	-	13	2293	c.1435C>T	c.(1435-1437)CAG>TAG	p.Q479*	SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Nonsense_Mutation_p.Q579*|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Nonsense_Mutation_p.Q383*|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Nonsense_Mutation_p.Q593*|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	479						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
CYP4V2	285440	broad.mit.edu	37	4	187118206	187118206	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187118206A>T	uc003iyw.3	+	4	830	c.526A>T	c.(526-528)AAA>TAA	p.K176*		NM_207352	NP_997235	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily v,	176					response to stimulus|visual perception	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187540563	187540563	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187540563G>A	uc003izf.2	-	10	7365	c.7177C>T	c.(7177-7179)CAG>TAG	p.Q2393*		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2393	Extracellular (Potential).|Cadherin 22.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
EXOC3	11336	broad.mit.edu	37	5	462121	462121	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:462121C>T	uc003jba.2	+	8	1566	c.1438C>T	c.(1438-1440)CGG>TGG	p.R480W		NM_007277	NP_009208	O60645	EXOC3_HUMAN	Sec6 protein	491					exocytosis|protein transport						0		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	482779	482779	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:482779G>A	uc003jbe.2	-	7	1352	c.1240C>T	c.(1240-1242)CTG>TTG	p.L414L	SLC9A3_uc011clx.1_Silent_p.L414L	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	414						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)															---	---	---	---
BRD9	65980	broad.mit.edu	37	5	865557	865557	+	Silent	SNP	G	A	A	rs146244980	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:865557G>A	uc003jbq.2	-	15	1832	c.1665C>T	c.(1663-1665)AAC>AAT	p.N555N	BRD9_uc003jbl.2_Silent_p.N439N|BRD9_uc003jbm.2_RNA|BRD9_uc003jbn.2_RNA|BRD9_uc011cmb.1_Silent_p.N502N|BRD9_uc003jbo.2_Silent_p.N459N	NM_023924	NP_076413	Q9H8M2	BRD9_HUMAN	bromodomain containing 9 isoform 1	555							nucleic acid binding				0			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)															---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1053577	1053577	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1053577C>T	uc003jbu.2	-	23	3113	c.3047G>A	c.(3046-3048)CGG>CAG	p.R1016Q		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	1016	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)													---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1081824	1081824	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1081824A>T	uc003jbu.2	-	9	1231	c.1165T>A	c.(1165-1167)TTT>ATT	p.F389I		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	389					potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)													---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7709395	7709395	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7709395G>A	uc003jdz.1	+	10	1540	c.1473G>A	c.(1471-1473)TCG>TCA	p.S491S	ADCY2_uc011cmo.1_Silent_p.S311S	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	491	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7709437	7709437	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7709437G>A	uc003jdz.1	+	10	1582	c.1515G>A	c.(1513-1515)AAG>AAA	p.K505K	ADCY2_uc011cmo.1_Silent_p.K325K	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	505	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9066571	9066571	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9066571T>C	uc003jek.2	-	17	2973	c.2261A>G	c.(2260-2262)TAC>TGC	p.Y754C		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	754	TSP type-1 4.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	10973659	10973659	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10973659C>A	uc003jfa.1	-	22	3729	c.3584G>T	c.(3583-3585)GGC>GTC	p.G1195V	CTNND2_uc010itt.2_Missense_Mutation_p.G1104V|CTNND2_uc011cmy.1_Missense_Mutation_p.G858V|CTNND2_uc011cmz.1_Missense_Mutation_p.G762V|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Missense_Mutation_p.G787V	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1195					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33576262	33576262	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33576262G>A	uc003jia.1	-	19	4032	c.3869C>T	c.(3868-3870)GCA>GTA	p.A1290V	ADAMTS12_uc010iuq.1_Missense_Mutation_p.A1205V	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1290	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
UGT3A1	133688	broad.mit.edu	37	5	35991338	35991338	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35991338A>G	uc003jjv.1	-	1	162	c.5T>C	c.(4-6)GTT>GCT	p.V2A	UGT3A1_uc003jjw.1_RNA|UGT3A1_uc011coq.1_Missense_Mutation_p.V2A|UGT3A1_uc011cor.1_Missense_Mutation_p.V2A|UGT3A1_uc003jjy.1_Intron	NM_152404	NP_689617	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	2						integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
SKP2	6502	broad.mit.edu	37	5	36168513	36168513	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36168513G>T	uc003jkc.1	+	5	817	c.635G>T	c.(634-636)AGC>ATC	p.S212I	SKP2_uc011cou.1_Intron|SKP2_uc003jkd.2_Missense_Mutation_p.S212I	NM_005983	NP_005974	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2 isoform 1	212	LRR 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G1/S transition of mitotic cell cycle|S phase of mitotic cell cycle	nucleoplasm|SCF ubiquitin ligase complex	protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
C5orf33	133686	broad.mit.edu	37	5	36197741	36197741	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36197741C>T	uc003jkf.3	-	11	1092	c.1092G>A	c.(1090-1092)CTG>CTA	p.L364L	C5orf33_uc003jke.3_RNA|C5orf33_uc010iux.2_Silent_p.L169L|C5orf33_uc003jkg.3_Silent_p.L201L|C5orf33_uc011cov.1_Silent_p.L223L	NM_001085411	NP_001078880	Q4G0N4	NAKD1_HUMAN	hypothetical protein LOC133686 isoform 1	364							NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
OSMR	9180	broad.mit.edu	37	5	38883960	38883960	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38883960C>T	uc003jln.1	+	5	817	c.450C>T	c.(448-450)TTC>TTT	p.F150F	OSMR_uc003jlm.1_Silent_p.F150F	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor	150	Extracellular (Potential).				cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)																	---	---	---	---
C7	730	broad.mit.edu	37	5	40964984	40964984	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40964984C>T	uc003jmh.2	+						C7_uc011cpn.1_Intron	NM_000587	NP_000578			complement component 7 precursor						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)																---	---	---	---
MAP3K1	4214	broad.mit.edu	37	5	56180553	56180553	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56180553G>T	uc003jqw.3	+	16	4383	c.3882G>T	c.(3880-3882)GAG>GAT	p.E1294D		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	1294	Protein kinase.				cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)														---	---	---	---
ELOVL7	79993	broad.mit.edu	37	5	60050586	60050586	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60050586G>T	uc003jsi.3	-	9	911	c.711C>A	c.(709-711)GTC>GTA	p.V237V	ELOVL7_uc011cqo.1_Silent_p.V150V|ELOVL7_uc010iwk.2_Silent_p.V237V|ELOVL7_uc003jsj.3_Silent_p.V224V	NM_024930	NP_079206	A1L3X0	ELOV7_HUMAN	elongation of very long chain fatty acids-like	237	Helical; (Potential).				fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)																---	---	---	---
HTR1A	3350	broad.mit.edu	37	5	63257163	63257163	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63257163G>A	uc011cqt.1	-	1	384	c.384C>T	c.(382-384)TGC>TGT	p.C128C		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	128	Helical; Name=3; (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66437997	66437997	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66437997G>T	uc003jut.1	+	19	2050	c.1982G>T	c.(1981-1983)AGT>ATT	p.S661I	MAST4_uc003juu.1_Missense_Mutation_p.S671I|MAST4_uc011cra.1_Missense_Mutation_p.S644I|MAST4_uc003juv.2_Missense_Mutation_p.S656I|MAST4_uc003juw.2_Missense_Mutation_p.S656I	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	853	AGC-kinase C-terminal.					cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
CCDC125	202243	broad.mit.edu	37	5	68595925	68595925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68595925C>T	uc003jvv.1	-	7	773	c.730G>A	c.(730-732)GCC>ACC	p.A244T	CCDC125_uc003jvx.1_Missense_Mutation_p.A243T|CCDC125_uc003jvy.1_RNA|CCDC125_uc003jvw.2_Missense_Mutation_p.A119T	NM_176816	NP_789786	Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	244						cytoplasm					0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73181709	73181709	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73181709G>A	uc011csq.1	+	24	3101	c.3090G>A	c.(3088-3090)GCG>GCA	p.A1030A	RGNEF_uc003kcx.2_Silent_p.A1030A|RGNEF_uc010izf.2_Silent_p.A1030A|RGNEF_uc011csr.1_Silent_p.A717A|RGNEF_uc003kcz.3_5'UTR|RGNEF_uc003kda.3_5'UTR	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor	1030	DH.				cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73188016	73188016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73188016G>A	uc011csq.1	+	26	3538	c.3527G>A	c.(3526-3528)CGC>CAC	p.R1176H	RGNEF_uc003kcx.2_Missense_Mutation_p.R1176H|RGNEF_uc010izf.2_Missense_Mutation_p.R1176H|RGNEF_uc011csr.1_Missense_Mutation_p.R863H|RGNEF_uc003kcz.3_Missense_Mutation_p.R140H|RGNEF_uc003kda.3_Missense_Mutation_p.R140H	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor	1176	PH.				cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)														---	---	---	---
SPZ1	84654	broad.mit.edu	37	5	79616234	79616234	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79616234A>G	uc003kgn.2	+	1	445	c.200A>G	c.(199-201)CAG>CGG	p.Q67R	uc011ctk.1_RNA	NM_032567	NP_115956	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	67	Potential.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(1)	1		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)														---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80419487	80419487	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80419487C>A	uc003kha.1	+	16	2497	c.2497C>A	c.(2497-2499)CGA>AGA	p.R833R	RASGRF2_uc011ctn.1_RNA	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	833					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
CKMT2	1160	broad.mit.edu	37	5	80548618	80548618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80548618C>T	uc003khc.3	+	4	499	c.257C>T	c.(256-258)ACG>ATG	p.T86M	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Missense_Mutation_p.T86M|CKMT2_uc003khd.3_Missense_Mutation_p.T86M|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	86	Phosphagen kinase N-terminal.				creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)													---	---	---	---
RPS23	6228	broad.mit.edu	37	5	81572238	81572238	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81572238G>A	uc003khu.2	-	3	357	c.264C>T	c.(262-264)GAC>GAT	p.D88D		NM_001025	NP_001016	P62266	RS23_HUMAN	ribosomal protein S23	88					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82843820	82843820	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82843820G>A	uc003kii.3	+	10	9766	c.9410G>A	c.(9409-9411)CGT>CAT	p.R3137H	VCAN_uc003kij.3_Missense_Mutation_p.R2150H|VCAN_uc010jau.2_Missense_Mutation_p.R1383H|VCAN_uc003kik.3_Missense_Mutation_p.R396H|VCAN_uc003kil.3_Missense_Mutation_p.R1801H	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	3137	EGF-like 2; calcium-binding (Potential).				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86659246	86659246	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86659246G>A	uc003kiw.2	+	11	1653	c.1535G>A	c.(1534-1536)CGA>CAA	p.R512Q	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Missense_Mutation_p.R335Q|RASA1_uc011ctv.1_Missense_Mutation_p.R345Q|RASA1_uc011ctw.1_Missense_Mutation_p.R346Q|RASA1_uc010jaw.2_Missense_Mutation_p.R334Q	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	512	PH.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89931070	89931070	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89931070T>A	uc003kju.2	+	10	2075	c.1979T>A	c.(1978-1980)ATT>AAT	p.I660N	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	660	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95103798	95103798	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95103798T>C	uc003klm.2	+	8	1747	c.1210T>C	c.(1210-1212)TGG>CGG	p.W404R		NM_014899	NP_055714	O94955	RHBT3_HUMAN	rho-related BTB domain containing 3	404					retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96116192	96116192	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96116192A>G	uc003kmm.2	-	18	2952	c.2605T>C	c.(2605-2607)TCT>CCT	p.S869P	ERAP1_uc003kml.2_Missense_Mutation_p.S869P|ERAP1_uc010jbm.1_Missense_Mutation_p.S681P|ERAP1_uc003kmn.2_Missense_Mutation_p.S869P	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding	869	Lumenal (Potential).				angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)														---	---	---	---
LIX1	167410	broad.mit.edu	37	5	96430690	96430690	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96430690C>T	uc003kmy.3	-	6	851	c.611G>A	c.(610-612)AGC>AAC	p.S204N		NM_153234	NP_694966	Q8N485	LIX1_HUMAN	limb expression 1	204										ovary(1)	1		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)														---	---	---	---
RIOK2	55781	broad.mit.edu	37	5	96514861	96514861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96514861C>T	uc003kmz.2	-	2	213	c.103G>A	c.(103-105)GGC>AGC	p.G35S	RIOK2_uc003kna.3_Missense_Mutation_p.G35S	NM_018343	NP_060813	Q9BVS4	RIOK2_HUMAN	RIO kinase 2 isoform 1	35							ATP binding|protein serine/threonine kinase activity			kidney(1)	1		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)														---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109125159	109125159	+	Splice_Site	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109125159A>T	uc003kou.1	+	12	2839	c.1876_splice	c.e12-2	p.D626_splice		NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
WDR36	134430	broad.mit.edu	37	5	110443069	110443069	+	Nonsense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110443069T>G	uc003kpd.2	+	12	1542	c.1425T>G	c.(1423-1425)TAT>TAG	p.Y475*	WDR36_uc010jbu.2_RNA	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	475					response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)														---	---	---	---
APC	324	broad.mit.edu	37	5	112174945	112174945	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112174945G>A	uc010jby.2	+	16	4034	c.3654G>A	c.(3652-3654)ACG>ACA	p.T1218T	APC_uc011cvt.1_Silent_p.T1200T|APC_uc003kpz.3_Silent_p.T1218T|APC_uc003kpy.3_Silent_p.T1218T|APC_uc010jbz.2_Silent_p.T935T|APC_uc010jca.2_Silent_p.T518T	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1218	Ser-rich.|Responsible for down-regulation through a process mediated by direct ubiquitination.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.K1192fs*3(1)|p.?(1)		large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)			12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			---	---	---	---
APC	324	broad.mit.edu	37	5	112176079	112176079	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112176079G>T	uc010jby.2	+	16	5168	c.4788G>T	c.(4786-4788)CAG>CAT	p.Q1596H	APC_uc011cvt.1_Missense_Mutation_p.Q1578H|APC_uc003kpz.3_Missense_Mutation_p.Q1596H|APC_uc003kpy.3_Missense_Mutation_p.Q1596H|APC_uc010jbz.2_Missense_Mutation_p.Q1313H|APC_uc010jca.2_Missense_Mutation_p.Q896H	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1596	Ser-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.K1192fs*3(1)|p.?(1)		large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)			12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			---	---	---	---
MCC	4163	broad.mit.edu	37	5	112384867	112384867	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112384867C>T	uc003kqj.3	-	14	2538	c.2008G>A	c.(2008-2010)GAG>AAG	p.E670K	MCC_uc003kqk.3_RNA|MCC_uc003kql.3_Missense_Mutation_p.E860K|MCC_uc011cwb.1_Missense_Mutation_p.E670K	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2	670					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112418583	112418583	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112418583A>G	uc003kqj.3	-	9	1718	c.1188T>C	c.(1186-1188)TTT>TTC	p.F396F	MCC_uc003kqk.3_RNA|MCC_uc003kql.3_Silent_p.F586F|MCC_uc011cwb.1_Silent_p.F396F|MCC_uc010jcd.1_Silent_p.F358F	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2	396					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115833073	115833073	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115833073A>G	uc010jck.2	-	4	938	c.229T>C	c.(229-231)TAT>CAT	p.Y77H	SEMA6A_uc003krx.3_Missense_Mutation_p.Y77H	NM_020796	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and	77	Sema.|Extracellular (Potential).				apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
FTMT	94033	broad.mit.edu	37	5	121187652	121187652	+	5'UTR	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121187652C>T	uc003kss.2	+	1						NM_177478	NP_803431			ferritin mitochondrial precursor						cellular iron ion homeostasis|iron ion transport|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)														---	---	---	---
PPIC	5480	broad.mit.edu	37	5	122365088	122365088	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122365088T>C	uc003kth.2	-	2	248	c.143A>G	c.(142-144)GAC>GGC	p.D48G	PPIC_uc011cwp.1_Missense_Mutation_p.D48G	NM_000943	NP_000934	P45877	PPIC_HUMAN	peptidylprolyl isomerase C	48	PPIase cyclophilin-type.				protein folding|signal transduction	cytoplasm	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding			ovary(1)	1		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)													---	---	---	---
PHAX	51808	broad.mit.edu	37	5	125952952	125952952	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125952952G>A	uc003kua.1	+	4	864	c.842G>A	c.(841-843)CGA>CAA	p.R281Q		NM_032177	NP_115553	Q9H814	PHAX_HUMAN	RNA U, small nuclear RNA export adaptor	281	Necessary for interaction with CBP80 (By similarity).|Sufficient for poly U RNA-binding.|Necessary for poly U RNA-binding and snRNA export (By similarity).				ncRNA metabolic process|protein transport|snRNA export from nucleus|spliceosomal snRNP assembly	Cajal body|cytosol	RNA binding				0																		---	---	---	---
LMNB1	4001	broad.mit.edu	37	5	126141336	126141336	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126141336G>A	uc003kud.1	+	3	958	c.590G>A	c.(589-591)CGT>CAT	p.R197H	LMNB1_uc003kuc.2_Missense_Mutation_p.R197H|LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_5'UTR	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1	197	Coil 1B.|Rod.				cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)														---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126676262	126676262	+	Missense_Mutation	SNP	A	G	G	rs41298304	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126676262A>G	uc003kuh.3	+	5	621	c.259A>G	c.(259-261)ATG>GTG	p.M87V	MEGF10_uc010jdc.1_Missense_Mutation_p.M87V|MEGF10_uc010jdd.1_Missense_Mutation_p.M87V|MEGF10_uc003kui.3_Missense_Mutation_p.M87V	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	87	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.|EMI.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)														---	---	---	---
SLC12A2	6558	broad.mit.edu	37	5	127469864	127469864	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127469864C>T	uc003kus.2	+	6	1360	c.1196C>T	c.(1195-1197)TCC>TTC	p.S399F	SLC12A2_uc010jdf.2_RNA|SLC12A2_uc010jdg.2_Missense_Mutation_p.S399F	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12	399	Extracellular (Potential).				potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
P4HA2	8974	broad.mit.edu	37	5	131554233	131554233	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131554233C>T	uc003kwh.2	-						P4HA2_uc003kwg.2_Intron|P4HA2_uc003kwi.2_Intron|P4HA2_uc003kwk.2_Intron|P4HA2_uc003kwl.2_Intron|P4HA2_uc003kwj.2_Intron	NM_004199	NP_004190			prolyl 4-hydroxylase, alpha II subunit isoform 1							endoplasmic reticulum lumen	electron carrier activity|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity|protein binding				0		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)													---	---	---	---
SHROOM1	134549	broad.mit.edu	37	5	132159958	132159958	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132159958C>T	uc003kxx.2	-	7	2200	c.1395G>A	c.(1393-1395)AGG>AGA	p.R465R	SHROOM1_uc003kxy.1_Silent_p.R465R	NM_133456	NP_597713	Q2M3G4	SHRM1_HUMAN	shroom family member 1	465					actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding			pancreas(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132648387	132648387	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132648387C>T	uc003kyn.1	-	6	904	c.686G>A	c.(685-687)AGT>AAT	p.S229N		NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor	229						extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
PITX1	5307	broad.mit.edu	37	5	134364881	134364881	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134364881C>T	uc010jea.2	-	3	926	c.533G>A	c.(532-534)GGC>GAC	p.G178D	PITX1_uc011cxy.1_Missense_Mutation_p.G178D	NM_002653	NP_002644	P78337	PITX1_HUMAN	paired-like homeodomain transcription factor 1	178	Interacts with PIT-1 (By similarity).					nucleolus	sequence-specific DNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)														---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136324222	136324222	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136324222A>G	uc003lbo.2	-	7	1008	c.817T>C	c.(817-819)TAC>CAC	p.Y273H	SPOCK1_uc003lbp.2_Missense_Mutation_p.Y273H	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains	273					cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137354674	137354674	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137354674G>A	uc003lbz.2	-	3	661	c.127C>T	c.(127-129)CGC>TGC	p.R43C	FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Missense_Mutation_p.R43C	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	43	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
CDC23	8697	broad.mit.edu	37	5	137525556	137525556	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137525556C>T	uc003lcl.2	-	14	1495	c.1464G>A	c.(1462-1464)CAG>CAA	p.Q488Q		NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	cell division cycle protein 23	488	TPR 9.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137722064	137722064	+	Silent	SNP	A	G	G	rs144389568	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137722064A>G	uc003lcy.1	+	7	1334	c.1134A>G	c.(1132-1134)ACA>ACG	p.T378T	KDM3B_uc010jew.1_Silent_p.T34T|KDM3B_uc011cys.1_5'UTR	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	378					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
CXXC5	51523	broad.mit.edu	37	5	139060294	139060294	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139060294C>T	uc010jfg.1	+	2	476	c.186C>T	c.(184-186)AGC>AGT	p.S62S	CXXC5_uc003let.2_Silent_p.S62S	NM_016463	NP_057547	Q7LFL8	CXXC5_HUMAN	CXXC finger 5	62					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|nucleus	DNA binding|signal transducer activity|zinc ion binding			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139216523	139216523	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139216523G>A	uc003leu.1	+	10	1736	c.1531G>A	c.(1531-1533)GCC>ACC	p.A511T		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	511					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139908543	139908543	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139908543A>G	uc003lfs.1	+	29	6136	c.6012A>G	c.(6010-6012)CTA>CTG	p.L2004L	ANKHD1_uc003lfr.2_Silent_p.L2004L|ANKHD1-EIF4EBP3_uc011czh.1_Silent_p.L743L|ANKHD1_uc003lfw.2_Silent_p.L642L|ANKHD1_uc010jfl.2_Silent_p.L439L|ANKHD1-EIF4EBP3_uc003lfx.1_Silent_p.L141L	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	2004						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
IK	3550	broad.mit.edu	37	5	140028074	140028074	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140028074C>A	uc003lgq.2	+	2	145	c.35C>A	c.(34-36)CCT>CAT	p.P12H	NDUFA2_uc003lgp.2_5'Flank|IK_uc011czk.1_Missense_Mutation_p.P12H	NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein	12					cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140182189	140182189	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182189G>A	uc003lhf.2	+	1	1407	c.1407G>A	c.(1405-1407)CCG>CCA	p.P469P	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.P469P	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	469	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA7	56141	broad.mit.edu	37	5	140215899	140215899	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215899G>A	uc003lhq.2	+	1	1931	c.1931G>A	c.(1930-1932)CGC>CAC	p.R644H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.R644H	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	644	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA9	9752	broad.mit.edu	37	5	140228264	140228264	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140228264C>T	uc003lhu.2	+	1	908	c.184C>T	c.(184-186)CGC>TGC	p.R62C	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lht.1_Missense_Mutation_p.R62C	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	62	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA10	56139	broad.mit.edu	37	5	140235929	140235929	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140235929T>C	uc003lhx.2	+	1	296	c.296T>C	c.(295-297)GTG>GCG	p.V99A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Missense_Mutation_p.V99A|PCDHA10_uc011dad.1_Missense_Mutation_p.V99A	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	99	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA10	56139	broad.mit.edu	37	5	140235939	140235939	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140235939C>T	uc003lhx.2	+	1	306	c.306C>T	c.(304-306)AGC>AGT	p.S102S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Silent_p.S102S|PCDHA10_uc011dad.1_Silent_p.S102S	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	102	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA12	56137	broad.mit.edu	37	5	140256160	140256160	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140256160T>C	uc003lic.2	+	1	1230	c.1103T>C	c.(1102-1104)GTC>GCC	p.V368A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Missense_Mutation_p.V368A	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	368	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHAC1	56135	broad.mit.edu	37	5	140307186	140307186	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140307186G>A	uc003lih.2	+	1	885	c.709G>A	c.(709-711)GTA>ATA	p.V237I	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lig.1_Missense_Mutation_p.V237I	NM_018898	NP_061721	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1 isoform 1	237	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB2	56133	broad.mit.edu	37	5	140474566	140474566	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140474566G>T	uc003lil.2	+	1	330	c.192G>T	c.(190-192)AGG>AGT	p.R64S	PCDHB2_uc003lim.1_Intron	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	64	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB6	56130	broad.mit.edu	37	5	140531429	140531429	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140531429G>A	uc003lir.2	+	1	1591	c.1591G>A	c.(1591-1593)GCC>ACC	p.A531T	PCDHB6_uc011dah.1_Missense_Mutation_p.A395T	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	531	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB16	57717	broad.mit.edu	37	5	140564000	140564000	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564000C>T	uc003liv.2	+	1	3021	c.1866C>T	c.(1864-1866)GGC>GGT	p.G622G	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	622	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB9	56127	broad.mit.edu	37	5	140568392	140568392	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140568392G>A	uc003liw.1	+	3	1501	c.1501G>A	c.(1501-1503)GCC>ACC	p.A501T		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	501	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB12	56124	broad.mit.edu	37	5	140588663	140588663	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140588663C>T	uc003liz.2	+	1	373	c.184C>T	c.(184-186)CGG>TGG	p.R62W	PCDHB12_uc011dak.1_Intron	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	62	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA2	56113	broad.mit.edu	37	5	140719242	140719242	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140719242C>T	uc003ljk.1	+	1	889	c.704C>T	c.(703-705)GCG>GTG	p.A235V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.A235V	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	235	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140723889	140723889	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140723889G>A	uc003ljm.1	+	1	289	c.289G>A	c.(289-291)GCT>ACT	p.A97T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Missense_Mutation_p.A97T	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	97	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA5	56110	broad.mit.edu	37	5	140746266	140746266	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140746266C>T	uc003lju.1	+	1	2369	c.2369C>T	c.(2368-2370)CCT>CTT	p.P790L	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.P790L	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	790	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA6	56109	broad.mit.edu	37	5	140755536	140755536	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140755536C>T	uc003ljy.1	+	1	1886	c.1886C>T	c.(1885-1887)GCG>GTG	p.A629V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Missense_Mutation_p.A629V	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	629	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA8	9708	broad.mit.edu	37	5	140774185	140774185	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140774185C>T	uc003lkd.1	+	1	2703	c.1805C>T	c.(1804-1806)GCC>GTC	p.A602V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.3_Missense_Mutation_p.A602V	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	602	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA11	56105	broad.mit.edu	37	5	140802535	140802535	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140802535C>T	uc003lkq.1	+	1	1999	c.1741C>T	c.(1741-1743)CGC>TGC	p.R581C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.R581C|PCDHGA11_uc003lkp.1_Missense_Mutation_p.R581C	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	581	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA12	26025	broad.mit.edu	37	5	140810564	140810564	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140810564C>T	uc003lkt.1	+	1	407	c.238C>T	c.(238-240)CGC>TGC	p.R80C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc011dba.1_Missense_Mutation_p.R80C	NM_003735	NP_003726	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12 isoform 1	80	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142513640	142513640	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142513640C>T	uc011dbj.1	+	19	1842	c.1807C>T	c.(1807-1809)CTC>TTC	p.L603F	ARHGAP26_uc003lmt.2_Missense_Mutation_p.L603F|ARHGAP26_uc003lmw.2_Missense_Mutation_p.L603F	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	603	Ser-rich.				actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SH3RF2	153769	broad.mit.edu	37	5	145393418	145393418	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145393418C>A	uc003lnt.2	+	5	1091	c.853C>A	c.(853-855)CTC>ATC	p.L285I	SH3RF2_uc011dbl.1_Missense_Mutation_p.L285I	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	285							ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147889382	147889382	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147889382C>T	uc003lpn.2	-	6	877	c.713G>A	c.(712-714)AGC>AAC	p.S238N	HTR4_uc010jgu.1_RNA|HTR4_uc003lpi.1_Missense_Mutation_p.S238N|HTR4_uc003lpj.1_Missense_Mutation_p.S238N|HTR4_uc003lpk.2_Missense_Mutation_p.S238N|HTR4_uc011dby.1_Missense_Mutation_p.S238N|HTR4_uc003lpl.2_Missense_Mutation_p.S252N|HTR4_uc003lpm.2_Missense_Mutation_p.S238N|HTR4_uc010jgv.2_RNA|HTR4_uc003lpo.1_Missense_Mutation_p.S238N	NM_000870	NP_000861	Q13639	5HT4R_HUMAN	serotonin 5-HT4 receptor isoform b	238	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
PCYOX1L	78991	broad.mit.edu	37	5	148747942	148747942	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148747942C>T	uc003lqk.2	+	6	1272	c.1210C>T	c.(1210-1212)CGG>TGG	p.R404W	PCYOX1L_uc003lql.2_Missense_Mutation_p.R387W|PCYOX1L_uc010jgz.2_Missense_Mutation_p.R328W|PCYOX1L_uc003lqm.2_Missense_Mutation_p.R286W|PCYOX1L_uc003lqn.2_Missense_Mutation_p.R314W	NM_024028	NP_076933	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like precursor	404					prenylcysteine catabolic process	extracellular region	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)													OREG0016912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC6A7	6534	broad.mit.edu	37	5	149576268	149576268	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149576268G>A	uc003lrr.2	+							NM_014228	NP_055043			solute carrier family 6, member 7							integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity				0		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)													---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150934236	150934236	+	Splice_Site	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150934236T>C	uc003lue.3	-	4	3647	c.3634_splice	c.e4-1	p.V1212_splice	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438			FAT tumor suppressor 2 precursor						epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153065857	153065857	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153065857G>A	uc003lva.3	+	8	1467	c.1102G>A	c.(1102-1104)GTG>ATG	p.V368M	GRIA1_uc003luy.3_Missense_Mutation_p.V368M|GRIA1_uc003luz.3_Missense_Mutation_p.V273M|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Missense_Mutation_p.V288M|GRIA1_uc011dcx.1_Missense_Mutation_p.V299M|GRIA1_uc011dcy.1_Missense_Mutation_p.V378M|GRIA1_uc011dcz.1_Missense_Mutation_p.V378M|GRIA1_uc010jia.1_Missense_Mutation_p.V348M	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	368	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154271254	154271254	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154271254G>A	uc003lvx.3	-	26	3892	c.3809C>T	c.(3808-3810)ACA>ATA	p.T1270I	GEMIN5_uc011ddk.1_Missense_Mutation_p.T1269I	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	1270					ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156816239	156816239	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156816239C>T	uc003lwq.2	+	31	3388	c.3250C>T	c.(3250-3252)CGG>TGG	p.R1084W	CYFIP2_uc011ddn.1_Missense_Mutation_p.R1058W|CYFIP2_uc011ddo.1_Missense_Mutation_p.R888W|CYFIP2_uc003lwr.2_Missense_Mutation_p.R1084W|CYFIP2_uc003lws.2_Missense_Mutation_p.R1084W|CYFIP2_uc003lwt.2_Missense_Mutation_p.R987W|CYFIP2_uc011ddp.1_Missense_Mutation_p.R818W|CYFIP2_uc003lwv.2_Missense_Mutation_p.R39W	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	1109					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
KCNMB1	3779	broad.mit.edu	37	5	169805828	169805828	+	Silent	SNP	G	A	A	rs145466654		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169805828G>A	uc003maq.1	-	4	856	c.456C>T	c.(454-456)TAC>TAT	p.Y152Y	KCNIP1_uc003map.2_Intron	NM_004137	NP_004128	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated	152	Extracellular (Potential).				platelet activation|synaptic transmission		calcium-activated potassium channel activity|potassium channel regulator activity			ovary(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)														---	---	---	---
STK10	6793	broad.mit.edu	37	5	171481568	171481568	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171481568G>A	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
ARL10	285598	broad.mit.edu	37	5	175793590	175793590	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175793590C>T	uc003mec.1	+						ARL10_uc003meb.2_Intron|MIR1271_hsa-mir-1271|MI0003814_5'Flank	NM_173664	NP_775935			ADP-ribosylation factor-like 10								GTP binding			ovary(1)	1	all_cancers(89;0.0064)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)														---	---	---	---
FAF2	23197	broad.mit.edu	37	5	175926019	175926019	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175926019G>A	uc003mej.3	+	9	997	c.944G>A	c.(943-945)CGG>CAG	p.R315Q		NM_014613	NP_055428	Q96CS3	FAF2_HUMAN	UBX domain containing 8	315	Potential.				response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1																		---	---	---	---
CDHR2	54825	broad.mit.edu	37	5	176002180	176002180	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176002180C>T	uc003mem.1	+	8	657	c.591C>T	c.(589-591)AGC>AGT	p.S197S	CDHR2_uc003men.1_Silent_p.S197S	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor	197	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2																		---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176675253	176675253	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176675253C>A	uc003mfr.3	+	11	4707	c.4569C>A	c.(4567-4569)CCC>CCA	p.P1523P	NSD1_uc003mft.3_Silent_p.P1254P|NSD1_uc003mfs.1_Silent_p.P1420P|NSD1_uc011dfx.1_Silent_p.P1171P	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1523					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
RGS14	10636	broad.mit.edu	37	5	176798908	176798908	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176798908C>T	uc003mgf.2	+	15	1715	c.1533C>T	c.(1531-1533)AGC>AGT	p.S511S	RGS14_uc003mgh.2_Silent_p.S359S|RGS14_uc003mgi.2_Silent_p.S282S|RGS14_uc003mgj.2_RNA	NM_006480	NP_006471	O43566	RGS14_HUMAN	regulator of G-protein signalling 14	511	GoLoco.				chromosome segregation|long-term memory|long-term synaptic potentiation|negative regulation of ERK1 and ERK2 cascade|negative regulation of MAP kinase activity|negative regulation of synaptic plasticity|nucleocytoplasmic transport|platelet-derived growth factor receptor signaling pathway|positive regulation of neurogenesis|regulation of DNA-dependent transcription in response to stress|regulation of G-protein coupled receptor protein signaling pathway|response to oxidative stress|spindle organization|visual learning|zygote asymmetric cell division	cell junction|centrosome|dendritic spine|microtubule|PML body|postsynaptic density|postsynaptic membrane|spindle pole	GDP-dissociation inhibitor activity|GTPase activator activity|microtubule binding|receptor signaling complex scaffold activity|receptor signaling protein activity			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
DOK3	79930	broad.mit.edu	37	5	176936799	176936799	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176936799G>A	uc003mhk.2	-						DOK3_uc003mhh.3_5'Flank|DOK3_uc003mhi.3_Intron|DOK3_uc003mhj.3_Intron|DOK3_uc003mhl.2_Intron	NM_024872	NP_079148			docking protein 3 isoform 1							cytoplasm|plasma membrane	insulin receptor binding				0	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)															---	---	---	---
RMND5B	64777	broad.mit.edu	37	5	177574868	177574868	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177574868C>T	uc003mim.2	+	10	1282	c.1102C>T	c.(1102-1104)CTC>TTC	p.L368F	RMND5B_uc003min.2_Missense_Mutation_p.L368F|RMND5B_uc003mio.2_Missense_Mutation_p.L355F|RMND5B_uc003mip.2_Missense_Mutation_p.L368F|RMND5B_uc011dgf.1_Missense_Mutation_p.L409F|RMND5B_uc003miq.2_Missense_Mutation_p.L308F	NM_022762	NP_073599	Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog	368										ovary(1)|skin(1)	2	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177688741	177688741	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177688741C>A	uc003mje.2	-	11	1042	c.684G>T	c.(682-684)AAG>AAT	p.K228N	COL23A1_uc010jkt.2_Missense_Mutation_p.R76M	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	228	Extracellular (Potential).|Collagen-like 1.|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
ADAMTS2	9509	broad.mit.edu	37	5	178553053	178553053	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178553053G>A	uc003mjw.2	-	18	2696	c.2696C>T	c.(2695-2697)TCG>TTG	p.S899L		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	899	TSP type-1 2.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)														---	---	---	---
HNRNPH1	3187	broad.mit.edu	37	5	179045245	179045245	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179045245G>A	uc003mkf.3	-	6	722	c.616C>T	c.(616-618)CGG>TGG	p.R206W	HNRNPH1_uc011dgn.1_5'Flank|HNRNPH1_uc003mkg.3_Missense_Mutation_p.R114W|HNRNPH1_uc003mke.3_Missense_Mutation_p.R206W|HNRNPH1_uc003mkh.3_Missense_Mutation_p.R206W	NM_005520	NP_005511	P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1	206					regulation of RNA splicing	actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|poly(U) RNA binding|protein binding				0																		---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179294813	179294813	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179294813G>A	uc003mlh.2	-	18	2865	c.2828C>T	c.(2827-2829)GCG>GTG	p.A943V	TBC1D9B_uc003mli.2_Missense_Mutation_p.A943V|TBC1D9B_uc003mlj.2_Missense_Mutation_p.A943V|TBC1D9B_uc003mlf.2_5'Flank|TBC1D9B_uc003mlg.2_Missense_Mutation_p.A119V|TBC1D9B_uc011dgv.1_Missense_Mutation_p.A119V|TBC1D9B_uc011dgw.1_Missense_Mutation_p.A119V	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	943						integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
GFPT2	9945	broad.mit.edu	37	5	179762846	179762846	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179762846G>A	uc003mlw.1	-	4	420	c.322C>T	c.(322-324)CGC>TGC	p.R108C		NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	108	Glutamine amidotransferase type-2.				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)													---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16326907	16326907	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16326907T>C	uc003nbt.2	-	8	2606	c.1635A>G	c.(1633-1635)CCA>CCG	p.P545P	ATXN1_uc010jpi.2_Silent_p.P545P|ATXN1_uc010jpj.1_Intron	NM_000332	NP_000323	P54253	ATX1_HUMAN	ataxin 1	545	Self-association.|Interaction with USP7.|RNA-binding.				cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
DEK	7913	broad.mit.edu	37	6	18258623	18258623	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18258623G>A	uc003ncr.1	-	3	352	c.159C>T	c.(157-159)ATC>ATT	p.I53I	DEK_uc011djf.1_Intron|DEK_uc011djg.1_RNA	NM_003472	NP_003463	P35659	DEK_HUMAN	DEK oncogene isoform 1	53					chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding			kidney(1)	1	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)					T	NUP214	AML								---	---	---	---
HIST1H3A	8350	broad.mit.edu	37	6	26020914	26020914	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26020914T>C	uc003nfp.1	+	1	197	c.197T>C	c.(196-198)CTA>CCA	p.L66P	HIST1H1A_uc003nfo.2_5'Flank|HIST1H4A_uc003nfq.2_5'Flank	NM_003529	NP_003520	P68431	H31_HUMAN	histone cluster 1, H3a	66					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)|pancreas(1)	2																		---	---	---	---
HIST1H3C	8352	broad.mit.edu	37	6	26045904	26045904	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26045904C>T	uc003nfv.2	+	1	266	c.266C>T	c.(265-267)GCG>GTG	p.A89V	HIST1H2BB_uc003nfu.2_5'Flank	NM_003531	NP_003522	P68431	H31_HUMAN	histone cluster 1, H3c	89					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1																		---	---	---	---
HIST1H3E	8353	broad.mit.edu	37	6	26225402	26225402	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26225402C>T	uc003nhb.2	+	2	380	c.20C>T	c.(19-21)ACG>ATG	p.T7M	HIST1H3E_uc003nhc.3_Missense_Mutation_p.T7M	NM_021018	NP_066298	P68431	H31_HUMAN	histone cluster 1, H3f	7					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding				0		all_hematologic(11;0.0223)|Acute lymphoblastic leukemia(11;0.0351)																---	---	---	---
PRSS16	10279	broad.mit.edu	37	6	27219688	27219688	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27219688G>A	uc003nja.2	+	8	889	c.877G>A	c.(877-879)GGA>AGA	p.G293R	PRSS16_uc011dkt.1_Intron|PRSS16_uc003njb.2_Intron|PRSS16_uc010jqq.1_Intron|PRSS16_uc010jqr.1_Intron|PRSS16_uc003njc.1_Intron|PRSS16_uc003njd.2_RNA	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16 precursor	293					protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity			ovary(2)|central_nervous_system(2)|skin(1)	5																		---	---	---	---
HIST1H2AJ	8331	broad.mit.edu	37	6	27782269	27782269	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27782269G>A	uc003njn.1	-	1	250	c.250C>T	c.(250-252)CTC>TTC	p.L84F	HIST1H2BM_uc003njo.2_5'Flank	NM_021066	NP_066544	Q99878	H2A1J_HUMAN	histone cluster 1, H2aj	84					nucleosome assembly	nucleosome|nucleus	DNA binding				0																		---	---	---	---
HIST1H3I	8354	broad.mit.edu	37	6	27839685	27839685	+	Nonstop_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27839685A>T	uc003njy.2	-	1	415	c.409T>A	c.(409-411)TAA>AAA	p.*137K		NM_003533	NP_003524	P68431	H31_HUMAN	histone cluster 1, H3i	137					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1																		---	---	---	---
GABBR1	2550	broad.mit.edu	37	6	29598334	29598334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29598334G>A	uc003nmt.3	-	4	712	c.376C>T	c.(376-378)CGG>TGG	p.R126W	GABBR1_uc003nmp.3_5'Flank|GABBR1_uc003nms.3_5'Flank|GABBR1_uc003nmu.3_Intron|GABBR1_uc011dlr.1_5'UTR|GABBR1_uc011dls.1_Missense_Mutation_p.R126W	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	126	Extracellular (Potential).|Sushi 2.				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)													---	---	---	---
NRM	11270	broad.mit.edu	37	6	30657122	30657122	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30657122G>A	uc003nrc.2	-	3	456	c.438C>T	c.(436-438)GTC>GTT	p.V146V	KIAA1949_uc003nra.2_5'Flank|KIAA1949_uc003nrb.3_5'Flank|NRM_uc003nrd.2_RNA|NRM_uc003nre.2_Silent_p.V34V	NM_007243	NP_009174	Q8IXM6	NRM_HUMAN	nurim	146	Leu-rich.|Helical; (Potential).					integral to membrane|nuclear inner membrane					0																		---	---	---	---
BAT4	7918	broad.mit.edu	37	6	31630239	31630239	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31630239T>A	uc003nvn.2	-	3	1520	c.875A>T	c.(874-876)GAC>GTC	p.D292V	C6orf47_uc003nvm.1_5'Flank|BAT4_uc003nvo.3_Missense_Mutation_p.D292V|BAT4_uc003nvp.3_Missense_Mutation_p.D292V|BAT4_uc003nvq.2_Missense_Mutation_p.D292V	NM_033177	NP_149417	O95872	GPAN1_HUMAN	HLA-B associated transcript 4	292	G-patch.					intracellular	nucleic acid binding				0																		---	---	---	---
C6orf25	80739	broad.mit.edu	37	6	31691724	31691724	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31691724G>A	uc011doc.1	+	2	370	c.370G>A	c.(370-372)GGG>AGG	p.G124R	LY6G6C_uc003nwh.2_5'Flank|LY6G6C_uc010jtd.2_5'Flank|C6orf25_uc003nwk.2_Missense_Mutation_p.G124R|C6orf25_uc011dod.1_Missense_Mutation_p.G124R|C6orf25_uc011doe.1_Missense_Mutation_p.G124R|C6orf25_uc003nwo.2_Missense_Mutation_p.G124R|C6orf25_uc003nwn.2_Missense_Mutation_p.G124R	NM_138272	NP_612116	O95866	G6B_HUMAN	G6B protein isoform G6b-B precursor	124	Extracellular (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	heparin binding|receptor activity				0																		---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31728555	31728555	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31728555G>A	uc003nwv.1	+	20	1980	c.1901G>A	c.(1900-1902)CGA>CAA	p.R634Q	MSH5_uc003nwt.1_Missense_Mutation_p.R651Q|MSH5_uc003nwu.1_Missense_Mutation_p.R634Q|MSH5_uc003nww.1_Missense_Mutation_p.R634Q|MSH5_uc003nwx.1_Missense_Mutation_p.R651Q|MSH5_uc011dof.1_Missense_Mutation_p.R333Q|MSH5_uc003nwy.1_Missense_Mutation_p.R308Q|MSH5_uc003nwz.3_RNA|C6orf26_uc003nxa.3_5'Flank	NM_172166	NP_751898	O43196	MSH5_HUMAN	mutS homolog 5 isoform c	634					chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32036881	32036881	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32036881C>T	uc003nzl.2	-	16	5822	c.5620G>A	c.(5620-5622)GCC>ACC	p.A1874T		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1956					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33133490	33133490	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33133490G>A	uc003ocx.1	-	63	4814	c.4586C>T	c.(4585-4587)CCG>CTG	p.P1529L	COL11A2_uc010jul.1_Missense_Mutation_p.P99L|COL11A2_uc003ocy.1_Missense_Mutation_p.P1443L|COL11A2_uc003ocz.1_Missense_Mutation_p.P1422L	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1529					cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33134297	33134297	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33134297C>T	uc003ocx.1	-	60	4613	c.4385G>A	c.(4384-4386)GGC>GAC	p.G1462D	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Missense_Mutation_p.G1376D|COL11A2_uc003ocz.1_Missense_Mutation_p.G1355D	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1462	Triple-helical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33139294	33139294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33139294G>A	uc003ocx.1	-	43	3436	c.3208C>T	c.(3208-3210)CTT>TTT	p.L1070F	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Missense_Mutation_p.L984F|COL11A2_uc003ocz.1_Missense_Mutation_p.L963F	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1070	Triple-helical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
RGL2	5863	broad.mit.edu	37	6	33264022	33264022	+	Missense_Mutation	SNP	C	T	T	rs138299795		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33264022C>T	uc003odv.2	-	6	684	c.551G>A	c.(550-552)CGG>CAG	p.R184Q	RGL2_uc003odu.2_5'UTR|RGL2_uc010jur.2_Intron|RGL2_uc003odw.2_Missense_Mutation_p.R102Q|RGL2_uc011drb.1_Missense_Mutation_p.R102Q	NM_004761	NP_004752	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation	184	N-terminal Ras-GEF.				Ras protein signal transduction|regulation of small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity			skin(3)|lung(1)|breast(1)|pancreas(1)	6																		---	---	---	---
ZBTB22	9278	broad.mit.edu	37	6	33284127	33284127	+	Silent	SNP	C	T	T	rs141471574		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33284127C>T	uc003oeb.2	-	2	719	c.567G>A	c.(565-567)GCG>GCA	p.A189A	TAPBP_uc003odx.1_5'Flank|TAPBP_uc010jus.1_5'Flank|TAPBP_uc003ody.2_5'Flank|TAPBP_uc003odz.2_5'Flank|TAPBP_uc010jut.1_5'Flank|TAPBP_uc011drc.1_5'Flank|ZBTB22_uc010juu.2_Silent_p.A189A	NM_005453	NP_005444	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	189					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PHF1	5252	broad.mit.edu	37	6	33382863	33382863	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33382863G>T	uc003oeh.2	+	12	1417	c.1181G>T	c.(1180-1182)CGC>CTC	p.R394L	PHF1_uc011drh.1_RNA|PHF1_uc003oei.2_Silent_p.A390A|PHF1_uc010jux.2_Missense_Mutation_p.R194L	NM_024165	NP_077084	O43189	PHF1_HUMAN	PHD finger protein 1 isoform b	394					chromatin modification	nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Ovarian(999;0.0443)														OREG0017346	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33652449	33652449	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33652449C>T	uc011drk.1	+	38	5340	c.5121C>T	c.(5119-5121)CCC>CCT	p.P1707P	ITPR3_uc003oey.2_5'Flank	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	1707	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
TCP11	6954	broad.mit.edu	37	6	35088325	35088325	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35088325C>T	uc003okd.2	-	7	1034	c.853G>A	c.(853-855)GCT>ACT	p.A285T	TCP11_uc003ojz.1_Missense_Mutation_p.A210T|TCP11_uc003oka.2_Missense_Mutation_p.A210T|TCP11_uc003okb.2_Missense_Mutation_p.A209T|TCP11_uc003okc.2_Missense_Mutation_p.A209T|TCP11_uc011dsu.1_Missense_Mutation_p.A267T|TCP11_uc011dsv.1_Missense_Mutation_p.A234T|TCP11_uc011dsw.1_Missense_Mutation_p.A239T	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	272					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5																		---	---	---	---
TCP11	6954	broad.mit.edu	37	6	35096947	35096947	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35096947C>A	uc003okd.2	-	4	469	c.288G>T	c.(286-288)AAG>AAT	p.K96N	TCP11_uc003ojz.1_Missense_Mutation_p.K21N|TCP11_uc003oka.2_Missense_Mutation_p.K21N|TCP11_uc003okb.2_Missense_Mutation_p.K20N|TCP11_uc003okc.2_Missense_Mutation_p.K20N|TCP11_uc011dsu.1_Missense_Mutation_p.K78N|TCP11_uc011dsv.1_Missense_Mutation_p.K45N|TCP11_uc011dsw.1_Missense_Mutation_p.K50N	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	83					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38862485	38862485	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38862485G>A	uc003ooe.1	+	57	8541	c.7941G>A	c.(7939-7941)ATG>ATA	p.M2647I		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
DAAM2	23500	broad.mit.edu	37	6	39855302	39855302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39855302G>A	uc003oow.2	+	16	2150	c.1994G>A	c.(1993-1995)CGC>CAC	p.R665H	DAAM2_uc003oox.2_Missense_Mutation_p.R665H|uc003ooz.1_5'Flank	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of	665	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42235995	42235995	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42235995C>A	uc003osd.2	-	5	1897	c.1334G>T	c.(1333-1335)AGC>ATC	p.S445I	TRERF1_uc011duq.1_Missense_Mutation_p.S445I|TRERF1_uc003osb.2_Missense_Mutation_p.S284I|TRERF1_uc003osc.2_Missense_Mutation_p.S284I|TRERF1_uc003ose.2_Missense_Mutation_p.S445I	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	445	Interacts with CREBBP.				cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
KLHDC3	116138	broad.mit.edu	37	6	42985287	42985287	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42985287T>C	uc003otl.2	+	3	354	c.185T>C	c.(184-186)GTG>GCG	p.V62A	KLHDC3_uc003otm.2_RNA|KLHDC3_uc010jyf.2_Missense_Mutation_p.V62A|KLHDC3_uc003otn.2_5'UTR|KLHDC3_uc003oto.2_Intron	NM_057161	NP_476502	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	62	Kelch 1.				reciprocal meiotic recombination	cytoplasm|nuclear chromatin	chromatin binding|protein binding			upper_aerodigestive_tract(1)	1			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
KLHDC3	116138	broad.mit.edu	37	6	42985348	42985348	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42985348C>T	uc003otl.2	+	3	415	c.246C>T	c.(244-246)ACC>ACT	p.T82T	KLHDC3_uc003otm.2_RNA|KLHDC3_uc010jyf.2_Silent_p.T82T|KLHDC3_uc003otn.2_Missense_Mutation_p.P5L|KLHDC3_uc003oto.2_Intron	NM_057161	NP_476502	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	82					reciprocal meiotic recombination	cytoplasm|nuclear chromatin	chromatin binding|protein binding			upper_aerodigestive_tract(1)	1			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
CUL7	9820	broad.mit.edu	37	6	43020031	43020031	+	Missense_Mutation	SNP	G	A	A	rs111471694	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43020031G>A	uc003otq.2	-	2	799	c.496C>T	c.(496-498)CTC>TTC	p.L166F	CUL7_uc011dvb.1_Missense_Mutation_p.L218F|CUL7_uc010jyh.2_Intron|KLC4_uc003otr.1_Intron	NM_014780	NP_055595	Q14999	CUL7_HUMAN	cullin 7	166					interspecies interaction between organisms|ubiquitin-dependent protein catabolic process|vasculogenesis	anaphase-promoting complex|mitochondrion	ubiquitin protein ligase binding			ovary(3)|kidney(1)	4			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
KLC4	89953	broad.mit.edu	37	6	43038549	43038549	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43038549C>T	uc003otv.1	+	8	1178	c.1101C>T	c.(1099-1101)TAC>TAT	p.Y367Y	KLC4_uc003otr.1_RNA|KLC4_uc011dvd.1_Silent_p.Y290Y|KLC4_uc003otw.1_Silent_p.Y385Y|KLC4_uc003otx.1_Silent_p.Y367Y|KLC4_uc003oty.1_Silent_p.Y367Y|KLC4_uc003otz.1_Silent_p.Y367Y	NM_201521	NP_958929	Q9NSK0	KLC4_HUMAN	kinesin-like 8 isoform a	367	TPR 5.					cytoplasm|kinesin complex|microtubule	microtubule motor activity|protein binding			skin(3)|ovary(1)	4			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43107208	43107208	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43107208G>T	uc003oub.1	+	10	1761	c.1563G>T	c.(1561-1563)ACG>ACT	p.T521T	PTK7_uc003ouc.1_Silent_p.T521T|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Silent_p.T529T|PTK7_uc010jyj.1_Intron	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	521	Ig-like C2-type 6.|Extracellular (Potential).				actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)															---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43305961	43305961	+	Silent	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43305961A>T	uc003oux.2	-	10	5853	c.5775T>A	c.(5773-5775)GCT>GCA	p.A1925A	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1925					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
AARS2	57505	broad.mit.edu	37	6	44272192	44272192	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44272192G>A	uc010jza.1	-	13	1834	c.1831C>T	c.(1831-1833)CGG>TGG	p.R611W	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial	611					alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		L-Alanine(DB00160)											OREG0017473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RCAN2	10231	broad.mit.edu	37	6	46191032	46191032	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46191032T>G	uc003oyb.1	-	4	755	c.440A>C	c.(439-441)AAG>ACG	p.K147T	RCAN2_uc003oyc.1_Missense_Mutation_p.K193T|RCAN2_uc003oyd.1_Missense_Mutation_p.K193T	NM_005822	NP_005813	Q14206	RCAN2_HUMAN	Down syndrome critical region gene 1-like 1	147					calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0																		---	---	---	---
GPR116	221395	broad.mit.edu	37	6	46834811	46834811	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46834811A>G	uc003oyo.3	-	13	1974	c.1685T>C	c.(1684-1686)GTT>GCT	p.V562A	GPR116_uc011dwj.1_Missense_Mutation_p.V117A|GPR116_uc011dwk.1_5'UTR|GPR116_uc003oyp.3_Missense_Mutation_p.V420A|GPR116_uc003oyq.3_Missense_Mutation_p.V562A|GPR116_uc010jzi.1_Missense_Mutation_p.V234A	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	562	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)															---	---	---	---
GPR115	221393	broad.mit.edu	37	6	47682301	47682301	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47682301C>T	uc003oza.1	+	6	1578	c.1320C>T	c.(1318-1320)CAC>CAT	p.H440H	GPR115_uc003oyz.1_Silent_p.H497H|GPR115_uc003ozb.1_Silent_p.H438H	NM_153838	NP_722580	Q8IZF3	GP115_HUMAN	G-protein coupled receptor 115 precursor	440	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8																		---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51774262	51774262	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51774262C>T	uc003pah.1	-	40	6777	c.6501G>A	c.(6499-6501)CAG>CAA	p.Q2167Q	PKHD1_uc010jzn.1_Silent_p.Q192Q|PKHD1_uc003pai.2_Silent_p.Q2167Q	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2167	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51918008	51918008	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51918008C>T	uc003pah.1	-	21	2282	c.2006G>A	c.(2005-2007)CGT>CAT	p.R669H	PKHD1_uc003pai.2_Missense_Mutation_p.R669H	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	669	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
EFHC1	114327	broad.mit.edu	37	6	52373024	52373024	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52373024G>A	uc011dwv.1	+						TRAM2_uc003paq.2_Intron|TRAM2_uc003par.1_5'Flank					SubName: Full=cDNA FLJ51667, highly similar to EF-hand domain-containing protein 1;							axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)|skin(1)	3	Lung NSC(77;0.109)																	---	---	---	---
FAM83B	222584	broad.mit.edu	37	6	54804497	54804497	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54804497T>C	uc003pck.2	+							NM_001010872	NP_001010872			hypothetical protein LOC222584											ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)																	---	---	---	---
DST	667	broad.mit.edu	37	6	56392287	56392287	+	Intron	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56392287T>G	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56472756	56472756	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56472756C>A	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Nonsense_Mutation_p.G1687*	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64422093	64422093	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64422093T>C	uc003pep.1	+	15	4635	c.4609T>C	c.(4609-4611)TCA>CCA	p.S1537P	PHF3_uc003pen.2_Missense_Mutation_p.S1449P|PHF3_uc011dxs.1_Missense_Mutation_p.S806P	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1537					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72967845	72967845	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72967845G>A	uc003pga.2	+	17	2865	c.2788G>A	c.(2788-2790)GCT>ACT	p.A930T	RIMS1_uc011dyb.1_Missense_Mutation_p.A555T|RIMS1_uc003pgc.2_Missense_Mutation_p.A556T|RIMS1_uc010kaq.2_Missense_Mutation_p.A403T|RIMS1_uc011dyc.1_Missense_Mutation_p.A404T|RIMS1_uc010kar.2_Missense_Mutation_p.A323T|RIMS1_uc011dyd.1_Missense_Mutation_p.A389T|RIMS1_uc003pgf.2_Missense_Mutation_p.A146T|RIMS1_uc003pgg.2_Missense_Mutation_p.A147T|RIMS1_uc003pgi.2_Missense_Mutation_p.A146T|RIMS1_uc003pgh.2_Missense_Mutation_p.A146T|RIMS1_uc003pgd.2_Missense_Mutation_p.A147T|RIMS1_uc003pge.2_Missense_Mutation_p.A147T|RIMS1_uc011dye.1_5'UTR|RIMS1_uc011dyf.1_5'Flank|RIMS1_uc003pgb.3_Missense_Mutation_p.A556T|RIMS1_uc010kas.1_Missense_Mutation_p.A389T	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	930					calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
C6orf150	115004	broad.mit.edu	37	6	74150030	74150030	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74150030C>T	uc003pgx.1	-	3	1155	c.1016G>A	c.(1015-1017)CGC>CAC	p.R339H		NM_138441	NP_612450	Q8N884	M21D1_HUMAN	hypothetical protein LOC115004	339											0																		---	---	---	---
MTO1	25821	broad.mit.edu	37	6	74191907	74191907	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74191907C>T	uc003pgy.3	+	9	1604	c.1480C>T	c.(1480-1482)CGA>TGA	p.R494*	MTO1_uc010kav.2_Nonsense_Mutation_p.R509*|MTO1_uc003pgz.3_Nonsense_Mutation_p.R469*|MTO1_uc003pha.3_Nonsense_Mutation_p.R131*|MTO1_uc003phb.3_Nonsense_Mutation_p.R420*	NM_133645	NP_598400	Q9Y2Z2	MTO1_HUMAN	mitochondrial translation optimization 1 homolog	494					tRNA processing	mitochondrion	flavin adenine dinucleotide binding			ovary(3)|skin(2)|pancreas(1)	6																		---	---	---	---
SLC17A5	26503	broad.mit.edu	37	6	74310100	74310100	+	Missense_Mutation	SNP	C	T	T	rs74360232	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74310100C>T	uc003phn.3	-	10	1452	c.1324G>A	c.(1324-1326)GTC>ATC	p.V442I	SLC17A5_uc010kax.2_Missense_Mutation_p.V101I|SLC17A5_uc010kay.2_RNA|SLC17A5_uc011dyo.1_Silent_p.P261P	NM_012434	NP_036566	Q9NRA2	S17A5_HUMAN	sialin	442	Helical; (Potential).				anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75861578	75861578	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75861578C>T	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
LCA5	167691	broad.mit.edu	37	6	80196908	80196908	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80196908G>T	uc003pix.2	-	8	2342	c.1907C>A	c.(1906-1908)CCT>CAT	p.P636H	LCA5_uc003piy.2_Missense_Mutation_p.P636H	NM_001122769	NP_001116241	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	636					protein transport	cilium axoneme|microtubule basal body	protein binding				0		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)														---	---	---	---
RARS2	57038	broad.mit.edu	37	6	88251634	88251634	+	Splice_Site	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88251634A>T	uc003pme.2	-	8	672	c.612_splice	c.e8+1	p.E204_splice	RARS2_uc003pmb.2_Splice_Site_p.E29_splice|RARS2_uc003pmc.2_Splice_Site_p.E29_splice|RARS2_uc003pmd.2_Splice_Site|RARS2_uc003pmf.2_Splice_Site	NM_020320	NP_064716			arginyl-tRNA synthetase 2, mitochondrial						arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90340310	90340310	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90340310G>A	uc003pni.3	+	16	2112	c.1771G>A	c.(1771-1773)GTC>ATC	p.V591I	ANKRD6_uc003pne.3_Missense_Mutation_p.V586I|ANKRD6_uc003pnf.3_Missense_Mutation_p.V556I|ANKRD6_uc011dzy.1_Missense_Mutation_p.V591I|ANKRD6_uc010kcd.2_Missense_Mutation_p.V527I|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.3_Missense_Mutation_p.V187I|LYRM2_uc010kcf.1_Intron|ANKRD6_uc003pnj.3_Missense_Mutation_p.V187I	NM_014942	NP_055757	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	591							protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90489947	90489947	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90489947A>T	uc003pnn.1	-	11	1825	c.1709T>A	c.(1708-1710)TTA>TAA	p.L570*	MDN1_uc003pno.1_5'UTR	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	570					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
FUT9	10690	broad.mit.edu	37	6	96651245	96651245	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96651245C>A	uc003pop.3	+	3	555	c.214C>A	c.(214-216)CCA>ACA	p.P72T		NM_006581	NP_006572	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3)	72	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101053542	101053542	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101053542C>T	uc003pqk.2	-	33	5408	c.5079G>A	c.(5077-5079)CCG>CCA	p.P1693P		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	1693	Helicase C-terminal 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102376410	102376410	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102376410G>A	uc003pqp.3	+	13	2237	c.1988G>A	c.(1987-1989)CGC>CAC	p.R663H	GRIK2_uc003pqo.3_Missense_Mutation_p.R663H|GRIK2_uc010kcw.2_Missense_Mutation_p.R663H	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	663	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
TRAF3IP2	10758	broad.mit.edu	37	6	111887690	111887690	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111887690T>C	uc011ebc.1	-	8	2048	c.1433A>G	c.(1432-1434)GAC>GGC	p.D478G	TRAF3IP2_uc011ebb.1_Missense_Mutation_p.D22G|TRAF3IP2_uc003pvd.2_Missense_Mutation_p.D70G|TRAF3IP2_uc003pvg.2_Missense_Mutation_p.D477G|TRAF3IP2_uc003pvf.2_Missense_Mutation_p.D478G	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	487	SEFIR.				intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)														---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112476858	112476858	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112476858G>A	uc003pvu.2	-	15	2177	c.1868C>T	c.(1867-1869)GCA>GTA	p.A623V	LAMA4_uc003pvv.2_Missense_Mutation_p.A616V|LAMA4_uc003pvt.2_Missense_Mutation_p.A616V	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	623	Domain II and I.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
GPRC6A	222545	broad.mit.edu	37	6	117113849	117113849	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117113849T>C	uc003pxj.1	-	6	2259	c.2237A>G	c.(2236-2238)GAG>GGG	p.E746G	GPRC6A_uc003pxk.1_Missense_Mutation_p.E571G|GPRC6A_uc003pxl.1_Missense_Mutation_p.E675G	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,	746	Extracellular (Potential).				response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)|skin(2)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)														---	---	---	---
GPRC6A	222545	broad.mit.edu	37	6	117127635	117127635	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117127635G>A	uc003pxj.1	-	3	1255	c.1233C>T	c.(1231-1233)CTC>CTT	p.L411L	GPRC6A_uc003pxk.1_Intron|GPRC6A_uc003pxl.1_Silent_p.L411L	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,	411	Extracellular (Potential).				response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)|skin(2)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)														---	---	---	---
RFX6	222546	broad.mit.edu	37	6	117241610	117241610	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117241610C>T	uc003pxm.2	+	12	1383	c.1320C>T	c.(1318-1320)TAC>TAT	p.Y440Y		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	440					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
RFX6	222546	broad.mit.edu	37	6	117244396	117244396	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117244396C>T	uc003pxm.2	+							NM_173560	NP_775831			regulatory factor X, 6						glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
HSF2	3298	broad.mit.edu	37	6	122753259	122753259	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122753259G>A	uc003pyu.2	+	13	1692	c.1505G>A	c.(1504-1506)CGC>CAC	p.R502H	HSF2_uc003pyv.2_Missense_Mutation_p.R484H	NM_004506	NP_004497	Q03933	HSF2_HUMAN	heat shock transcription factor 2 isoform a	502					response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)														---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127797044	127797044	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127797044G>A	uc003qbd.2	-	6	2992	c.2127C>T	c.(2125-2127)CGC>CGT	p.R709R	C6orf174_uc003qbc.2_5'Flank	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor	709	Potential.					integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130399738	130399738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130399738G>A	uc003qbt.2	+	14	1450	c.1280G>A	c.(1279-1281)GGT>GAT	p.G427D	L3MBTL3_uc003qbu.2_Missense_Mutation_p.G402D	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a	427	MBT 2.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)														---	---	---	---
MED23	9439	broad.mit.edu	37	6	131924311	131924311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131924311G>A	uc003qcs.1	-	16	1964	c.1790C>T	c.(1789-1791)GCA>GTA	p.A597V	MED23_uc003qcq.2_Missense_Mutation_p.A603V|MED23_uc011eca.1_Missense_Mutation_p.A238V|MED23_uc003qct.1_Missense_Mutation_p.A603V|MED23_uc011ecb.1_RNA	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	597					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
TAAR1	134864	broad.mit.edu	37	6	132966641	132966641	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132966641C>T	uc003qdm.1	-	1	502	c.502G>A	c.(502-504)GCT>ACT	p.A168T		NM_138327	NP_612200	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	168	Extracellular (Potential).					plasma membrane					0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)													---	---	---	---
BCLAF1	9774	broad.mit.edu	37	6	136599544	136599544	+	Nonsense_Mutation	SNP	G	A	A	rs140155621	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136599544G>A	uc003qgx.1	-	4	728	c.475C>T	c.(475-477)CGA>TGA	p.R159*	BCLAF1_uc003qgw.1_Nonsense_Mutation_p.R159*|BCLAF1_uc003qgy.1_Nonsense_Mutation_p.R157*|BCLAF1_uc011edc.1_RNA|BCLAF1_uc011edd.1_RNA|BCLAF1_uc011ede.1_Nonsense_Mutation_p.R157*	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	159					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)														---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139202243	139202243	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139202243G>A	uc003qif.1	+	13	1918	c.1815G>A	c.(1813-1815)GCG>GCA	p.A605A	ECT2L_uc011edq.1_Silent_p.A536A	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2	605	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
TXLNB	167838	broad.mit.edu	37	6	139583871	139583871	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139583871T>C	uc011eds.1	-	5	892	c.727A>G	c.(727-729)AGG>GGG	p.R243G		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	243	Potential.					cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143074547	143074547	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143074547G>A	uc003qjd.2	-	10	7781	c.7038C>T	c.(7036-7038)CTC>CTT	p.L2346L		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	2346					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146231594	146231594	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146231594A>T	uc003qlf.2	-	25	4904	c.4505T>A	c.(4504-4506)ATC>AAC	p.I1502N	SHPRH_uc003qld.2_Missense_Mutation_p.I1506N|SHPRH_uc003qle.2_Missense_Mutation_p.I1506N|SHPRH_uc003qlg.1_Missense_Mutation_p.I1058N	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1502					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
RBM16	22828	broad.mit.edu	37	6	155131216	155131216	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155131216C>T	uc003qqa.2	+	13	1526	c.1294C>T	c.(1294-1296)CGC>TGC	p.R432C	RBM16_uc011efj.1_Missense_Mutation_p.R498C|RBM16_uc011efk.1_Missense_Mutation_p.R477C|RBM16_uc003qpz.2_Missense_Mutation_p.R432C|RBM16_uc010kji.2_Missense_Mutation_p.R453C	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	432	Arg-rich.				mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155577970	155577970	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155577970T>C	uc003qqb.2	+	29	6094	c.4821T>C	c.(4819-4821)GCT>GCC	p.A1607A	TIAM2_uc003qqe.2_Silent_p.A1607A|TIAM2_uc010kjj.2_Silent_p.A1169A|TIAM2_uc003qqf.2_Silent_p.A983A|TIAM2_uc011efl.1_Silent_p.A951A|TIAM2_uc003qqg.2_Silent_p.A919A|TIAM2_uc003qqh.2_Silent_p.A532A|uc003qqi.1_5'Flank	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1607					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157502183	157502183	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157502183G>T	uc003qqn.2	+	12	3314	c.3162G>T	c.(3160-3162)TGG>TGT	p.W1054C	ARID1B_uc003qqo.2_Missense_Mutation_p.W1014C|ARID1B_uc003qqp.2_Missense_Mutation_p.W1001C|ARID1B_uc010kjl.2_Missense_Mutation_p.W199C	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1059	ARID.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157522231	157522231	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157522231A>G	uc003qqn.2	+	18	4601	c.4449A>G	c.(4447-4449)GTA>GTG	p.V1483V	ARID1B_uc003qqo.2_Silent_p.V1443V|ARID1B_uc003qqp.2_Silent_p.V1430V	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1488	Pro-rich.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158454638	158454638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158454638C>T	uc003qqx.1	+	4	712	c.637C>T	c.(637-639)CGC>TGC	p.R213C	SYNJ2_uc011efm.1_RNA|SYNJ2_uc003qqw.1_Missense_Mutation_p.R213C|SYNJ2_uc003qqy.1_5'UTR|SYNJ2_uc011efn.1_Missense_Mutation_p.R162C|SYNJ2_uc010kjo.1_Missense_Mutation_p.R162C	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	213	SAC.						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158924597	158924597	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158924597G>A	uc003qrf.2	+	13	5259	c.3902G>A	c.(3901-3903)AGC>AAC	p.S1301N	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	1301					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
ACAT2	39	broad.mit.edu	37	6	160188151	160188151	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160188151C>T	uc010kjy.2	+	3	436	c.305C>T	c.(304-306)GCA>GTA	p.A102V	ACAT2_uc011efw.1_Missense_Mutation_p.A131V	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2	102						mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
PNLDC1	154197	broad.mit.edu	37	6	160229771	160229771	+	Splice_Site	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160229771G>T	uc003qsx.1	+	8	701	c.530_splice	c.e8-1	p.G177_splice	PNLDC1_uc003qsy.1_Splice_Site_p.G188_splice	NM_173516	NP_775787			poly(A)-specific ribonuclease (PARN)-like domain							integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
PNLDC1	154197	broad.mit.edu	37	6	160241544	160241544	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160241544A>G	uc003qsx.1	+	19	1729	c.1558A>G	c.(1558-1560)ACC>GCC	p.T520A	PNLDC1_uc003qsy.1_Missense_Mutation_p.T531A	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain	520	Extracellular (Potential).					integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160468915	160468915	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160468915C>T	uc003qta.2	+	17	2469	c.2321C>T	c.(2320-2322)ACG>ATG	p.T774M		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	774	5.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
PLG	5340	broad.mit.edu	37	6	161139766	161139766	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161139766G>T	uc003qtm.3	+	9	1055	c.992G>T	c.(991-993)AGG>ATG	p.R331M		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	331	Kringle 3.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)													---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163735999	163735999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163735999G>A	uc003qua.2	+	7	1095	c.871G>A	c.(871-873)GAG>AAG	p.E291K	PACRG_uc003qub.2_Missense_Mutation_p.E252K|PACRG_uc003quc.2_Missense_Mutation_p.E252K|LOC285796_uc011egh.1_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1	291											0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169632132	169632132	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169632132G>A	uc003qwt.2	-	14	2342	c.2094C>T	c.(2092-2094)GAC>GAT	p.D698D		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	698	TSP type-3 1.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4088990	4088990	+	Silent	SNP	G	A	A	rs143539228	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4088990G>A	uc003smx.2	+	18	2752	c.2613G>A	c.(2611-2613)GCG>GCA	p.A871A	SDK1_uc010kso.2_Silent_p.A147A	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	871	Fibronectin type-III 3.				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)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4249804	4249804	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4249804G>A	uc003smx.2	+						SDK1_uc010kso.2_Intron|SDK1_uc003smy.2_Intron	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)														---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5265458	5265458	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5265458G>A	uc003snv.2	+	9	961	c.745G>A	c.(745-747)GTG>ATG	p.V249M	WIPI2_uc003snw.2_Missense_Mutation_p.V249M|WIPI2_uc003snx.2_Missense_Mutation_p.V231M|WIPI2_uc003sny.2_Missense_Mutation_p.V231M|WIPI2_uc010ksv.2_Missense_Mutation_p.V105M|WIPI2_uc003soa.2_Missense_Mutation_p.V190M|WIPI2_uc003sob.2_Translation_Start_Site	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	249	WD 2.				autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5751450	5751450	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5751450G>A	uc003soy.1	-	13	2022	c.1832C>T	c.(1831-1833)CCG>CTG	p.P611L	RNF216_uc010ksz.1_Missense_Mutation_p.P233L|RNF216_uc010kta.1_Missense_Mutation_p.P233L|RNF216_uc011jwj.1_Missense_Mutation_p.P233L|RNF216_uc003sox.1_Missense_Mutation_p.P668L	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b	611	IBR-type.				apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
PMS2	5395	broad.mit.edu	37	7	6043613	6043613	+	Silent	SNP	G	A	A	rs143162541		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6043613G>A	uc003spl.2	-	3	327	c.240C>T	c.(238-240)TTC>TTT	p.F80F	PMS2_uc003spj.2_Nonsense_Mutation_p.R9*|PMS2_uc003spk.2_5'UTR|PMS2_uc011jwl.1_5'UTR|PMS2_uc010ktg.2_5'UTR|PMS2_uc010kte.2_Silent_p.F80F|PMS2_uc010ktf.1_Silent_p.F80F	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	80					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)				Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
USP42	84132	broad.mit.edu	37	7	6178816	6178816	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6178816G>A	uc011jwo.1	+	5	770	c.647G>A	c.(646-648)GGC>GAC	p.G216D	USP42_uc011jwn.1_Missense_Mutation_p.G61D|USP42_uc010kth.1_Missense_Mutation_p.G149D|USP42_uc011jwp.1_Missense_Mutation_p.G216D|USP42_uc011jwq.1_5'UTR|USP42_uc011jwr.1_Missense_Mutation_p.G61D	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	216					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
USP42	84132	broad.mit.edu	37	7	6180567	6180567	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6180567C>T	uc011jwo.1	+	7	870	c.747C>T	c.(745-747)GGC>GGT	p.G249G	USP42_uc011jwn.1_Silent_p.G94G|USP42_uc010kth.1_Silent_p.G182G|USP42_uc011jwp.1_Silent_p.G249G|USP42_uc011jwq.1_Silent_p.G56G|USP42_uc011jwr.1_Silent_p.G94G	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	249					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11062581	11062581	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11062581T>C	uc003sry.1	+	6	1727	c.1292T>C	c.(1291-1293)ATG>ACG	p.M431T	PHF14_uc011jxi.1_Missense_Mutation_p.M146T|PHF14_uc003srz.2_Missense_Mutation_p.M431T|PHF14_uc011jxj.1_Missense_Mutation_p.M146T	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	431							zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
MEOX2	4223	broad.mit.edu	37	7	15652114	15652114	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15652114C>T	uc003stc.2	-	3	1094	c.813G>A	c.(811-813)GAG>GAA	p.E271E	MEOX2_uc011jxw.1_Silent_p.E271E	NM_005924	NP_005915	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	271					blood circulation|multicellular organismal development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)														---	---	---	---
AHR	196	broad.mit.edu	37	7	17382640	17382640	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17382640G>A	uc011jxz.1	+	11	3112	c.2499G>A	c.(2497-2499)CCG>CCA	p.P833P	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	833				LNETYPAELNNINNTQTTTHLQPLHHPSEARPFPDLTSSGF L -> FK (in Ref. 1; BAA03857).	apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
SP4	6671	broad.mit.edu	37	7	21469572	21469572	+	Silent	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21469572A>T	uc003sva.2	+	3	970	c.789A>T	c.(787-789)GGA>GGT	p.G263G	SP4_uc003svb.2_5'UTR	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	263					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21923959	21923959	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21923959C>T	uc003svc.2	+	77	12490	c.12459C>T	c.(12457-12459)GGC>GGT	p.G4153G		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	4153					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
CDCA7L	55536	broad.mit.edu	37	7	21946056	21946056	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21946056G>A	uc010kuk.2	-	6	892	c.772C>T	c.(772-774)CGG>TGG	p.R258W	CDCA7L_uc003sve.3_Missense_Mutation_p.R224W|CDCA7L_uc010kul.2_Missense_Mutation_p.R212W|CDCA7L_uc003svf.3_Missense_Mutation_p.R257W	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1	258					positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0																		---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23381773	23381773	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23381773G>A	uc003swg.2	-	10	1379	c.1113C>T	c.(1111-1113)AAC>AAT	p.N371N	IGF2BP3_uc003swf.2_Translation_Start_Site	NM_006547	NP_006538	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding	371					anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2																		---	---	---	---
HNRNPA2B1	3181	broad.mit.edu	37	7	26236264	26236264	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26236264T>C	uc003sxr.3	-	6	742	c.526A>G	c.(526-528)ACC>GCC	p.T176A	HNRNPA2B1_uc003sxs.3_Missense_Mutation_p.T164A	NM_031243	NP_112533	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	176	RRM 2.				RNA transport	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3								T	ETV1	prostate								---	---	---	---
ADCYAP1R1	117	broad.mit.edu	37	7	31142894	31142894	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31142894A>T	uc003tca.1	+	14	1313	c.1090A>T	c.(1090-1092)ATC>TTC	p.I364F	ADCYAP1R1_uc003tcb.1_Missense_Mutation_p.I343F|ADCYAP1R1_uc003tcc.1_Missense_Mutation_p.I392F|ADCYAP1R1_uc003tcd.1_Missense_Mutation_p.I392F|ADCYAP1R1_uc003tce.1_Missense_Mutation_p.I391F|ADCYAP1R1_uc003tcf.1_Missense_Mutation_p.I122F	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1	364	Helical; Name=6; (Potential).				activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32582834	32582834	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32582834T>C	uc003tcv.1	+	2	321	c.175T>C	c.(175-177)TTC>CTC	p.F59L	AVL9_uc011kai.1_Missense_Mutation_p.F59L|AVL9_uc010kwj.1_5'Flank	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	59						integral to membrane					0																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35029496	35029496	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35029496C>A	uc003tem.3	-	7	748	c.603G>T	c.(601-603)GAG>GAT	p.E201D		NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1	201	Helical; (Potential).					integral to membrane					0																		---	---	---	---
TBX20	57057	broad.mit.edu	37	7	35242274	35242274	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35242274C>T	uc011kas.1	-	8	1123	c.1112G>A	c.(1111-1113)AGC>AAC	p.S371N		NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN	T-box transcription factor TBX20	371						nucleus	DNA binding			central_nervous_system(1)	1																		---	---	---	---
GPR141	353345	broad.mit.edu	37	7	37780065	37780065	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37780065T>C	uc003tfm.1	+	1	70	c.70T>C	c.(70-72)TAC>CAC	p.Y24H	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	24	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3																		---	---	---	---
TARP	445347	broad.mit.edu	37	7	38304986	38304986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38304986C>T	uc003tge.1	-	5	1098	c.721G>A	c.(721-723)GTT>ATT	p.V241I	uc003tfz.1_Intron|TARP_uc003tgb.2_Missense_Mutation_p.V37I|TARP_uc003tgc.1_Missense_Mutation_p.V37I|TARP_uc003tgd.1_Missense_Mutation_p.V37I|TARP_uc010kxi.1_RNA|TARP_uc003tgf.1_RNA|TARP_uc003tgj.1_RNA|TARP_uc003tgh.1_RNA|TARP_uc003tgi.1_RNA|TARP_uc003tgg.1_RNA			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.	Error:Variant_position_missing_in_A2JGV3_after_alignment											0																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40789045	40789045	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40789045G>T	uc003thn.1	+	13	1147	c.1102G>T	c.(1102-1104)GGC>TGC	p.G368C	C7orf10_uc003thm.1_Missense_Mutation_p.G364C|C7orf10_uc003tho.1_Missense_Mutation_p.G320C	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13	375							transferase activity			ovary(2)	2																		---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42005557	42005557	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42005557G>A	uc011kbh.1	-	15	3205	c.3114C>T	c.(3112-3114)TCC>TCT	p.S1038S	GLI3_uc011kbg.1_Silent_p.S979S	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1038					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
MYL7	58498	broad.mit.edu	37	7	44178553	44178553	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44178553G>A	uc003tkg.2	-	7	507	c.495C>T	c.(493-495)TAC>TAT	p.Y165Y		NM_021223	NP_067046	Q01449	MLRA_HUMAN	myosin light chain 2a	165	EF-hand 3.				actin filament-based movement|smooth muscle contraction	A band|myosin complex	ATPase activity, coupled|calcium ion binding|microfilament motor activity				0																		---	---	---	---
NUDCD3	23386	broad.mit.edu	37	7	44425623	44425623	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44425623G>A	uc003tkz.2	-	6	1259	c.1073C>T	c.(1072-1074)GCT>GTT	p.A358V	NUDCD3_uc010kye.2_RNA	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	358											0																		---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44733452	44733452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44733452C>T	uc003tln.2	+	11	1473	c.1364C>T	c.(1363-1365)GCC>GTC	p.A455V	OGDH_uc011kbx.1_Missense_Mutation_p.A451V|OGDH_uc011kby.1_Missense_Mutation_p.A305V|OGDH_uc003tlp.2_Missense_Mutation_p.A466V|OGDH_uc011kbz.1_Missense_Mutation_p.A250V|OGDH_uc003tlo.1_Missense_Mutation_p.A288V	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	455					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)													---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45747986	45747986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45747986C>T	uc003tne.3	+	18	2873	c.2855C>T	c.(2854-2856)GCG>GTG	p.A952V		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	952	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55241708	55241708	+	Missense_Mutation	SNP	G	A	A	rs121913428		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55241708G>A	uc003tqk.2	+	18	2402	c.2156G>A	c.(2155-2157)GGC>GAC	p.G719D	EGFR_uc010kzg.1_Missense_Mutation_p.G674D|EGFR_uc011kco.1_Missense_Mutation_p.G666D	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	719	Cytoplasmic (Potential).|Protein kinase.|ATP.		G -> A (found in a lung cancer sample).|G -> D (found in a lung cancer sample).|G -> S (found in a lung cancer sample; somatic mutation; strongly increased kinase activity).		activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.G719S(61)|p.G719A(52)|p.G719C(31)|p.G719?(9)|p.G719D(6)|p.G719V(1)|p.G719fs*29(1)		lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
LANCL2	55915	broad.mit.edu	37	7	55492992	55492992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55492992G>A	uc003tqp.2	+	7	1632	c.1054G>A	c.(1054-1056)GAT>AAT	p.D352N		NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2	352					negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)															---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56088834	56088834	+	Silent	SNP	C	T	T	rs145408555	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56088834C>T	uc003trg.2	-	3	435	c.72G>A	c.(70-72)ACG>ACA	p.T24T	PSPH_uc003trh.2_Silent_p.T24T|PSPH_uc003tri.2_Silent_p.T24T|PSPH_uc003trj.2_Silent_p.T53T	NM_004577	NP_004568	P78330	SERB_HUMAN	phosphoserine phosphatase	24					L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
GUSB	2990	broad.mit.edu	37	7	65435316	65435316	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65435316G>A	uc003tun.2	-	9	1505	c.1429C>T	c.(1429-1431)CGG>TGG	p.R477W	GUSB_uc011kdt.1_Missense_Mutation_p.R331W	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	477			R -> W (in MPS7).		glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0																		---	---	---	---
TBL2	26608	broad.mit.edu	37	7	72985146	72985146	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72985146G>A	uc003tyh.2	-	7	1169	c.1035C>T	c.(1033-1035)GTC>GTT	p.V345V	TBL2_uc011kex.1_Silent_p.V309V|TBL2_uc010lbg.2_Silent_p.V250V|TBL2_uc003tyi.2_Silent_p.V180V|TBL2_uc011key.1_Silent_p.V216V|TBL2_uc010lbh.2_Silent_p.V250V	NM_012453	NP_036585	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	345	WD 6.										0		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
STX1A	6804	broad.mit.edu	37	7	73117219	73117219	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73117219G>A	uc003tyx.2	-	8	661	c.634C>T	c.(634-636)CTA>TTA	p.L212L	WBSCR22_uc003tyw.1_Intron|STX1A_uc003tyy.2_Silent_p.L212L|STX1A_uc010lbj.1_Silent_p.L212L	NM_004603	NP_004594	Q16623	STX1A_HUMAN	syntaxin 1A isoform 1	212	Cytoplasmic (Potential).|t-SNARE coiled-coil homology.				energy reserve metabolic process|glutamate secretion|intracellular protein transport|regulation of insulin secretion	cell junction|extracellular region|integral to membrane|neuron projection|synaptic vesicle membrane|synaptosome	SNAP receptor activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
STX1A	6804	broad.mit.edu	37	7	73119544	73119544	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73119544C>A	uc003tyx.2	-	4	246	c.219G>T	c.(217-219)GAG>GAT	p.E73D	STX1A_uc003tyy.2_Missense_Mutation_p.E73D|STX1A_uc010lbj.1_Missense_Mutation_p.E73D	NM_004603	NP_004594	Q16623	STX1A_HUMAN	syntaxin 1A isoform 1	73	Potential.|Cytoplasmic (Potential).			E -> V (in Ref. 8; AAA20940).	energy reserve metabolic process|glutamate secretion|intracellular protein transport|regulation of insulin secretion	cell junction|extracellular region|integral to membrane|neuron projection|synaptic vesicle membrane|synaptosome	SNAP receptor activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
WBSCR28	135886	broad.mit.edu	37	7	73279571	73279571	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73279571G>A	uc003tzk.2	+	2	357	c.321G>A	c.(319-321)AAG>AAA	p.K107K	RFC2_uc011kfa.1_Intron|WBSCR28_uc003tzl.2_Silent_p.K6K	NM_182504	NP_872310	Q6UE05	WBS28_HUMAN	hypothetical protein LOC135886	107						integral to membrane				breast(1)	1		Lung NSC(55;0.159)																---	---	---	---
LIMK1	3984	broad.mit.edu	37	7	73520485	73520485	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73520485G>A	uc003uaa.1	+	7	958	c.793G>A	c.(793-795)GGG>AGG	p.G265R	RFC2_uc011kfa.1_Intron|LIMK1_uc010lbl.1_RNA|LIMK1_uc003uab.2_Missense_Mutation_p.G231R|LIMK1_uc003uac.1_Missense_Mutation_p.G57R	NM_002314	NP_002305	P53667	LIMK1_HUMAN	LIM domain kinase 1	265					actin cytoskeleton organization|axon guidance|negative regulation of ubiquitin-protein ligase activity|positive regulation of actin filament bundle assembly|positive regulation of axon extension|Rho protein signal transduction	cytosol|growth cone|nucleus	ATP binding|heat shock protein binding|protein serine/threonine kinase activity|zinc ion binding			stomach(2)|ovary(1)	3		Lung NSC(55;0.137)																---	---	---	---
LIMK1	3984	broad.mit.edu	37	7	73535239	73535239	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73535239C>T	uc003uaa.1	+	15	1806	c.1641C>T	c.(1639-1641)AAC>AAT	p.N547N	RFC2_uc011kfa.1_Intron|LIMK1_uc010lbl.1_RNA|LIMK1_uc003uab.2_Silent_p.N513N	NM_002314	NP_002305	P53667	LIMK1_HUMAN	LIM domain kinase 1	547	Protein kinase.				actin cytoskeleton organization|axon guidance|negative regulation of ubiquitin-protein ligase activity|positive regulation of actin filament bundle assembly|positive regulation of axon extension|Rho protein signal transduction	cytosol|growth cone|nucleus	ATP binding|heat shock protein binding|protein serine/threonine kinase activity|zinc ion binding			stomach(2)|ovary(1)	3		Lung NSC(55;0.137)																---	---	---	---
SRRM3	222183	broad.mit.edu	37	7	75890723	75890723	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75890723G>A	uc010ldi.2	+	7	838	c.629G>A	c.(628-630)CGC>CAC	p.R210H		NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0																		---	---	---	---
YWHAG	7532	broad.mit.edu	37	7	75959098	75959098	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75959098G>A	uc011kgj.1	-	2	757	c.540C>T	c.(538-540)TCC>TCT	p.S180S		NM_012479	NP_036611	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan	180					G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity			ovary(1)|lung(1)	2																		---	---	---	---
SRCRB4D	136853	broad.mit.edu	37	7	76019438	76019438	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76019438G>A	uc003ufb.2	-	11	2014	c.1666C>T	c.(1666-1668)CGC>TGC	p.R556C	SRCRB4D_uc003ufa.2_Silent_p.S57S	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	556	SRCR 4.					extracellular region|membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
PTPN12	5782	broad.mit.edu	37	7	77212874	77212874	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77212874C>T	uc003ugh.2	+	4	379	c.288C>T	c.(286-288)GGC>GGT	p.G96G	PTPN12_uc011kgp.1_5'UTR|PTPN12_uc011kgq.1_Intron|PTPN12_uc010ldq.1_RNA|PTPN12_uc010ldr.1_Intron	NM_002835	NP_002826	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type	96	Tyrosine-protein phosphatase.					soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82544630	82544630	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82544630A>G	uc003uhx.2	-	7	12961	c.12672T>C	c.(12670-12672)ACT>ACC	p.T4224T	PCLO_uc003uhv.2_Silent_p.T4224T|PCLO_uc010lec.2_Silent_p.T1189T	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4155					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82581897	82581897	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82581897G>T	uc003uhx.2	-	5	8661	c.8372C>A	c.(8371-8373)GCC>GAC	p.A2791D	PCLO_uc003uhv.2_Missense_Mutation_p.A2791D|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2722					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82583097	82583097	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82583097C>T	uc003uhx.2	-	5	7461	c.7172G>A	c.(7171-7173)CGC>CAC	p.R2391H	PCLO_uc003uhv.2_Missense_Mutation_p.R2391H|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2322	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82784604	82784604	+	Silent	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82784604A>C	uc003uhx.2	-	2	1642	c.1353T>G	c.(1351-1353)GCT>GCG	p.A451A	PCLO_uc003uhv.2_Silent_p.A451A	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	402	Gln-rich.|Pro-rich.|10 X 10 AA tandem approximate repeats of P-A-K-P-Q-P-Q-Q-P-X.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
GRM3	2913	broad.mit.edu	37	7	86416033	86416033	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86416033A>G	uc003uid.2	+	3	2024	c.925A>G	c.(925-927)ATC>GTC	p.I309V	GRM3_uc010lef.2_Missense_Mutation_p.I307V|GRM3_uc010leg.2_Missense_Mutation_p.I181V|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	309	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
ABCB4	5244	broad.mit.edu	37	7	87041227	87041227	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87041227C>T	uc003uiv.1	-	23	2982	c.2906G>A	c.(2905-2907)CGC>CAC	p.R969H	ABCB4_uc003uiw.1_Missense_Mutation_p.R969H|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	969	Extracellular (By similarity).|ABC transmembrane type-1 2.				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)																	---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88964130	88964130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88964130G>A	uc011khi.1	+	4	2372	c.1834G>A	c.(1834-1836)GGC>AGC	p.G612S		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	612						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
FZD1	8321	broad.mit.edu	37	7	90895367	90895367	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90895367G>A	uc003ula.2	+	1	1585	c.1172G>A	c.(1171-1173)CGC>CAC	p.R391H		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	391	Extracellular (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)															---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91714121	91714121	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91714121T>C	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron|AKAP9_uc003ulk.2_Intron	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
COL1A2	1278	broad.mit.edu	37	7	94054967	94054967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94054967G>A	uc003ung.1	+	43	3298	c.2827G>A	c.(2827-2829)GGA>AGA	p.G943R	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	943					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)										HNSCC(75;0.22)			---	---	---	---
PEG10	23089	broad.mit.edu	37	7	94293260	94293260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94293260G>A	uc011kie.1	+	2	837	c.620G>A	c.(619-621)CGT>CAT	p.R207H		NM_001040152	NP_001035242	Q86TG7	PEG10_HUMAN	paternally expressed 10 isoform RF1	131	Necessary for interaction with ALK1.				apoptosis|cell differentiation|negative regulation of transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
ASNS	440	broad.mit.edu	37	7	97484728	97484728	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97484728G>A	uc003uot.3	-	9	1580	c.1074C>T	c.(1072-1074)AGC>AGT	p.S358S	ASNS_uc011kin.1_Silent_p.S275S|ASNS_uc003uou.3_Silent_p.S358S|ASNS_uc003uov.3_Silent_p.S358S|ASNS_uc011kio.1_Silent_p.S337S|ASNS_uc003uow.3_Silent_p.S337S|ASNS_uc003uox.3_Silent_p.S275S	NM_133436	NP_597680	P08243	ASNS_HUMAN	asparagine synthetase	358	Asparagine synthetase.			RKNTDSVV -> GRTQIAWL (in Ref. 8; AAA36781).	cellular response to glucose starvation|glutamine metabolic process|negative regulation of apoptosis|positive regulation of mitotic cell cycle	cytosol|soluble fraction	asparagine synthase (glutamine-hydrolyzing) activity|ATP binding			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
ZNF394	84124	broad.mit.edu	37	7	99092193	99092193	+	Silent	SNP	C	T	T	rs145455958		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99092193C>T	uc003uqs.2	-	3	806	c.645G>A	c.(643-645)GCG>GCA	p.A215A	ZNF394_uc003uqt.2_Silent_p.A8A	NM_032164	NP_115540	Q53GI3	ZN394_HUMAN	zinc finger protein 394	215	KRAB.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)																	---	---	---	---
PILRB	29990	broad.mit.edu	37	7	99964982	99964982	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99964982G>A	uc003uuk.2	+	18	3162	c.666G>A	c.(664-666)GCG>GCA	p.A222A	PILRB_uc003uul.2_3'UTR|PILRB_uc003uun.2_Silent_p.A222A	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta	222	Cytoplasmic (Potential).				activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
MOSPD3	64598	broad.mit.edu	37	7	100210559	100210559	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100210559A>C	uc003uvq.2	+	2	347	c.145A>C	c.(145-147)AGC>CGC	p.S49R	MOSPD3_uc003uvr.2_Missense_Mutation_p.S49R|MOSPD3_uc003uvs.2_Missense_Mutation_p.S49R|MOSPD3_uc003uvt.2_Missense_Mutation_p.S49R	NM_001040097	NP_001035186	O75425	MSPD3_HUMAN	motile sperm domain containing 3 isoform a	49	MSP.					integral to membrane	structural molecule activity			ovary(2)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
LRWD1	222229	broad.mit.edu	37	7	102110260	102110260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102110260G>A	uc003uzn.2	+	11	1511	c.1373G>A	c.(1372-1374)CGC>CAC	p.R458H	LRWD1_uc003uzo.2_Missense_Mutation_p.R306H	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain	458	WD 2.				chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1																		---	---	---	---
NAPEPLD	222236	broad.mit.edu	37	7	102760494	102760494	+	Silent	SNP	C	T	T	rs144069186		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102760494C>T	uc003vbc.2	-	3	799	c.471G>A	c.(469-471)TCG>TCA	p.S157S	NAPEPLD_uc003vbd.2_Silent_p.S157S|NAPEPLD_uc011klj.1_Silent_p.S230S|NAPEPLD_uc003vbe.2_RNA	NM_198990	NP_945341	Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	157					phospholipid catabolic process	membrane	metal ion binding			skin(1)	1																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103368572	103368572	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103368572C>T	uc003vca.2	-	7	899	c.739G>A	c.(739-741)GGC>AGC	p.G247S	RELN_uc010liz.2_Missense_Mutation_p.G247S	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	247					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107414557	107414557	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107414557G>A	uc003ver.2	-	17	2026	c.1815C>T	c.(1813-1815)GAC>GAT	p.D605D	SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3	605	STAS.				excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107613491	107613491	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107613491T>A	uc003vew.2	-	13	1843	c.1508A>T	c.(1507-1509)GAT>GTT	p.D503V	LAMB1_uc003vev.2_Missense_Mutation_p.D527V|LAMB1_uc003vex.2_Missense_Mutation_p.D503V|LAMB1_uc010ljn.1_Missense_Mutation_p.D589V	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	503	Laminin EGF-like 4.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107638873	107638873	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107638873C>T	uc003vew.2	-	4	613	c.278G>A	c.(277-279)AGC>AAC	p.S93N	LAMB1_uc003vev.2_Missense_Mutation_p.S117N|LAMB1_uc003vex.2_Missense_Mutation_p.S93N|LAMB1_uc010ljn.1_Missense_Mutation_p.S179N	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	93	Laminin N-terminal.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110762960	110762960	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110762960A>G	uc003vft.3	+	4	1178	c.132A>G	c.(130-132)AGA>AGG	p.R44R	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Silent_p.R44R|LRRN3_uc003vfs.3_Silent_p.R44R	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	44	Extracellular (Potential).|LRRNT.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110764861	110764861	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110764861C>G	uc003vft.3	+	4	3079	c.2033C>G	c.(2032-2034)CCT>CGT	p.P678R	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.P678R|LRRN3_uc003vfs.3_Missense_Mutation_p.P678R	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	678	Cytoplasmic (Potential).					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111629110	111629110	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111629110C>T	uc003vfx.2	-	6	693	c.424G>A	c.(424-426)GTG>ATG	p.V142M	DOCK4_uc003vfy.2_Missense_Mutation_p.V142M|DOCK4_uc003vga.1_Translation_Start_Site|DOCK4_uc010ljt.1_Missense_Mutation_p.V142M|DOCK4_uc003vgb.1_Missense_Mutation_p.V66M	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	142					cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
TMEM168	64418	broad.mit.edu	37	7	112407288	112407288	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112407288C>A	uc003vgn.2	-	5	2450	c.2058G>T	c.(2056-2058)CTG>CTT	p.L686L	TMEM168_uc010lju.2_Silent_p.L686L|TMEM168_uc011kmr.1_Silent_p.L302L	NM_022484	NP_071929	Q9H0V1	TM168_HUMAN	transmembrane protein 168	686						integral to membrane|transport vesicle				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C7orf60	154743	broad.mit.edu	37	7	112462155	112462155	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112462155T>C	uc003vgo.1	-	5	989	c.862A>G	c.(862-864)ATG>GTG	p.M288V	C7orf60_uc011kms.1_Missense_Mutation_p.M314V	NM_152556	NP_689769	Q1RMZ1	CG060_HUMAN	hypothetical protein LOC154743	288										ovary(2)|skin(1)	3																		---	---	---	---
MET	4233	broad.mit.edu	37	7	116435720	116435720	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116435720C>T	uc003vij.2	+	20	3997	c.3810C>T	c.(3808-3810)GGC>GGT	p.G1270G	MET_uc010lkh.2_Silent_p.G1288G|MET_uc011knj.1_Silent_p.G840G	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	1270	Protein kinase.|Interaction with RANBP9.|Cytoplasmic (Potential).				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)					Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)		OREG0003446	type=REGULATORY REGION|Gene=MET|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117306983	117306983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117306983C>T	uc003vjd.2	+	27	4396	c.4264C>T	c.(4264-4266)CGG>TGG	p.R1422W	CFTR_uc011knq.1_Missense_Mutation_p.R828W	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	1422	Cytoplasmic (Potential).|ABC transporter 2.				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120884296	120884296	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120884296G>A	uc003vjq.3	+	18	2661	c.2214G>A	c.(2212-2214)AGG>AGA	p.R738R	C7orf58_uc003vjs.3_Silent_p.R738R|C7orf58_uc003vjt.3_Silent_p.R518R	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	738						endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)																	---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121659304	121659304	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121659304G>A	uc003vjy.2	+	13	5365	c.4970G>A	c.(4969-4971)GGT>GAT	p.G1657D	PTPRZ1_uc003vjz.2_Missense_Mutation_p.G797D|PTPRZ1_uc011knt.1_Missense_Mutation_p.G247D	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1657	Helical; (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
SLC13A1	6561	broad.mit.edu	37	7	122839969	122839969	+	Missense_Mutation	SNP	C	T	T	rs143242073	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122839969C>T	uc003vkm.2	-	1	57	c.32G>A	c.(31-33)CGC>CAC	p.R11H	SLC13A1_uc010lks.2_5'UTR	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	11						integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)													---	---	---	---
ZNF800	168850	broad.mit.edu	37	7	127014259	127014259	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127014259A>G	uc003vlx.1	-	5	1394	c.1131T>C	c.(1129-1131)CAT>CAC	p.H377H	ZNF800_uc003vlw.1_Silent_p.H280H|ZNF800_uc003vly.1_Silent_p.H377H|ZNF800_uc010lla.2_Silent_p.H377H	NM_176814	NP_789784	Q2TB10	ZN800_HUMAN	zinc finger protein 800	377	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
FSCN3	29999	broad.mit.edu	37	7	127235708	127235708	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127235708C>T	uc003vmd.1	+	2	711	c.492C>T	c.(490-492)GGC>GGT	p.G164G	FSCN3_uc003vmc.1_Silent_p.G119G|FSCN3_uc011kog.1_RNA|FSCN3_uc011koh.1_Silent_p.G30G|FSCN3_uc010llc.1_Silent_p.G164G	NM_020369	NP_065102	Q9NQT6	FSCN3_HUMAN	fascin 3	164						actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128478828	128478828	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128478828G>A	uc003vnz.3	+	8	1591	c.1382G>A	c.(1381-1383)CGC>CAC	p.R461H	FLNC_uc003voa.3_Missense_Mutation_p.R461H	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	461	Filamin 2.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128492747	128492747	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128492747G>A	uc003vnz.3	+	36	6154	c.5945G>A	c.(5944-5946)CGT>CAT	p.R1982H	FLNC_uc003voa.3_Missense_Mutation_p.R1949H	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1982	Filamin 18.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
IRF5	3663	broad.mit.edu	37	7	128586626	128586626	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128586626G>T	uc003vog.2	+						IRF5_uc010llr.1_Intron|IRF5_uc011kot.1_3'UTR|IRF5_uc011kou.1_Intron|IRF5_uc010lls.1_Intron|IRF5_uc003voh.2_Intron|IRF5_uc010llt.2_Intron|IRF5_uc003voi.2_Intron|IRF5_uc010llu.1_Intron|IRF5_uc003vok.2_Intron|IRF5_uc003voj.3_Intron|IRF5_uc010llv.1_Intron|IRF5_uc010llw.1_Intron	NM_002200	NP_002191			interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
FAM40B	57464	broad.mit.edu	37	7	129122880	129122880	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129122880C>T	uc011koy.1	+	20	2287	c.2247C>T	c.(2245-2247)TAC>TAT	p.Y749Y	FAM40B_uc003vow.2_Silent_p.Y749Y|FAM40B_uc011koz.1_Silent_p.Y241Y	NM_020704	NP_065755	Q9ULQ0	FA40B_HUMAN	hypothetical protein LOC57464 isoform a	749											0																		---	---	---	---
ZC3HC1	51530	broad.mit.edu	37	7	129662198	129662198	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129662198C>T	uc003vpi.2	-	9	1428	c.1401G>A	c.(1399-1401)GCG>GCA	p.A467A	ZC3HC1_uc003vph.2_Silent_p.A311A|ZC3HC1_uc010lma.2_Silent_p.A283A	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1	467					cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)																	---	---	---	---
CPA5	93979	broad.mit.edu	37	7	130007391	130007391	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130007391C>T	uc010lmd.1	+	12	1637	c.1017C>T	c.(1015-1017)CCC>CCT	p.P339P	CPA5_uc003vps.2_Silent_p.P339P|CPA5_uc003vpt.2_Silent_p.P339P|CPA5_uc010lme.1_Silent_p.P339P|CPA5_uc003vpu.1_Silent_p.P339P|uc003vpv.1_RNA	NM_001127441	NP_001120913	Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5 isoform 1	339					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134882825	134882825	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134882825C>T	uc003vsp.2	-	7	1032	c.970G>A	c.(970-972)GGT>AGT	p.G324S	WDR91_uc010lmq.2_5'UTR|WDR91_uc010lmr.2_RNA	NM_014149	NP_054868	A4D1P6	WDR91_HUMAN	WD repeat domain 91	324										breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135282121	135282121	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135282121G>A	uc003vsw.2	+	14	2050	c.2019G>A	c.(2017-2019)CTG>CTA	p.L673L		NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	673					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
SLC13A4	26266	broad.mit.edu	37	7	135384232	135384232	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135384232T>C	uc003vta.2	-	8	1465	c.776A>G	c.(775-777)CAC>CGC	p.H259R	SLC13A4_uc003vtb.2_Missense_Mutation_p.H260R	NM_012450	NP_036582	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate	259						integral to plasma membrane	sodium:sulfate symporter activity				0																		---	---	---	---
CHRM2	1129	broad.mit.edu	37	7	136700642	136700642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700642G>A	uc003vtf.1	+	4	1653	c.1030G>A	c.(1030-1032)GTG>ATG	p.V344M	CHRM2_uc003vtg.1_Missense_Mutation_p.V344M|CHRM2_uc003vtj.1_Missense_Mutation_p.V344M|CHRM2_uc003vtk.1_Missense_Mutation_p.V344M|CHRM2_uc003vtl.1_Missense_Mutation_p.V344M|CHRM2_uc003vtm.1_Missense_Mutation_p.V344M|CHRM2_uc003vti.1_Missense_Mutation_p.V344M|CHRM2_uc003vto.1_Missense_Mutation_p.V344M|CHRM2_uc003vtn.1_Missense_Mutation_p.V344M|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	344	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)													---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138602777	138602777	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138602777G>A	uc011kql.1	-	2	1644	c.1595C>T	c.(1594-1596)GCG>GTG	p.A532V	KIAA1549_uc003vuk.3_Missense_Mutation_p.A482V|KIAA1549_uc011kqj.1_Missense_Mutation_p.A532V	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	532	Ser-rich.					integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
TRPV5	56302	broad.mit.edu	37	7	142622773	142622773	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142622773C>T	uc003wby.1	-	8	1237	c.973G>A	c.(973-975)GGC>AGC	p.G325S	TRPV5_uc003wbz.2_Missense_Mutation_p.G325S	NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,	325	Cytoplasmic (Potential).				protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|skin(1)	6	Melanoma(164;0.059)																	---	---	---	---
OR2F2	135948	broad.mit.edu	37	7	143632600	143632600	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143632600T>A	uc011ktv.1	+	1	275	c.275T>A	c.(274-276)ATC>AAC	p.I92N		NM_001004685	NP_001004685	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F,	92	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	Melanoma(164;0.0903)																	---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146741074	146741074	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146741074C>T	uc003weu.1	+	4	994	c.478C>T	c.(478-480)CGC>TGC	p.R160C		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	160	F5/8 type C.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146805342	146805342	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146805342G>A	uc003weu.1	+	5	1170	c.654G>A	c.(652-654)ACG>ACA	p.T218T		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	218	Laminin G-like 1.|Extracellular (Potential).		T -> M.		behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	147675066	147675066	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147675066C>T	uc003weu.1	+	15	2884	c.2368C>T	c.(2368-2370)CGC>TGC	p.R790C		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	790	Extracellular (Potential).|Fibrinogen C-terminal.				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	148963903	148963903	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148963903G>A	uc003wfr.3	+											Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																														---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149476709	149476709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149476709C>T	uc010lpk.2	+	10	1159	c.1159C>T	c.(1159-1161)CGG>TGG	p.R387W	SSPO_uc010lpl.1_Intron	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	387	VWFD 1.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
GIMAP1	170575	broad.mit.edu	37	7	150417581	150417581	+	Silent	SNP	C	T	T	rs142477944	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150417581C>T	uc003whq.2	+	3	576	c.489C>T	c.(487-489)CAC>CAT	p.H163H	GIMAP1_uc003whp.2_Silent_p.H171H	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	163	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151802440	151802440	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151802440G>A	uc010lqg.1	+	5	927	c.697G>A	c.(697-699)GCG>ACG	p.A233T	GALNT11_uc011kvm.1_Missense_Mutation_p.A152T|GALNT11_uc003wku.2_Missense_Mutation_p.A233T|GALNT11_uc011kvn.1_RNA|GALNT11_uc003wkw.1_5'Flank	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	233	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)														---	---	---	---
ZNF596	169270	broad.mit.edu	37	8	195432	195432	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:195432G>A	uc003wot.2	+	6	873	c.585G>A	c.(583-585)TTG>TTA	p.L195L	ZNF596_uc003wou.2_Silent_p.L94L|ZNF596_uc003wov.2_Silent_p.L195L|ZNF596_uc003wow.2_Silent_p.L195L	NM_173539	NP_775810	Q8TC21	ZN596_HUMAN	zinc finger protein 596	195	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2026978	2026978	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2026978G>T	uc003wpx.3	+	12	1564	c.1426G>T	c.(1426-1428)GCT>TCT	p.A476S	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	476					muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3045488	3045488	+	Splice_Site	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3045488C>G	uc011kwk.1	-	36	5917	c.5527_splice	c.e36-1	p.I1843_splice	CSMD1_uc011kwj.1_Splice_Site_p.I1235_splice|CSMD1_uc003wqe.2_Splice_Site_p.I999_splice|CSMD1_uc010lrg.2_Splice_Site	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3216709	3216709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3216709C>T	uc011kwk.1	-	21	3662	c.3272G>A	c.(3271-3273)CGC>CAC	p.R1091H	CSMD1_uc011kwj.1_Missense_Mutation_p.R483H|CSMD1_uc003wqe.2_Missense_Mutation_p.R247H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1091	Sushi 6.|Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	4277535	4277535	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4277535T>C	uc011kwk.1	-	3	745	c.355A>G	c.(355-357)ACT>GCT	p.T119A		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	119	Extracellular (Potential).|CUB 1.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10466772	10466772	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10466772G>A	uc003wtc.2	-	4	5065	c.4836C>T	c.(4834-4836)GGC>GGT	p.G1612G		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1612					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10470173	10470173	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10470173C>T	uc003wtc.2	-	4	1664	c.1435G>A	c.(1435-1437)GGG>AGG	p.G479R		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	479					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10470278	10470278	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10470278C>T	uc003wtc.2	-	4	1559	c.1330G>A	c.(1330-1332)GGG>AGG	p.G444R		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	444					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10470720	10470720	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10470720C>T	uc003wtc.2	-	4	1117	c.888G>A	c.(886-888)ACG>ACA	p.T296T		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	296					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
USP17L2	377630	broad.mit.edu	37	8	11996040	11996040	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11996040G>A	uc003wvc.1	-	1	230	c.230C>T	c.(229-231)GCG>GTG	p.A77V	FAM66D_uc011kxp.1_Intron|FAM66D_uc011kxo.1_Intron	NM_201402	NP_958804	Q6R6M4	U17L2_HUMAN	deubiquitinating enzyme 3	77					apoptosis|cell cycle|G2/M transition checkpoint|mitotic cell cycle G1/S transition checkpoint|protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18393319	18393319	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18393319C>T	uc003wza.2	-	16	3181	c.3078G>A	c.(3076-3078)AAG>AAA	p.K1026K	PSD3_uc003wyx.3_Silent_p.K355K|PSD3_uc003wyy.2_Silent_p.K492K|PSD3_uc003wyz.2_Silent_p.K327K	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	1027					regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18656809	18656809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18656809C>T	uc003wza.2	-	8	2181	c.2078G>A	c.(2077-2079)GGC>GAC	p.G693D	PSD3_uc003wyy.2_Missense_Mutation_p.G159D|PSD3_uc003wyz.2_5'UTR	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	693	SEC7.				regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
HR	55806	broad.mit.edu	37	8	21984573	21984573	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21984573G>A	uc003xas.2	-	3	2047	c.1382C>T	c.(1381-1383)TCG>TTG	p.S461L	HR_uc003xat.2_Missense_Mutation_p.S461L	NM_005144	NP_005135	O43593	HAIR_HUMAN	hairless protein isoform a	461							DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22146070	22146070	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22146070A>C	uc003xbn.2	+	8	1025	c.877A>C	c.(877-879)AGT>CGT	p.S293R	PIWIL2_uc011kzf.1_Missense_Mutation_p.S293R|PIWIL2_uc010ltv.2_Missense_Mutation_p.S293R	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	293					DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
ADAM28	10863	broad.mit.edu	37	8	24187575	24187575	+	Silent	SNP	C	T	T	rs151133749	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24187575C>T	uc003xdy.2	+	11	1133	c.1050C>T	c.(1048-1050)GAC>GAT	p.D350D	ADAM28_uc003xdx.2_Silent_p.D350D|ADAM28_uc011kzz.1_Silent_p.D117D|ADAM28_uc011laa.1_RNA|ADAM28_uc010lua.2_Silent_p.D37D	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	350	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)														---	---	---	---
NEFM	4741	broad.mit.edu	37	8	24775222	24775222	+	Silent	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24775222A>C	uc003xed.3	+	3	1887	c.1854A>C	c.(1852-1854)CCA>CCC	p.P618P	NEFM_uc011lac.1_Intron|NEFM_uc010lue.2_Silent_p.P242P	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	618	6 X 13 AA approximate tandem repeats of K-S-P-V-[PS]-K-S-P-V-E-E-[KA]-[GAK].|1.|Tail.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
NEFM	4741	broad.mit.edu	37	8	24775225	24775225	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24775225A>G	uc003xed.3	+	3	1890	c.1857A>G	c.(1855-1857)AAA>AAG	p.K619K	NEFM_uc011lac.1_Intron|NEFM_uc010lue.2_Silent_p.K243K	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	619	6 X 13 AA approximate tandem repeats of K-S-P-V-[PS]-K-S-P-V-E-E-[KA]-[GAK].|1.|Tail.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
CDCA2	157313	broad.mit.edu	37	8	25341605	25341605	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25341605G>A	uc003xep.1	+	10	1723	c.1244G>A	c.(1243-1245)CGT>CAT	p.R415H	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_Missense_Mutation_p.R415H|CDCA2_uc003xeq.1_Missense_Mutation_p.R400H|CDCA2_uc003xer.1_Missense_Mutation_p.R78H	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	415					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26484126	26484126	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26484126G>A	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27277536	27277536	+	Missense_Mutation	SNP	C	T	T	rs149715605		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27277536C>T	uc003xfn.1	+	8	1137	c.329C>T	c.(328-330)ACG>ATG	p.T110M	PTK2B_uc003xfo.1_Missense_Mutation_p.T110M|PTK2B_uc003xfp.1_Missense_Mutation_p.T110M|PTK2B_uc003xfq.1_Missense_Mutation_p.T110M	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	110	FERM.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27288494	27288494	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27288494C>T	uc003xfn.1	+	13	1579	c.771C>T	c.(769-771)TTC>TTT	p.F257F	PTK2B_uc003xfo.1_Silent_p.F257F|PTK2B_uc003xfp.1_Silent_p.F257F|PTK2B_uc003xfq.1_Silent_p.F257F|PTK2B_uc010luq.1_Silent_p.F28F|PTK2B_uc003xfr.1_5'Flank	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	257	FERM.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
CHRNA2	1135	broad.mit.edu	37	8	27327303	27327303	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27327303A>G	uc010lur.2	-	3	878	c.269T>C	c.(268-270)CTG>CCG	p.L90P	CHRNA2_uc011lal.1_Intron|CHRNA2_uc010lus.2_5'UTR	NM_000742	NP_000733	Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha	90	Extracellular.					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(1)	1		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Gallamine Triethiodide(DB00483)|Levallorphan(DB00504)|Mecamylamine(DB00657)|Metocurine(DB01336)|Metocurine Iodide(DB00416)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Rocuronium(DB00728)|Tubocurarine(DB01199)													---	---	---	---
ESCO2	157570	broad.mit.edu	37	8	27660935	27660935	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27660935G>A	uc003xgg.2	+	11	1869	c.1786G>A	c.(1786-1788)GTA>ATA	p.V596I	ESCO2_uc010luy.1_Intron	NM_001017420	NP_001017420	Q56NI9	ESCO2_HUMAN	establishment of cohesion 1 homolog 2	596					cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding			central_nervous_system(1)	1		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)										SC_Phocomelia_syndrome				---	---	---	---
EXTL3	2137	broad.mit.edu	37	8	28574459	28574459	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28574459C>T	uc003xgz.1	+	3	1476	c.883C>T	c.(883-885)CGT>TGT	p.R295C		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	295	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding			skin(2)	2		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)														---	---	---	---
TMEM66	51669	broad.mit.edu	37	8	29927396	29927396	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29927396G>A	uc003xhs.2	-	3	646	c.462C>T	c.(460-462)GGC>GGT	p.G154G	TMEM66_uc003xht.2_Silent_p.G154G|TMEM66_uc003xhu.2_Silent_p.G118G|TMEM66_uc003xhv.2_5'UTR	NM_016127	NP_057211	Q96BY9	TMM66_HUMAN	transmembrane protein 66 precursor	154						integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)														---	---	---	---
BRF2	55290	broad.mit.edu	37	8	37702171	37702171	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37702171G>A	uc003xkk.2	-	4	1207	c.1097C>T	c.(1096-1098)CCG>CTG	p.P366L		NM_018310	NP_060780	Q9HAW0	BRF2_HUMAN	RNA polymerase III transcription initiation	366					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter|transcription initiation, DNA-dependent	nucleoplasm	protein binding|zinc ion binding				0		Lung NSC(58;0.118)|all_lung(54;0.195)	BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;1.81e-10)															---	---	---	---
AGPAT6	137964	broad.mit.edu	37	8	41456754	41456754	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41456754G>A	uc003xnz.2	+	2	1035	c.96G>A	c.(94-96)GTG>GTA	p.V32V		NM_178819	NP_848934	Q86UL3	GPAT4_HUMAN	lysophosphatidic acid acyltransferase zeta	32					acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity				0	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48710933	48710933	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48710933C>T	uc003xqi.2	-	74	10380	c.10323G>A	c.(10321-10323)GCG>GCA	p.A3441A	PRKDC_uc003xqj.2_Silent_p.A3441A|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	3441	FAT.				cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51415426	51415426	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51415426A>G	uc010lxy.1	+	10	823	c.452A>G	c.(451-453)AAT>AGT	p.N151S	SNTG1_uc003xqs.1_Missense_Mutation_p.N151S|SNTG1_uc010lxz.1_Missense_Mutation_p.N151S|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	151					cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)																---	---	---	---
RPS20	6224	broad.mit.edu	37	8	56985778	56985778	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56985778C>A	uc003xsn.2	-	4	429	c.231G>T	c.(229-231)TGG>TGT	p.W77C	RPS20_uc003xsm.2_Missense_Mutation_p.W77C	NM_001023	NP_001014	P60866	RS20_HUMAN	ribosomal protein S20 isoform 2	77					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.155)	Epithelial(17;0.00117)|all cancers(17;0.00879)															---	---	---	---
VCPIP1	80124	broad.mit.edu	37	8	67577776	67577776	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67577776C>T	uc003xwn.2	-	1	1677	c.1418G>A	c.(1417-1419)GGT>GAT	p.G473D	SGK3_uc003xwp.2_5'Flank|C8orf44_uc003xwo.1_5'Flank	NM_025054	NP_079330	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex	473					protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1)	8		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69021830	69021830	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69021830G>A	uc003xxv.1	+	25	3145	c.3118G>A	c.(3118-3120)GTG>ATG	p.V1040M	PREX2_uc011lez.1_Missense_Mutation_p.V975M	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1040					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69058592	69058592	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69058592A>G	uc003xxv.1	+							NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
PEX2	5828	broad.mit.edu	37	8	77896094	77896094	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77896094A>G	uc003yax.2	-	4	779	c.321T>C	c.(319-321)GCT>GCC	p.A107A	PEX2_uc003yay.2_Silent_p.A107A|PEX2_uc003yaz.2_Silent_p.A107A	NM_000318	NP_000309	P28328	PEX2_HUMAN	peroxin 2	107					peroxisome organization	integral to peroxisomal membrane	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81555315	81555315	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81555315G>A	uc003yby.1	-	8	1314	c.1082C>T	c.(1081-1083)GCG>GTG	p.A361V		NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	361						intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
LRRCC1	85444	broad.mit.edu	37	8	86041538	86041538	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86041538A>G	uc003ycw.2	+	10	1704	c.1550A>G	c.(1549-1551)CAC>CGC	p.H517R	LRRCC1_uc010lzz.1_Intron|LRRCC1_uc010maa.1_Missense_Mutation_p.H218R|LRRCC1_uc003ycx.2_Missense_Mutation_p.H424R|LRRCC1_uc003ycy.2_Missense_Mutation_p.H497R	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	517	Potential.				cell division|mitosis	centriole|nucleus					0																		---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94776096	94776096	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94776096T>A	uc011lgk.1	+	4	504	c.433T>A	c.(433-435)TTG>ATG	p.L145M	TMEM67_uc010mat.1_Missense_Mutation_p.L60M|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Missense_Mutation_p.L64M	NM_153704	NP_714915	Q5HYA8	MKS3_HUMAN	meckelin isoform 1	145					cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95524241	95524241	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95524241G>T	uc003ygo.1	-	12	2841	c.2828C>A	c.(2827-2829)CCA>CAA	p.P943Q	KIAA1429_uc003ygp.2_Missense_Mutation_p.P943Q|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	943	Poly-Pro.				mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95854570	95854570	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95854570T>C	uc003yhb.2	+						INTS8_uc003yha.1_Intron|INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
C8orf37	157657	broad.mit.edu	37	8	96281258	96281258	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96281258T>C	uc003yho.1	-							NM_177965	NP_808880			hypothetical protein LOC157657												0	Breast(36;3.41e-05)																	---	---	---	---
GDF6	392255	broad.mit.edu	37	8	97157019	97157019	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97157019G>T	uc003yhp.2	-	2	1240	c.1140C>A	c.(1138-1140)GCC>GCA	p.A380A		NM_001001557	NP_001001557	Q6KF10	GDF6_HUMAN	growth differentiation factor 6 precursor	380					activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(1)|breast(1)|pancreas(1)	3	Breast(36;2.67e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	98155278	98155278	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98155278A>G	uc003yhw.2	+	8	1452	c.1286A>G	c.(1285-1287)TAT>TGT	p.Y429C		NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor	429					peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
MATN2	4147	broad.mit.edu	37	8	99045884	99045884	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99045884C>T	uc003yic.2	+	18	3043	c.2812C>T	c.(2812-2814)CGC>TGC	p.R938C	MATN2_uc010mbh.1_Missense_Mutation_p.R897C|MATN2_uc003yid.2_Missense_Mutation_p.R919C|MATN2_uc003yie.1_Missense_Mutation_p.R938C|MATN2_uc010mbi.1_Missense_Mutation_p.R752C|MATN2_uc010mbj.1_Missense_Mutation_p.R299C|RPL30_uc010mbk.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	938	Potential.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
EIF3E	3646	broad.mit.edu	37	8	109260837	109260837	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109260837C>A	uc003ymu.2	-						EIF3E_uc003ymv.2_Intron|EIF3E_uc010mci.1_Intron|EIF3E_uc010mcj.1_Intron	NM_001568	NP_001559			eukaryotic translation initiation factor 3,						negative regulation of translational initiation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|eukaryotic translation initiation factor 3 complex|PML body	protein N-terminus binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110420412	110420412	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110420412A>G	uc003yne.2	+	18	2052	c.1948A>G	c.(1948-1950)ACT>GCT	p.T650A		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	650	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116426926	116426926	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116426926T>C	uc003ynz.2	-	6	3630	c.3171A>G	c.(3169-3171)GAA>GAG	p.E1057E	TRPS1_uc011lhy.1_Silent_p.E1061E|TRPS1_uc003yny.2_Silent_p.E1070E|TRPS1_uc010mcy.2_Silent_p.E1057E	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	1057	Mediates interaction with RNF4 (By similarity).				negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125520860	125520860	+	Silent	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125520860T>G	uc003yrd.2	-	7	501	c.459A>C	c.(457-459)TCA>TCC	p.S153S	TATDN1_uc003yre.2_RNA|TATDN1_uc010mdm.2_Silent_p.S106S|TATDN1_uc003yrf.2_Silent_p.S153S	NM_032026	NP_114415	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1 isoform a	153						nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131200388	131200388	+	Silent	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131200388A>T	uc003yta.1	-	5	475	c.447T>A	c.(445-447)TCT>TCA	p.S149S	ASAP1_uc011liw.1_Silent_p.S142S	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor	149					cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131793086	131793086	+	Silent	SNP	G	A	A	rs145809062		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131793086G>A	uc003ytd.3	-	18	3562	c.3306C>T	c.(3304-3306)GGC>GGT	p.G1102G	ADCY8_uc010mds.2_Silent_p.G971G	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	1102	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
TG	7038	broad.mit.edu	37	8	133900380	133900380	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133900380G>A	uc003ytw.2	+	10	2369	c.2328G>A	c.(2326-2328)GGG>GGA	p.G776G		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	776	Thyroglobulin type-1 7.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135521968	135521968	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135521968A>G	uc003yup.2	-	15	3561	c.3386T>C	c.(3385-3387)GTG>GCG	p.V1129A	ZFAT_uc011ljj.1_Missense_Mutation_p.V248A|ZFAT_uc003yun.2_Missense_Mutation_p.V1117A|ZFAT_uc003yuo.2_Missense_Mutation_p.V1117A|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.V1117A|ZFAT_uc010mej.2_Missense_Mutation_p.V1067A	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	1129					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
SLC45A4	57210	broad.mit.edu	37	8	142229106	142229106	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142229106G>A	uc003ywd.1	-	4	788	c.480C>T	c.(478-480)TAC>TAT	p.Y160Y	SLC45A4_uc003ywc.1_Silent_p.Y160Y|SLC45A4_uc010meq.1_Silent_p.Y158Y	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	211	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
RHPN1	114822	broad.mit.edu	37	8	144459618	144459618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144459618C>T	uc003yyb.2	+	4	507	c.374C>T	c.(373-375)CCG>CTG	p.P125L		NM_052924	NP_443156	Q8TCX5	RHPN1_HUMAN	rhophilin 1	125	BRO1.				signal transduction	intracellular				large_intestine(1)	1	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)															---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144663495	144663495	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144663495A>G	uc011lki.1	-	4	462	c.193T>C	c.(193-195)TCA>CCA	p.S65P	NAPRT1_uc003yym.3_5'Flank|NAPRT1_uc003yyn.3_5'Flank|NAPRT1_uc011lkh.1_5'Flank|NAPRT1_uc003yyo.3_5'Flank|EEF1D_uc003yyp.1_Missense_Mutation_p.S407P|EEF1D_uc003yyq.1_Missense_Mutation_p.S481P|EEF1D_uc011lkj.1_Missense_Mutation_p.S430P|EEF1D_uc003yyr.2_Missense_Mutation_p.S431P|EEF1D_uc003yyt.2_Missense_Mutation_p.S431P|EEF1D_uc011lkk.1_Missense_Mutation_p.S65P|EEF1D_uc003yys.2_Missense_Mutation_p.S65P|EEF1D_uc003yyv.2_Missense_Mutation_p.S41P|EEF1D_uc003yyu.2_Missense_Mutation_p.S65P|EEF1D_uc011lkl.1_Missense_Mutation_p.S65P	NM_001130057	NP_001123529	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	65					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144941064	144941064	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144941064G>A	uc003zaa.1	-	1	6371	c.6358C>T	c.(6358-6360)CCA>TCA	p.P2120S		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	2120						cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
ZNF250	58500	broad.mit.edu	37	8	146107196	146107196	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146107196G>A	uc003zeq.3	-	6	1504	c.1387C>T	c.(1387-1389)CGC>TGC	p.R463C	COMMD5_uc010mgf.2_Intron|ZNF250_uc003zer.3_Missense_Mutation_p.R458C|ZNF250_uc010mgg.2_Missense_Mutation_p.R458C	NM_021061	NP_066405	P15622	ZN250_HUMAN	zinc finger protein 250 isoform a	463	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)														---	---	---	---
C8orf33	65265	broad.mit.edu	37	8	146279467	146279467	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146279467G>A	uc003zfc.3	+	5	668	c.614G>A	c.(613-615)TGC>TAC	p.C205Y	C8orf33_uc003zfd.2_RNA	NM_023080	NP_075568	Q9H7E9	CH033_HUMAN	hypothetical protein LOC65265	205											0	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)														---	---	---	---
CBWD1	55871	broad.mit.edu	37	9	164038	164038	+	Splice_Site	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:164038C>G	uc003zga.3	-	5	537	c.431_splice	c.e5-1	p.G144_splice	CBWD1_uc010mgs.2_Splice_Site|CBWD1_uc003zgb.3_Splice_Site_p.G108_splice|CBWD1_uc003zgc.3_Splice_Site_p.G144_splice|CBWD1_uc011llr.1_Splice_Site_p.G108_splice	NM_018491	NP_060961			COBW domain containing 1 isoform 1								ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2047443	2047443	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2047443A>T	uc003zhc.2	+	5	1104	c.1005A>T	c.(1003-1005)CAA>CAT	p.Q335H	SMARCA2_uc003zhd.2_Missense_Mutation_p.Q335H|SMARCA2_uc010mha.2_Missense_Mutation_p.Q326H	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	335					chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
KIAA0020	9933	broad.mit.edu	37	9	2829880	2829880	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2829880G>A	uc003zhp.1	-	8	842	c.746C>T	c.(745-747)GCG>GTG	p.A249V	KIAA0020_uc010mhc.1_Missense_Mutation_p.A248V|KIAA0020_uc003zhq.1_Missense_Mutation_p.A248V	NM_014878	NP_055693	Q15397	K0020_HUMAN	KIAA0020 protein	249	Pumilio 3.|PUM-HD.					endoplasmic reticulum|nucleolus	RNA binding			ovary(1)	1				GBM - Glioblastoma multiforme(50;0.0319)														---	---	---	---
JAK2	3717	broad.mit.edu	37	9	5080673	5080673	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5080673G>A	uc010mhm.2	+	17	2537	c.2424G>A	c.(2422-2424)TTG>TTA	p.L808L	JAK2_uc003ziw.2_Silent_p.L808L	NM_004972	NP_004963	O60674	JAK2_HUMAN	Janus kinase 2	808	Protein kinase 1.				actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)			1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6554767	6554767	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6554767G>T	uc003zkc.2	-	19	2410	c.2217C>A	c.(2215-2217)CGC>CGA	p.R739R		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	739					glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
TTC39B	158219	broad.mit.edu	37	9	15175042	15175042	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15175042C>T	uc003zlr.1	-	19	1856	c.1735G>A	c.(1735-1737)GCC>ACC	p.A579T	TTC39B_uc003zlq.1_Missense_Mutation_p.A548T|TTC39B_uc011lmp.1_Missense_Mutation_p.A480T|TTC39B_uc010mie.1_Missense_Mutation_p.A577T|TTC39B_uc011lmq.1_Missense_Mutation_p.A566T|TTC39B_uc011lmr.1_Missense_Mutation_p.A510T|TTC39B_uc003zlp.1_Missense_Mutation_p.A162T	NM_152574	NP_689787	Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	579	TPR 3.						binding			ovary(1)	1																		---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16552745	16552745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16552745G>A	uc003zml.2	-	5	592	c.452C>T	c.(451-453)ACG>ATG	p.T151M	BNC2_uc011lmw.1_Missense_Mutation_p.T56M|BNC2_uc003zmm.2_Missense_Mutation_p.T109M|BNC2_uc003zmq.1_Missense_Mutation_p.T165M|BNC2_uc003zmr.1_Missense_Mutation_p.T188M|BNC2_uc003zmp.1_Missense_Mutation_p.T179M|BNC2_uc010mij.1_Missense_Mutation_p.T73M|BNC2_uc011lmv.1_Translation_Start_Site|BNC2_uc003zmo.1_Missense_Mutation_p.T73M	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	151					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)														---	---	---	---
IFNA14	3448	broad.mit.edu	37	9	21239945	21239945	+	5'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21239945G>A	uc010mis.2	-	1					IFNA14_uc003zoo.1_RNA	NM_002172	NP_002163			interferon, alpha 14 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
ELAVL2	1993	broad.mit.edu	37	9	23705013	23705013	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23705013G>T	uc003zpu.2	-	4	665	c.390C>A	c.(388-390)AGC>AGA	p.S130R	ELAVL2_uc003zps.2_Missense_Mutation_p.S130R|ELAVL2_uc003zpt.2_Missense_Mutation_p.S130R|ELAVL2_uc003zpv.2_Missense_Mutation_p.S130R|ELAVL2_uc003zpw.2_Missense_Mutation_p.S130R	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,	130	RRM 2.				regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)														---	---	---	---
PLAA	9373	broad.mit.edu	37	9	26905649	26905649	+	Missense_Mutation	SNP	C	T	T	rs76067929		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26905649C>T	uc003zqd.2	-	14	2673	c.2248G>A	c.(2248-2250)GGA>AGA	p.G750R		NM_001031689	NP_001026859	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	750	PUL.				phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)														---	---	---	---
PLAA	9373	broad.mit.edu	37	9	26905803	26905803	+	Silent	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26905803A>T	uc003zqd.2	-	14	2519	c.2094T>A	c.(2092-2094)ATT>ATA	p.I698I		NM_001031689	NP_001026859	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	698	PUL.				phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)														---	---	---	---
C9orf72	203228	broad.mit.edu	37	9	27556595	27556595	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27556595G>A	uc003zqq.2	-	8	1152	c.1055C>T	c.(1054-1056)ACG>ATG	p.T352M		NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a	352										ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)														---	---	---	---
ACO1	48	broad.mit.edu	37	9	32423420	32423420	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32423420A>G	uc003zqw.3	+						ACO1_uc010mjh.1_Intron|ACO1_uc003zqx.3_Intron|ACO1_uc003zqy.3_Intron	NM_002197	NP_002188			aconitase 1						citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)														---	---	---	---
NOL6	65083	broad.mit.edu	37	9	33468956	33468956	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33468956C>A	uc003zsz.2	-	7	1127	c.1026G>T	c.(1024-1026)AAG>AAT	p.K342N	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zta.2_Missense_Mutation_p.K342N|NOL6_uc010mjv.2_Missense_Mutation_p.K342N|NOL6_uc011lob.1_Missense_Mutation_p.K282N|NOL6_uc003ztb.1_Missense_Mutation_p.K342N	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	342					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)														---	---	---	---
CNTFR	1271	broad.mit.edu	37	9	34556287	34556287	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34556287C>T	uc003zup.1	-	7	1015	c.734G>A	c.(733-735)CGC>CAC	p.R245H	CNTFR_uc003zuq.1_Missense_Mutation_p.R245H	NM_147164	NP_671693	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	245	Fibronectin type-III 2.				nervous system development	anchored to membrane|extrinsic to membrane|plasma membrane	ciliary neurotrophic factor receptor activity|receptor binding			ovary(3)|central_nervous_system(1)|skin(1)	5	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)														---	---	---	---
DCTN3	11258	broad.mit.edu	37	9	34617907	34617907	+	Silent	SNP	G	T	T	rs150631162	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34617907G>T	uc003zux.1	-	3	278	c.243C>A	c.(241-243)GCC>GCA	p.A81A	DCTN3_uc003zuw.1_Silent_p.A81A	NM_007234	NP_009165	O75935	DCTN3_HUMAN	dynactin 3 isoform 1	81					cytokinesis|G2/M transition of mitotic cell cycle|mitosis	centrosome|cleavage furrow|condensed chromosome kinetochore|cytosol|dynactin complex|midbody|perinuclear region of cytoplasm|spindle	protein binding|structural molecule activity				0	all_epithelial(49;0.0863)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.0388)														---	---	---	---
CCL27	10850	broad.mit.edu	37	9	34662306	34662306	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34662306C>T	uc003zvm.1	-	2	237	c.178G>A	c.(178-180)GGG>AGG	p.G60R		NM_006664	NP_006655	Q9Y4X3	CCL27_HUMAN	small inducible cytokine A27 precursor	60					cell-cell signaling|chemotaxis|immune response	extracellular space	chemokine activity				0	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)														---	---	---	---
FANCG	2189	broad.mit.edu	37	9	35076548	35076548	+	Silent	SNP	C	T	T	rs145092954	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35076548C>T	uc003zwb.1	-	8	1449	c.957G>A	c.(955-957)CCG>CCA	p.P319P	FANCG_uc003zwa.1_Silent_p.P61P|FANCG_uc010mkj.1_Silent_p.P61P|FANCG_uc011lot.1_Silent_p.P319P	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	319					cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)					Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
CD72	971	broad.mit.edu	37	9	35612975	35612975	+	Missense_Mutation	SNP	G	A	A	rs139792014		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35612975G>A	uc003zxb.2	-	6	828	c.704C>T	c.(703-705)TCG>TTG	p.S235L	CD72_uc003zxc.1_Missense_Mutation_p.S20L|CD72_uc010mkt.1_Missense_Mutation_p.S20L|CD72_uc010mku.2_Missense_Mutation_p.S235L	NM_001782	NP_001773	P21854	CD72_HUMAN	CD72 molecule	235	C-type lectin.|Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	receptor binding|sugar binding|transmembrane receptor activity				0			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
FBXO10	26267	broad.mit.edu	37	9	37518203	37518203	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37518203G>A	uc004aab.2	-	9	2482	c.2433C>T	c.(2431-2433)GGC>GGT	p.G811G	FBXO10_uc004aac.2_Silent_p.G827G|FBXO10_uc004aad.2_Silent_p.G361G	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10	811						ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(5)	5				GBM - Glioblastoma multiforme(29;0.0107)														---	---	---	---
FAM74A3	728495	broad.mit.edu	37	9	40716214	40716214	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40716214G>A	uc010mmk.2	+	1		c.691G>A				NR_026801				Homo sapiens family with sequence similarity 74, member A3 (FAM74A3), non-coding RNA.											skin(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
C9orf71	169693	broad.mit.edu	37	9	71155449	71155449	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71155449G>A	uc004agt.2	-							NM_153237	NP_694969			hypothetical protein LOC169693							integral to membrane					0																		---	---	---	---
APBA1	320	broad.mit.edu	37	9	72047481	72047481	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72047481C>T	uc004ahh.2	-	12	2689	c.2413G>A	c.(2413-2415)GTC>ATC	p.V805I		NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,	805	PDZ 2.				axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79324547	79324547	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79324547A>G	uc010mpk.2	-	8	2767	c.2643T>C	c.(2641-2643)AAT>AAC	p.N881N		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	881					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79325137	79325137	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79325137A>T	uc010mpk.2	-	8	2177	c.2053T>A	c.(2053-2055)TCA>ACA	p.S685T		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	685					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82187735	82187735	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82187735G>A	uc004ald.2	+	1	858	c.9G>A	c.(7-9)CCG>CCA	p.P3P	TLE4_uc004alc.2_Silent_p.P10P|TLE4_uc010mpr.2_5'UTR|TLE4_uc004ale.2_5'UTR|TLE4_uc011lsq.1_Silent_p.P3P|TLE4_uc010mps.2_Silent_p.P3P|TLE4_uc004alf.2_5'Flank	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4	Error:Variant_position_missing_in_O60756_after_alignment										lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82337487	82337487	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82337487G>A	uc004ald.2	+	19	3032	c.2183G>A	c.(2182-2184)TGT>TAT	p.C728Y	TLE4_uc004alc.2_Missense_Mutation_p.C703Y|TLE4_uc010mpr.2_Missense_Mutation_p.C582Y|TLE4_uc004ale.2_Missense_Mutation_p.C340Y|TLE4_uc011lsq.1_Missense_Mutation_p.C671Y|TLE4_uc010mps.2_Missense_Mutation_p.C627Y|TLE4_uc004alf.2_Missense_Mutation_p.C642Y	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4	42										lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84226744	84226744	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84226744C>T	uc004aly.2	-	13	1635	c.1194G>A	c.(1192-1194)TCG>TCA	p.S398S	TLE1_uc004alz.2_Silent_p.S408S|TLE1_uc011lsr.1_Silent_p.S383S|TLE1_uc004ama.1_Silent_p.S397S|TLE1_uc011lss.1_Silent_p.S324S	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1	398	Pro/Ser-rich.				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84607526	84607526	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84607526G>A	uc004amn.2	+	4	2188	c.2141G>A	c.(2140-2142)CGT>CAT	p.R714H		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	714						integral to membrane					0																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86502116	86502116	+	Intron	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86502116A>T	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86590403	86590403	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86590403T>C	uc004ang.3	-	6	455	c.231A>G	c.(229-231)TCA>TCG	p.S77S	HNRNPK_uc011lsw.1_5'UTR|HNRNPK_uc004and.3_5'UTR|HNRNPK_uc004ank.3_Silent_p.S77S|HNRNPK_uc004anf.3_Silent_p.S77S|HNRNPK_uc004anh.3_Silent_p.S77S|HNRNPK_uc011lsx.1_Silent_p.S77S|HNRNPK_uc004ani.3_Silent_p.S77S|HNRNPK_uc004anj.3_Silent_p.S77S|HNRNPK_uc004ann.3_Silent_p.S77S|HNRNPK_uc004anl.3_Silent_p.S77S|HNRNPK_uc004anm.3_Silent_p.S77S	NM_031262	NP_112552	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	77	KH 1.|5 X 4 AA repeats of G-X-G-G.|Necessary for interaction with DDX1.|2 X 22 AA approximate repeats.|Interaction with ASFV p30.				interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1																		---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92007436	92007436	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92007436G>A	uc004aqo.1	-	10	1096	c.524C>T	c.(523-525)TCG>TTG	p.S175L	SEMA4D_uc011ltm.1_Missense_Mutation_p.S175L|SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aqp.1_Missense_Mutation_p.S173L	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	175	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95420923	95420923	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95420923C>T	uc004asl.1	-	2	399	c.122G>A	c.(121-123)AGG>AAG	p.R41K		NM_022755	NP_073592	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	41					inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
BICD2	23299	broad.mit.edu	37	9	95482762	95482762	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95482762G>A	uc004aso.1	-	4	939	c.882C>T	c.(880-882)AAC>AAT	p.N294N	BICD2_uc004asp.1_Silent_p.N294N	NM_015250	NP_056065	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 isoform 2	294					microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1																		---	---	---	---
FBP2	8789	broad.mit.edu	37	9	97321346	97321346	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97321346C>A	uc004auv.2	-	7	961	c.894G>T	c.(892-894)ACG>ACT	p.T298T	uc004aus.1_RNA|uc004aut.1_RNA|uc004auu.2_RNA	NM_003837	NP_003828	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	298					fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
FBP1	2203	broad.mit.edu	37	9	97369133	97369133	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97369133G>T	uc004auw.3	-	5	1000	c.669C>A	c.(667-669)GCC>GCA	p.A223A	FBP1_uc010mrl.2_Silent_p.A223A	NM_000507	NP_000498	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	223					gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	98774869	98774869	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98774869G>T	uc010msa.1	+	4	1856	c.980G>T	c.(979-981)AGA>ATA	p.R327I	uc011lun.1_Intron					RecName: Full=Uncharacterized protein C9orf102;																														---	---	---	---
TMOD1	7111	broad.mit.edu	37	9	100286498	100286498	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100286498T>A	uc004axk.1	+	2	241	c.28T>A	c.(28-30)TAC>AAC	p.Y10N	TMOD1_uc004axl.1_Missense_Mutation_p.Y10N	NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1	10					muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)														---	---	---	---
ANKS6	203286	broad.mit.edu	37	9	101544788	101544788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101544788A>G	uc004ayu.2	-	5	1201	c.1180T>C	c.(1180-1182)TAC>CAC	p.Y394H	ANKS6_uc004ayt.2_Missense_Mutation_p.Y93H|ANKS6_uc004ayw.1_5'Flank|ANKS6_uc004ayx.1_RNA|ANKS6_uc004ayy.1_RNA	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	394	ANK 11.									ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
ERP44	23071	broad.mit.edu	37	9	102782899	102782899	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102782899C>A	uc004bam.2	-	6	794	c.586G>T	c.(586-588)GGG>TGG	p.G196W	ERP44_uc010msy.2_RNA|ERP44_uc010msz.2_Missense_Mutation_p.G196W	NM_015051	NP_055866	Q9BS26	ERP44_HUMAN	thioredoxin domain containing 4 (endoplasmic	196					cell redox homeostasis|glycoprotein metabolic process|protein folding|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|ER-Golgi intermediate compartment	protein binding|protein disulfide isomerase activity				0																		---	---	---	---
ALDOB	229	broad.mit.edu	37	9	104184099	104184099	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104184099T>C	uc004bbk.2	-	9	1169	c.1087A>G	c.(1087-1089)ACC>GCC	p.T363A		NM_000035	NP_000026	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	363					fructose 1,6-bisphosphate metabolic process|fructose catabolic process|gluconeogenesis|glycolysis|NADH oxidation|positive regulation of ATPase activity|vacuolar proton-transporting V-type ATPase complex assembly	centriolar satellite|cytosol	ATPase binding|cytoskeletal protein binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106864708	106864708	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106864708A>G	uc004bbv.2	+	9	1162	c.874A>G	c.(874-876)ACT>GCT	p.T292A	SMC2_uc004bbu.1_Missense_Mutation_p.T292A|SMC2_uc004bbw.2_Missense_Mutation_p.T292A|SMC2_uc011lvl.1_Missense_Mutation_p.T292A|SMC2_uc010mtg.1_Missense_Mutation_p.T147A|SMC2_uc010mth.1_Missense_Mutation_p.T242A|SMC2_uc004bbx.2_Missense_Mutation_p.T292A	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	292	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107547859	107547859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107547859C>T	uc004bcl.2	-	49	6776	c.6463G>A	c.(6463-6465)GTC>ATC	p.V2155I	NIPSNAP3B_uc004bcj.1_Intron	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	2155					Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107584954	107584954	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107584954A>G	uc004bcl.2	-							NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109687602	109687602	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109687602A>G	uc004bcz.2	+	3	1698	c.1409A>G	c.(1408-1410)TAC>TGC	p.Y470C	ZNF462_uc010mto.2_Missense_Mutation_p.Y318C|ZNF462_uc004bda.2_Missense_Mutation_p.Y318C	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	470	C2H2-type 5.				transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
ACTL7A	10881	broad.mit.edu	37	9	111625337	111625337	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111625337G>A	uc004bdj.1	+	1	735	c.735G>A	c.(733-735)GCG>GCA	p.A245A		NM_006687	NP_006678	Q9Y615	ACL7A_HUMAN	actin-like 7A	245						cytoplasm|cytoskeleton|protein complex	structural constituent of cytoskeleton				0																		---	---	---	---
C9orf5	23731	broad.mit.edu	37	9	111812919	111812919	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111812919G>A	uc004bdt.3	-	13	1940	c.1908C>T	c.(1906-1908)ACC>ACT	p.T636T	C9orf5_uc004bds.3_RNA|C9orf5_uc004bdr.3_Silent_p.T628T	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731	636	Helical; (Potential).					integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)														---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113530330	113530330	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113530330C>A	uc004bey.2	+	8	1249	c.1151C>A	c.(1150-1152)CCT>CAT	p.P384H		NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase	384	FZ.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115232836	115232836	+	3'UTR	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115232836A>T	uc004bga.1	+	11					HSDL2_uc011lwv.1_3'UTR|HSDL2_uc004bgb.1_3'UTR|HSDL2_uc004bgc.1_3'UTR|HSDL2_uc011lww.1_3'UTR|uc004bge.1_Intron	NM_032303	NP_115679			hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
DFNB31	25861	broad.mit.edu	37	9	117168806	117168806	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117168806G>T	uc004biz.3	-	9	2714	c.2065C>A	c.(2065-2067)CTG>ATG	p.L689M	DFNB31_uc004bix.2_Missense_Mutation_p.L338M|DFNB31_uc004biy.3_Missense_Mutation_p.L306M|DFNB31_uc004bja.3_Missense_Mutation_p.L689M	NM_015404	NP_056219	Q9P202	WHRN_HUMAN	CASK-interacting protein CIP98 isoform 1	689	Pro-rich.				inner ear receptor stereocilium organization|retina homeostasis|sensory perception of light stimulus|sensory perception of sound	cytoplasm|growth cone|stereocilium				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
TNC	3371	broad.mit.edu	37	9	117849281	117849281	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117849281G>A	uc004bjj.3	-	3	1091	c.729C>T	c.(727-729)GCC>GCT	p.A243A	TNC_uc010mvf.2_Silent_p.A243A	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	243	EGF-like 3.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7																		---	---	---	---
DBC1	1620	broad.mit.edu	37	9	121976224	121976224	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121976224C>T	uc004bkc.2	-	6	1351	c.895G>A	c.(895-897)GAA>AAA	p.E299K	DBC1_uc004bkd.2_Missense_Mutation_p.E299K	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	299					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
C5	727	broad.mit.edu	37	9	123782301	123782301	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123782301T>C	uc004bkv.2	-	12	1489	c.1459A>G	c.(1459-1461)ACC>GCC	p.T487A	C5_uc010mvm.1_Missense_Mutation_p.T487A|C5_uc010mvn.1_Missense_Mutation_p.T487A	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein	487					activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
OR1L6	392390	broad.mit.edu	37	9	125512094	125512094	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125512094C>A	uc011lzc.1	+	1	76	c.76C>A	c.(76-78)CTT>ATT	p.L26I		NM_001004453	NP_001004453	Q8NGR2	OR1L6_HUMAN	olfactory receptor, family 1, subfamily L,	26	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
ZBTB34	403341	broad.mit.edu	37	9	129642061	129642061	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129642061G>T	uc004bqm.3	+	2	468	c.371G>T	c.(370-372)AGC>ATC	p.S124I		NM_001099270	NP_001092740	Q8NCN2	ZBT34_HUMAN	zinc finger and BTB domain containing 34	124					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
TTC16	158248	broad.mit.edu	37	9	130485392	130485392	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130485392C>A	uc004brq.1	+						PTRH1_uc011mah.1_Intron|TTC16_uc011mai.1_Intron|TTC16_uc004brr.1_Intron|TTC16_uc010mxn.1_Intron	NM_144965	NP_659402			tetratricopeptide repeat domain 16								binding				0																		---	---	---	---
GLE1	2733	broad.mit.edu	37	9	131271325	131271325	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131271325C>T	uc004bvj.2	+	2	384	c.270C>T	c.(268-270)GAC>GAT	p.D90D	GLE1_uc004bvi.2_Silent_p.D90D|GLE1_uc010myd.2_Translation_Start_Site	NM_001003722	NP_001003722	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator homolog isoform 1	90					poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0																		---	---	---	---
PKN3	29941	broad.mit.edu	37	9	131477689	131477689	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131477689C>T	uc004bvw.2	+	15	2151	c.1758C>T	c.(1756-1758)GCC>GCT	p.A586A	PKN3_uc010myh.2_Silent_p.A586A|PKN3_uc011mbk.1_Silent_p.A136A	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN	protein kinase PKNbeta	586	Protein kinase.				signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			stomach(2)|lung(2)	4																		---	---	---	---
C9orf50	375759	broad.mit.edu	37	9	132377792	132377792	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132377792G>A	uc004byc.3	-	4	1053	c.851C>T	c.(850-852)ACG>ATG	p.T284M	C9orf50_uc004byb.3_RNA	NM_199350	NP_955382	Q5SZB4	CI050_HUMAN	hypothetical protein LOC375759	284										ovary(1)|central_nervous_system(1)	2		Ovarian(14;0.00556)																---	---	---	---
DDX31	64794	broad.mit.edu	37	9	135505725	135505725	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135505725G>A	uc004cbq.1	-	16	2024	c.1872C>T	c.(1870-1872)TGC>TGT	p.C624C	DDX31_uc010mzu.1_Missense_Mutation_p.A616V	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	624	Helicase C-terminal.					nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)														---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136270019	136270019	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136270019C>T	uc004cdk.2	+	17	1900	c.1839C>T	c.(1837-1839)AAC>AAT	p.N613N	C9orf96_uc004cdl.2_RNA	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	613							ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
ADAMTSL2	9719	broad.mit.edu	37	9	136405775	136405775	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136405775C>T	uc011mdl.1	+	6	1025	c.468C>T	c.(466-468)GAC>GAT	p.D156D	ADAMTSL2_uc004cei.2_Silent_p.D156D	NM_001145320	NP_001138792	Q86TH1	ATL2_HUMAN	ADAMTS-like 2 precursor	156					negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136662938	136662938	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136662938G>A	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870			vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
KIAA0649	9858	broad.mit.edu	37	9	138378529	138378529	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138378529A>G	uc004cfr.1	+	4	2722	c.2173A>G	c.(2173-2175)AGC>GGC	p.S725G		NM_014811	NP_055626	Q5T8A7	K0649_HUMAN	1A6/DRIM (down-regulated in metastasis)	725						nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(145;6.91e-08)|Epithelial(140;4.69e-07)|all cancers(34;9.33e-06)														---	---	---	---
KCNT1	57582	broad.mit.edu	37	9	138676641	138676641	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138676641C>T	uc011mdq.1	+	27	3136	c.3062C>T	c.(3061-3063)ACG>ATG	p.T1021M	KCNT1_uc011mdr.1_Missense_Mutation_p.T848M|KCNT1_uc010nbf.2_Missense_Mutation_p.T976M|KCNT1_uc004cgo.1_Missense_Mutation_p.T770M	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	1021						membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)														---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138719367	138719367	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138719367C>T	uc004cgr.3	-	8	1109	c.1109G>A	c.(1108-1110)CGC>CAC	p.R370H	CAMSAP1_uc004cgq.3_Missense_Mutation_p.R260H|CAMSAP1_uc010nbg.2_Missense_Mutation_p.R92H	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	370						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
CARD9	64170	broad.mit.edu	37	9	139265329	139265329	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139265329G>A	uc004chg.3	-	4	757	c.591C>T	c.(589-591)GGC>GGT	p.G197G	CARD9_uc011mdw.1_Silent_p.G197G|CARD9_uc011mdx.1_Silent_p.G93G|CARD9_uc010nbj.2_Silent_p.G197G	NM_052813	NP_434700	Q9H257	CARD9_HUMAN	caspase recruitment domain protein 9 isoform 1	197	Potential.				positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of stress-activated MAPK cascade|regulation of apoptosis	cytoplasm	CARD domain binding|protein homodimerization activity			pancreas(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139391715	139391715	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139391715C>T	uc004chz.2	-	34	6476	c.6476G>A	c.(6475-6477)CGC>CAC	p.R2159H		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2159	Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	p.R2160H(1)		haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)				T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139910214	139910214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139910214G>A	uc011mem.1	-	22	3572	c.3424C>T	c.(3424-3426)CGC>TGC	p.R1142C	ABCA2_uc011mel.1_Missense_Mutation_p.R1143C|ABCA2_uc004ckl.1_Missense_Mutation_p.R1073C|ABCA2_uc004ckm.1_Missense_Mutation_p.R1173C|ABCA2_uc004ckn.1_RNA	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	1142	ABC transporter 1.				cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
ANAPC2	29882	broad.mit.edu	37	9	140069704	140069704	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140069704C>T	uc004clr.1	-	12	2314	c.2241G>A	c.(2239-2241)AAG>AAA	p.K747K	ANAPC2_uc004clq.1_Silent_p.K603K	NM_013366	NP_037498	Q9UJX6	ANC2_HUMAN	anaphase-promoting complex subunit 2	747					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cyclin catabolic process|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of synapse maturation|positive regulation of synaptic plasticity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of cyclin-dependent protein kinase activity	anaphase-promoting complex|cytosol|nucleoplasm	ubiquitin protein ligase binding|ubiquitin-protein ligase activity			ovary(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)														---	---	---	---
ANAPC2	29882	broad.mit.edu	37	9	140077656	140077656	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140077656C>T	uc004clr.1	-	6	1280	c.1207G>A	c.(1207-1209)GCC>ACC	p.A403T	ANAPC2_uc004clq.1_Missense_Mutation_p.A259T	NM_013366	NP_037498	Q9UJX6	ANC2_HUMAN	anaphase-promoting complex subunit 2	403					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cyclin catabolic process|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of synapse maturation|positive regulation of synaptic plasticity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of cyclin-dependent protein kinase activity	anaphase-promoting complex|cytosol|nucleoplasm	ubiquitin protein ligase binding|ubiquitin-protein ligase activity			ovary(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140250757	140250757	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140250757C>A	uc004cmp.2	-	8	916	c.720G>T	c.(718-720)CAG>CAT	p.Q240H	C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Translation_Start_Site|EXD3_uc004cmq.1_RNA|EXD3_uc010ncg.1_Missense_Mutation_p.Q179H	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	exonuclease 3'-5' domain containing 3	240					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140711915	140711915	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140711915G>A	uc011mfc.1	+	24	3436	c.3399G>A	c.(3397-3399)ACG>ACA	p.T1133T	EHMT1_uc004coe.2_Silent_p.T38T	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1133	SET.				DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1063133	1063133	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1063133G>T	uc001ift.2	+	17	1942	c.1871G>T	c.(1870-1872)GGG>GTG	p.G624V	GTPBP4_uc001ifu.2_RNA|GTPBP4_uc010qad.1_Missense_Mutation_p.G508V|GTPBP4_uc010qae.1_Missense_Mutation_p.G577V	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG	624					negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
PITRM1	10531	broad.mit.edu	37	10	3189762	3189762	+	Splice_Site	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3189762A>G	uc010qah.1	-	16	1973	c.1941_splice	c.e16+1	p.Q647_splice	PITRM1_uc001igr.1_Splice_Site_p.Q745_splice|PITRM1_uc001igs.1_5'Flank|PITRM1_uc001igt.1_Splice_Site_p.Q745_splice|PITRM1_uc009xhv.1_Splice_Site_p.Q311_splice|PITRM1_uc001igu.1_Splice_Site_p.Q671_splice|PITRM1_uc010qai.1_Splice_Site_p.Q716_splice|uc001igv.1_RNA					SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7618516	7618516	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7618516C>T	uc001ijq.2	-	10	1957	c.1878G>A	c.(1876-1878)CCG>CCA	p.P626P	ITIH5_uc001ijp.2_Silent_p.P412P|ITIH5_uc001ijr.1_Silent_p.P626P	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	626					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
OPTN	10133	broad.mit.edu	37	10	13151223	13151223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13151223C>T	uc001ilu.1	+	4	539	c.101C>T	c.(100-102)ACG>ATG	p.T34M	OPTN_uc001ilv.1_Missense_Mutation_p.T34M|OPTN_uc001ilw.1_Missense_Mutation_p.T34M|OPTN_uc001ilx.1_Missense_Mutation_p.T34M|OPTN_uc001ily.1_Missense_Mutation_p.T34M|OPTN_uc010qbr.1_Translation_Start_Site|OPTN_uc001ilz.1_Missense_Mutation_p.T34M	NM_001008213	NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	34					cell death|Golgi ribbon formation|Golgi to plasma membrane protein transport|protein targeting to Golgi|signal transduction	perinuclear region of cytoplasm|trans-Golgi network	protein C-terminus binding			ovary(2)	2																		---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17157487	17157487	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17157487G>A	uc001ioo.2	-	7	755	c.703C>T	c.(703-705)CGA>TGA	p.R235*		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	235					cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
C10orf140	387640	broad.mit.edu	37	10	21804424	21804424	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21804424C>A	uc009xkd.2	-	4	4581	c.2328G>T	c.(2326-2328)AGG>AGT	p.R776S	uc001iqp.1_Intron	NM_207371	NP_997254	Q1XH10	DLN1_HUMAN	hypothetical protein LOC387640	695						nucleus	nucleotide binding			ovary(1)	1																		---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22209884	22209884	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22209884T>A	uc001irc.2	-	4	667	c.380A>T	c.(379-381)GAT>GTT	p.D127V	DNAJC1_uc001ird.2_Missense_Mutation_p.D13V	NM_022365	NP_071760	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	127	Lumenal (By similarity).|J.				negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24832668	24832668	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24832668A>G	uc001iru.3	+	19	4872	c.4469A>G	c.(4468-4470)GAT>GGT	p.D1490G	KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc001irw.2_Intron|KIAA1217_uc001irz.2_Intron|KIAA1217_uc001irx.2_Missense_Mutation_p.D1173G|KIAA1217_uc001iry.2_Intron|KIAA1217_uc001isa.1_Missense_Mutation_p.D326G	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	1490	Potential.				embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27059469	27059469	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27059469T>C	uc001isx.2	-						ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Intron|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Intron|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Intron|ABI1_uc010qdj.1_Intron|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron|ABI1_uc010qdg.1_Intron	NM_005470	NP_005461			abl-interactor 1 isoform a						actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30318683	30318683	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30318683C>T	uc001iux.2	-	2	453	c.394G>A	c.(394-396)GAA>AAA	p.E132K	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_5'UTR|KIAA1462_uc009xle.1_Missense_Mutation_p.E132K	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	132										ovary(4)	4																		---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33469276	33469276	+	Missense_Mutation	SNP	C	T	T	rs150351789	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33469276C>T	uc001iwx.3	-	17	3023	c.2500G>A	c.(2500-2502)GAA>AAA	p.E834K	NRP1_uc001iwv.3_Missense_Mutation_p.E817K|NRP1_uc009xlz.2_Missense_Mutation_p.E828K|NRP1_uc001iww.3_Missense_Mutation_p.E646K|NRP1_uc001iwy.3_Missense_Mutation_p.E827K	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	834	Extracellular (Potential).				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33502517	33502517	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33502517A>G	uc001iwx.3	-	9	1934	c.1411T>C	c.(1411-1413)TGG>CGG	p.W471R	NRP1_uc001iwv.3_Missense_Mutation_p.W471R|NRP1_uc009xlz.2_Missense_Mutation_p.W471R|NRP1_uc001iww.3_Missense_Mutation_p.W290R|NRP1_uc001iwy.3_Missense_Mutation_p.W471R|NRP1_uc001iwz.2_Missense_Mutation_p.W471R|NRP1_uc001ixa.2_Missense_Mutation_p.W471R|NRP1_uc001ixb.1_Missense_Mutation_p.W471R|NRP1_uc001ixc.1_Missense_Mutation_p.W471R	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	471	Extracellular (Potential).|F5/8 type C 2.				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
ZNF33A	7581	broad.mit.edu	37	10	38343551	38343551	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38343551T>C	uc001izh.2	+	5	674	c.496T>C	c.(496-498)TCT>CCT	p.S166P	ZNF33A_uc001izg.2_Missense_Mutation_p.S167P|ZNF33A_uc010qev.1_Missense_Mutation_p.S173P|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	166						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ZNF37A	7587	broad.mit.edu	37	10	38404122	38404122	+	Splice_Site	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38404122G>T	uc001izk.2	+	7	962	c.143_splice	c.e7-1	p.G48_splice	ZNF37A_uc001izl.2_Splice_Site_p.G48_splice|ZNF37A_uc001izm.2_Splice_Site_p.G48_splice	NM_001007094	NP_001007095			zinc finger protein 37a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1																		---	---	---	---
CSGALNACT2	55454	broad.mit.edu	37	10	43657666	43657666	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43657666G>A	uc001jan.2	+						CSGALNACT2_uc001jam.1_Nonsense_Mutation_p.W333*	NM_018590	NP_061060			chondroitin sulfate						chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1																		---	---	---	---
ZNF485	220992	broad.mit.edu	37	10	44111933	44111933	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44111933C>G	uc010qfc.1	+	5	636	c.442C>G	c.(442-444)CAC>GAC	p.H148D	ZNF485_uc010qfd.1_Missense_Mutation_p.H57D	NM_145312	NP_660355	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	148	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
GDF2	2658	broad.mit.edu	37	10	48413916	48413916	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48413916T>C	uc001jfa.1	-	2	1115	c.952A>G	c.(952-954)AAA>GAA	p.K318E		NM_016204	NP_057288	Q9UK05	GDF2_HUMAN	growth differentiation factor 2 precursor	318					activin receptor signaling pathway|BMP signaling pathway|cartilage development|cellular iron ion homeostasis|growth|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of DNA replication|negative regulation of endothelial cell proliferation|ossification|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61828953	61828953	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61828953C>T	uc001jky.2	-	37	11878	c.11686G>A	c.(11686-11688)GAG>AAG	p.E3896K	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	3896					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61848114	61848114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61848114G>A	uc001jky.2	-	29	3523	c.3331C>T	c.(3331-3333)CTT>TTT	p.L1111F	ANK3_uc001jkw.2_Missense_Mutation_p.L245F|ANK3_uc009xpa.2_Missense_Mutation_p.L245F|ANK3_uc001jkx.2_Missense_Mutation_p.L289F|ANK3_uc010qih.1_Missense_Mutation_p.L1112F|ANK3_uc001jkz.3_Missense_Mutation_p.L1105F|ANK3_uc001jla.1_Missense_Mutation_p.L177F|ANK3_uc001jlb.1_Missense_Mutation_p.L629F	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1111					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
RHOBTB1	9886	broad.mit.edu	37	10	62634768	62634768	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62634768C>T	uc001jli.2	-	10	2197	c.1759G>A	c.(1759-1761)GCC>ACC	p.A587T	RHOBTB1_uc001jlh.2_Missense_Mutation_p.A587T|RHOBTB1_uc001jlj.2_Missense_Mutation_p.A587T|RHOBTB1_uc001jlk.2_Missense_Mutation_p.A587T|RHOBTB1_uc009xpe.1_Missense_Mutation_p.A525T|RHOBTB1_uc009xpd.2_Missense_Mutation_p.A52T|RHOBTB1_uc001jll.2_Missense_Mutation_p.A337T	NM_014836	NP_055651	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	587					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			upper_aerodigestive_tract(1)	1	Prostate(12;0.0112)																	---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	69366623	69366623	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69366623C>T	uc009xpn.1	-	3	407	c.284G>A	c.(283-285)CGC>CAC	p.R95H	CTNNA3_uc001jmw.2_Missense_Mutation_p.R95H|CTNNA3_uc001jmx.3_Missense_Mutation_p.R95H|CTNNA3_uc009xpo.1_Missense_Mutation_p.A11T|CTNNA3_uc001jna.2_Missense_Mutation_p.R107H	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3	95	Potential.				cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
MYPN	84665	broad.mit.edu	37	10	69957120	69957120	+	Missense_Mutation	SNP	G	A	A	rs150414382		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69957120G>A	uc001jnm.3	+	17	3355	c.3170G>A	c.(3169-3171)CGA>CAA	p.R1057Q	MYPN_uc001jnn.3_Missense_Mutation_p.R782Q|MYPN_uc001jno.3_Missense_Mutation_p.R1057Q|MYPN_uc009xpt.2_Missense_Mutation_p.R1057Q|MYPN_uc010qit.1_Missense_Mutation_p.R763Q|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	1057	Interaction with ACTN.					nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5																		---	---	---	---
HKDC1	80201	broad.mit.edu	37	10	71005920	71005920	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71005920G>T	uc001jpf.3	+	8	1094	c.961G>T	c.(961-963)GGT>TGT	p.G321C	HKDC1_uc010qje.1_Missense_Mutation_p.G184C	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	321					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71142486	71142486	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71142486G>A	uc001jpl.3	+	10	1610	c.1509G>A	c.(1507-1509)ACG>ACA	p.T503T	HK1_uc001jpg.3_Silent_p.T491T|HK1_uc001jph.3_Silent_p.T507T|HK1_uc001jpi.3_Silent_p.T507T|HK1_uc001jpj.3_Silent_p.T538T|HK1_uc001jpk.3_Silent_p.T502T|HK1_uc009xqd.2_Silent_p.T381T	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	503	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
TACR2	6865	broad.mit.edu	37	10	71175995	71175995	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71175995G>A	uc001jpn.2	-	1	680	c.85C>T	c.(85-87)CCC>TCC	p.P29S		NM_001057	NP_001048	P21452	NK2R_HUMAN	tachykinin receptor 2	29	Extracellular (Potential).				excretion|muscle contraction	integral to plasma membrane	tachykinin receptor activity			prostate(1)	1					Clonidine(DB00575)|Octreotide(DB00104)													---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72468468	72468468	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72468468C>T	uc001jrh.2	+	4	804	c.804C>T	c.(802-804)GAC>GAT	p.D268D	ADAMTS14_uc001jrg.2_Silent_p.D268D	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	268	Peptidase M12B.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72498708	72498708	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72498708C>T	uc001jrh.2	+	11	1710	c.1710C>T	c.(1708-1710)GGC>GGT	p.G570G	ADAMTS14_uc001jrg.2_Silent_p.G573G|ADAMTS14_uc001jri.1_Silent_p.G93G	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	570	TSP type-1 1.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
UNC5B	219699	broad.mit.edu	37	10	73047433	73047433	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73047433G>A	uc001jro.2	+	6	1257	c.812G>A	c.(811-813)CGG>CAG	p.R271Q	UNC5B_uc001jrp.2_Missense_Mutation_p.R271Q	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	271	TSP type-1 1.|Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane		p.R271W(1)		ovary(2)|lung(1)	3																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73326547	73326547	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73326547G>A	uc001jrx.3	+	7	855	c.478G>A	c.(478-480)GAC>AAC	p.D160N	CDH23_uc001jrw.3_Missense_Mutation_p.D160N|CDH23_uc001jrv.2_Missense_Mutation_p.D155N|CDH23_uc009xql.2_Missense_Mutation_p.D205N	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	160	Cadherin 2.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73377078	73377078	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73377078C>T	uc001jrx.3	+	11	1439	c.1062C>T	c.(1060-1062)AGC>AGT	p.S354S	CDH23_uc001jrw.3_Silent_p.S354S|CDH23_uc009xql.2_Silent_p.S399S	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	354	Cadherin 4.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73490248	73490248	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73490248T>C	uc001jrx.3	+	30	3979	c.3602T>C	c.(3601-3603)ATC>ACC	p.I1201T	CDH23_uc001jrz.2_Missense_Mutation_p.I817T|C10orf105_uc001jsb.1_Intron|CDH23_uc001jsc.1_Missense_Mutation_p.I9T	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1201	Cadherin 11.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
C10orf54	64115	broad.mit.edu	37	10	73521734	73521734	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73521734A>G	uc001jsd.2	-	2	273	c.132T>C	c.(130-132)TGT>TGC	p.C44C	CDH23_uc001jrx.3_Intron|C10orf54_uc001jse.2_Intron|C10orf54_uc009xqm.2_Intron|C10orf54_uc001jsf.1_Silent_p.C44C	NM_022153	NP_071436	Q9H7M9	GI24_HUMAN	platelet receptor Gi24 precursor	44	Ig-like.|Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74660172	74660172	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74660172C>A	uc001jte.1	+	3	692	c.474C>A	c.(472-474)AGC>AGA	p.S158R	OIT3_uc009xqs.1_RNA	NM_152635	NP_689848	Q8WWZ8	OIT3_HUMAN	oncoprotein-induced transcript 3 precursor	158						nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)																	---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74684140	74684140	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74684140G>A	uc001jte.1	+	7	1323	c.1105G>A	c.(1105-1107)GTT>ATT	p.V369I	OIT3_uc009xqs.1_Intron	NM_152635	NP_689848	Q8WWZ8	OIT3_HUMAN	oncoprotein-induced transcript 3 precursor	369	ZP.					nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)																	---	---	---	---
USP54	159195	broad.mit.edu	37	10	75335426	75335426	+	Translation_Start_Site	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75335426C>T	uc001juo.2	-	1	8	c.-9G>A	c.(-11--7)ATGTG>ATATG		USP54_uc001jup.2_Translation_Start_Site|USP54_uc010qkl.1_Translation_Start_Site	NM_152586	NP_689799			ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)																	---	---	---	---
NDST2	8509	broad.mit.edu	37	10	75565696	75565696	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75565696G>T	uc001jvk.2	-	7	2329	c.1525C>A	c.(1525-1527)CGA>AGA	p.R509R	NDST2_uc010qks.1_Silent_p.R135R|NDST2_uc010qkt.1_Silent_p.R386R|NDST2_uc001jvl.1_5'Flank|NDST2_uc009xro.2_Silent_p.R135R|NDST2_uc010qku.1_Silent_p.R384R	NM_003635	NP_003626	P52849	NDST2_HUMAN	heparan glucosaminyl	509	Lumenal (Potential).|Heparan sulfate N-deacetylase 2.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1	Prostate(51;0.0112)																	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76789272	76789272	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76789272G>A	uc001jwn.1	+	18	5183	c.4690G>A	c.(4690-4692)GAG>AAG	p.E1564K	MYST4_uc001jwo.1_Missense_Mutation_p.E1272K|MYST4_uc001jwp.1_Missense_Mutation_p.E1381K	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1564	Interaction with RUNX1 and RUNX2.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76789416	76789416	+	Missense_Mutation	SNP	C	T	T	rs140992439		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76789416C>T	uc001jwn.1	+	18	5327	c.4834C>T	c.(4834-4836)CGT>TGT	p.R1612C	MYST4_uc001jwo.1_Missense_Mutation_p.R1320C|MYST4_uc001jwp.1_Missense_Mutation_p.R1429C	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1612	Ser-rich.|Interaction with RUNX1 and RUNX2.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78869966	78869966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78869966G>A	uc001jxn.2	-	8	1273	c.1096C>T	c.(1096-1098)CGC>TGC	p.R366C	KCNMA1_uc001jxj.2_Missense_Mutation_p.R366C|KCNMA1_uc001jxk.1_Silent_p.G11G|KCNMA1_uc009xrt.1_Missense_Mutation_p.R186C|KCNMA1_uc001jxl.1_Missense_Mutation_p.R20C|KCNMA1_uc001jxo.2_Missense_Mutation_p.R366C|KCNMA1_uc001jxm.2_Missense_Mutation_p.R366C|KCNMA1_uc001jxq.2_Missense_Mutation_p.R366C	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	366	Extracellular (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
SFTPD	6441	broad.mit.edu	37	10	81701252	81701252	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81701252C>T	uc001kbh.2	-	6	612	c.569G>A	c.(568-570)GGT>GAT	p.G190D	MBL1P_uc001kbf.2_Intron	NM_003019	NP_003010	P35247	SFTPD_HUMAN	pulmonary surfactant-associated protein D	190	Collagen-like.				cell junction assembly|innate immune response|lung alveolus development|macrophage chemotaxis|negative regulation of interleukin-2 biosynthetic process|negative regulation of T cell proliferation|positive regulation of phagocytosis|reactive oxygen species metabolic process|receptor-mediated endocytosis|respiratory gaseous exchange|surfactant homeostasis	collagen|endocytic vesicle|extracellular space|lysosome	bacterial cell surface binding|protein binding|sugar binding			skin(1)	1	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)															---	---	---	---
ANXA11	311	broad.mit.edu	37	10	81930619	81930619	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81930619G>T	uc001kbq.1	-	5	933	c.108C>A	c.(106-108)CCC>CCA	p.P36P	ANXA11_uc010qlx.1_Silent_p.P136P|ANXA11_uc001kbr.1_Silent_p.P36P|ANXA11_uc001kbs.1_Silent_p.P36P|ANXA11_uc001kbt.1_Silent_p.P36P|ANXA11_uc010qly.1_Silent_p.P3P|ANXA11_uc009xsq.1_Silent_p.P36P|ANXA11_uc001kbu.1_Silent_p.P36P	NM_145869	NP_665876	P50995	ANX11_HUMAN	annexin A11	36					cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)															---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84745046	84745046	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84745046T>C	uc001kco.2	+	9	1803	c.1776T>C	c.(1774-1776)ATT>ATC	p.I592I	NRG3_uc010qlz.1_Silent_p.I591I|NRG3_uc001kcp.2_Silent_p.I395I|NRG3_uc001kcq.2_Silent_p.I242I|NRG3_uc001kcr.2_Silent_p.I266I	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	616	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88764072	88764072	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88764072C>T	uc001kee.2	+						AGAP11_uc001kef.2_Intron	NM_133447	NP_597704			ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
IFIT1	3434	broad.mit.edu	37	10	91162521	91162521	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91162521C>T	uc001kgi.2	+	2	637	c.489C>T	c.(487-489)TGC>TGT	p.C163C	LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|IFIT1_uc009xtt.2_Silent_p.C163C|IFIT1_uc001kgj.2_Silent_p.C132C	NM_001548	NP_001539	P09914	IFIT1_HUMAN	interferon-induced protein with	163	TPR 3.				cellular response to exogenous dsRNA|intracellular transport of viral proteins in host cell|negative regulation of defense response to virus by host|negative regulation of helicase activity|negative regulation of protein binding|negative regulation of viral genome replication|positive regulation of viral genome replication|response to virus|type I interferon-mediated signaling pathway	cytoplasm	protein binding				0																		---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93593768	93593768	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93593768G>A	uc001khp.2	+	12	1731	c.1434G>A	c.(1432-1434)CAG>CAA	p.Q478Q		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	478					positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95121308	95121308	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95121308C>T	uc001kin.2	-	28	2998	c.2875G>A	c.(2875-2877)GAT>AAT	p.D959N	MYOF_uc001kio.2_Missense_Mutation_p.D946N|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	959	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
ZNF518A	9849	broad.mit.edu	37	10	97917230	97917230	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97917230A>G	uc001klp.2	+	6	2008	c.1151A>G	c.(1150-1152)AAA>AGA	p.K384R	ZNF518A_uc001klo.1_Intron|ZNF518A_uc001klq.2_Missense_Mutation_p.K384R|ZNF518A_uc001klr.2_Missense_Mutation_p.K384R	NM_014803	NP_055618	Q6AHZ1	Z518A_HUMAN	zinc finger protein 518	384					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)														---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98743905	98743905	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98743905C>T	uc001kmv.2	+	1	2865	c.2758C>T	c.(2758-2760)CTA>TTA	p.L920L		NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	920										skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99218630	99218630	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99218630G>A	uc001kns.3	-	30	3217	c.2992C>T	c.(2992-2994)CGG>TGG	p.R998W	MMS19_uc001knq.2_Missense_Mutation_p.R261W|MMS19_uc009xvs.2_Missense_Mutation_p.R576W|MMS19_uc009xvt.2_Missense_Mutation_p.R742W|MMS19_uc001knr.2_Missense_Mutation_p.R839W|MMS19_uc010qox.1_Missense_Mutation_p.R976W|MMS19_uc001knt.2_Missense_Mutation_p.R998W	NM_022362	NP_071757	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog	998	HEAT 7.				chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)									Direct_reversal_of_damage|NER					---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101590174	101590174	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101590174C>T	uc001kqf.2	+	20	2870	c.2731C>T	c.(2731-2733)CGA>TGA	p.R911*		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	911	Cytoplasmic (By similarity).					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
SCD	6319	broad.mit.edu	37	10	102112215	102112215	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102112215C>T	uc001kqy.2	+	3	893	c.403C>T	c.(403-405)CGG>TGG	p.R135W		NM_005063	NP_005054	O00767	ACOD_HUMAN	stearoyl-CoA desaturase 1	135	Cytoplasmic (Potential).				fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)														---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103867933	103867933	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103867933C>A	uc009xwz.2	-	11	1496	c.1153G>T	c.(1153-1155)GGC>TGC	p.G385C	LDB1_uc001kuk.3_Missense_Mutation_p.G349C	NM_001113407	NP_001106878	Q86U70	LDB1_HUMAN	LIM domain binding 1 isoform 1	385					histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
TRIM8	81603	broad.mit.edu	37	10	104414974	104414974	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104414974G>T	uc001kvz.2	+	3	927	c.804G>T	c.(802-804)CAG>CAT	p.Q268H		NM_030912	NP_112174	Q9BZR9	TRIM8_HUMAN	tripartite motif-containing 8	268						cytoplasm|PML body	ligase activity|protein homodimerization activity|zinc ion binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
PCGF6	84108	broad.mit.edu	37	10	105073980	105073980	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105073980C>A	uc001kwt.2	-	9	1027	c.959G>T	c.(958-960)AGG>ATG	p.R320M	PCGF6_uc001kwu.2_Missense_Mutation_p.R245M|PCGF6_uc009xxk.2_RNA|PCGF6_uc009xxl.2_RNA|PCGF6_uc009xxm.2_RNA	NM_001011663	NP_001011663	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6 isoform a	320					negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)														---	---	---	---
NEURL	9148	broad.mit.edu	37	10	105349928	105349928	+	Silent	SNP	G	A	A	rs146023099		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105349928G>A	uc001kxh.2	+	6	1934	c.1524G>A	c.(1522-1524)TCG>TCA	p.S508S	SH3PXD2A_uc010qqr.1_Intron	NM_004210	NP_004201	O76050	NEU1A_HUMAN	neuralized-like	508					nervous system development	perinuclear region of cytoplasm	zinc ion binding				0				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)														---	---	---	---
SMC3	9126	broad.mit.edu	37	10	112364065	112364065	+	3'UTR	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112364065A>G	uc001kze.2	+	29						NM_005445	NP_005436			structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115347999	115347999	+	Silent	SNP	C	T	T	rs137990336	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115347999C>T	uc001lai.3	+	13	1657	c.1554C>T	c.(1552-1554)GAC>GAT	p.D518D		NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	518	Peptidase S1.				cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
AFAP1L2	84632	broad.mit.edu	37	10	116057096	116057096	+	Silent	SNP	G	A	A	rs115650575	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116057096G>A	uc001lbn.2	-	17	2491	c.2190C>T	c.(2188-2190)CGC>CGT	p.R730R	AFAP1L2_uc001lbo.2_Silent_p.R730R|AFAP1L2_uc010qse.1_Silent_p.R783R|AFAP1L2_uc001lbp.2_Silent_p.R758R|AFAP1L2_uc001lbm.2_Silent_p.R169R|AFAP1L2_uc010qsd.1_Silent_p.R296R|AFAP1L2_uc001lbq.1_Silent_p.R252R	NM_001001936	NP_001001936	Q8N4X5	AF1L2_HUMAN	KIAA1914 protein isoform 1	730	Potential.				inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding			ovary(1)|breast(1)	2		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)														---	---	---	---
FAM160B1	57700	broad.mit.edu	37	10	116605199	116605199	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116605199T>C	uc001lcb.2	+	8	1422	c.1087T>C	c.(1087-1089)TGG>CGG	p.W363R	FAM160B1_uc001lcc.2_Missense_Mutation_p.W363R	NM_020940	NP_065991	Q5W0V3	F16B1_HUMAN	hypothetical protein LOC57700 isoform a	363										lung(1)	1																		---	---	---	---
PRDX3	10935	broad.mit.edu	37	10	120931885	120931885	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120931885G>T	uc001lec.2	-							NM_006793	NP_006784			peroxiredoxin 3 isoform a precursor						cell redox homeostasis|hydrogen peroxide catabolic process|mitochondrion organization|myeloid cell differentiation|negative regulation of kinase activity|positive regulation of cell proliferation|positive regulation of NF-kappaB transcription factor activity|regulation of mitochondrial membrane potential|response to lipopolysaccharide	early endosome|mitochondrion	alkyl hydroperoxide reductase activity|caspase inhibitor activity|peroxidase activity|peroxiredoxin activity|protein C-terminus binding|protein kinase binding				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)														---	---	---	---
PRDX3	10935	broad.mit.edu	37	10	120936634	120936634	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120936634C>T	uc001lec.2	-	2	111	c.68G>A	c.(67-69)GGC>GAC	p.G23D		NM_006793	NP_006784	P30048	PRDX3_HUMAN	peroxiredoxin 3 isoform a precursor	23					cell redox homeostasis|hydrogen peroxide catabolic process|mitochondrion organization|myeloid cell differentiation|negative regulation of kinase activity|positive regulation of cell proliferation|positive regulation of NF-kappaB transcription factor activity|regulation of mitochondrial membrane potential|response to lipopolysaccharide	early endosome|mitochondrion	alkyl hydroperoxide reductase activity|caspase inhibitor activity|peroxidase activity|peroxiredoxin activity|protein C-terminus binding|protein kinase binding				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)														---	---	---	---
WDR11	55717	broad.mit.edu	37	10	122664223	122664223	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122664223A>G	uc010qtf.1	+	25	3331	c.3093A>G	c.(3091-3093)TCA>TCG	p.S1031S	WDR11_uc010qte.1_Silent_p.S633S|WDR11_uc001lfd.1_Silent_p.S549S|WDR11_uc009xzn.2_Silent_p.S322S|uc001lfe.1_5'Flank	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	1031						integral to membrane					0																		---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123843937	123843937	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123843937C>A	uc001lfv.2	+	4	2282	c.1922C>A	c.(1921-1923)GCT>GAT	p.A641D	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.A641D|TACC2_uc010qtv.1_Missense_Mutation_p.A641D	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	641						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
PLEKHA1	59338	broad.mit.edu	37	10	124189200	124189200	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124189200G>A	uc001lge.1	+	12	1084	c.961G>A	c.(961-963)GCC>ACC	p.A321T	PLEKHA1_uc001lgf.1_3'UTR|PLEKHA1_uc001lgg.1_Missense_Mutation_p.A321T	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A	321					B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	127730706	127730706	+	Intron	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127730706T>G	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Missense_Mutation_p.I738L|ADAM12_uc001ljn.2_Missense_Mutation_p.I735L|ADAM12_uc001ljl.3_Missense_Mutation_p.I737L	NM_003474	NP_003465			ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	133107449	133107449	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133107449T>G	uc001lkp.2	-	2	542	c.456A>C	c.(454-456)AAA>AAC	p.K152N		NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	152	WW 1.									large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
KNDC1	85442	broad.mit.edu	37	10	135020817	135020817	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135020817C>T	uc001llz.1	+	20	3757	c.3756C>T	c.(3754-3756)GCC>GCT	p.A1252A		NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	1252	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)														---	---	---	---
CYP2E1	1571	broad.mit.edu	37	10	135352393	135352393	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135352393C>T	uc001lnj.1	+	9	1440	c.1407C>T	c.(1405-1407)ATC>ATT	p.I469I	CYP2E1_uc001lnk.1_Silent_p.I332I|CYP2E1_uc009ybl.1_Silent_p.I270I|CYP2E1_uc009ybm.1_Silent_p.I123I|CYP2E1_uc001lnl.1_Intron	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	469					drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
HRAS	3265	broad.mit.edu	37	11	533504	533504	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:533504G>A	uc001lpv.2	-	4	587	c.399C>T	c.(397-399)CTC>CTT	p.L133L	HRAS_uc010qvw.1_Silent_p.L133L|HRAS_uc010qvx.1_Silent_p.L133L|HRAS_uc010qvy.1_RNA	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene	133					activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding			urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			---	---	---	---
PNPLA2	57104	broad.mit.edu	37	11	821958	821958	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:821958G>A	uc001lrt.2	+	4	623	c.421G>A	c.(421-423)GCC>ACC	p.A141T	PNPLA2_uc009ycl.2_5'Flank	NM_020376	NP_065109	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	141	Lumenal (Potential).|Patatin.				negative regulation of sequestering of triglyceride|positive regulation of triglyceride catabolic process	integral to membrane|lipid particle|plasma membrane	triglyceride lipase activity				0		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1015800	1015800	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1015800G>A	uc001lsw.2	-	31	7052	c.7001C>T	c.(7000-7002)CCG>CTG	p.P2334L		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	2334	Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1029611	1029611	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1029611C>A	uc001lsw.2	-	9	1071	c.1020G>T	c.(1018-1020)ACG>ACT	p.T340T		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	340	TIL.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1159011	1159011	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1159011G>A	uc009ycr.1	+	11	1315	c.1189G>A	c.(1189-1191)GTC>ATC	p.V397I		NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1159413	1159413	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1159413C>T	uc009ycr.1	+							NM_017511	NP_059981			SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	2356882	2356882	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2356882G>A	uc001lwe.2	-											Homo sapiens, clone IMAGE:4940779, mRNA.																														---	---	---	---
TRPM5	29850	broad.mit.edu	37	11	2429027	2429027	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2429027G>T	uc001lwm.3	-	19	2907	c.2898C>A	c.(2896-2898)ACC>ACA	p.T966T	TRPM5_uc010qxl.1_Silent_p.T966T|TRPM5_uc009ydn.2_Silent_p.T968T	NM_014555	NP_055370	Q9NZQ8	TRPM5_HUMAN	transient receptor potential cation channel,	966	Helical; (Potential).					integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)														---	---	---	---
CARS	833	broad.mit.edu	37	11	3047975	3047975	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3047975C>T	uc001lxh.2	-	9	909	c.835G>A	c.(835-837)GAG>AAG	p.E279K	CARS_uc001lxe.2_Missense_Mutation_p.E269K|CARS_uc001lxf.2_Missense_Mutation_p.E362K|CARS_uc001lxg.2_Missense_Mutation_p.E279K|CARS_uc010qxo.1_Missense_Mutation_p.E362K|CARS_uc010qxp.1_Missense_Mutation_p.E292K|uc001lxi.1_5'Flank	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b	279					cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)			T	ALK	ALCL								---	---	---	---
TRIM68	55128	broad.mit.edu	37	11	4621993	4621993	+	Missense_Mutation	SNP	C	T	T	rs147039003		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4621993C>T	uc001lzf.1	-	7	1209	c.971G>A	c.(970-972)CGT>CAT	p.R324H	TRIM68_uc001lzg.1_Missense_Mutation_p.R101H|TRIM68_uc010qyj.1_RNA	NM_018073	NP_060543	Q6AZZ1	TRI68_HUMAN	ring finger protein 137	324	B30.2/SPRY.				protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)														---	---	---	---
OR52J3	119679	broad.mit.edu	37	11	5068506	5068506	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5068506G>A	uc010qyv.1	+	1	751	c.751G>A	c.(751-753)GTT>ATT	p.V251I		NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J,	251	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|lung(1)|skin(1)	3		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52D1	390066	broad.mit.edu	37	11	5510028	5510028	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5510028C>T	uc010qzg.1	+	1	92	c.92C>T	c.(91-93)GCC>GTC	p.A31V	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D,	31	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR52D1	390066	broad.mit.edu	37	11	5510682	5510682	+	Missense_Mutation	SNP	G	T	T	rs147388113	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5510682G>T	uc010qzg.1	+	1	746	c.746G>T	c.(745-747)GGC>GTC	p.G249V	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D,	249	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR52B2	255725	broad.mit.edu	37	11	6190954	6190954	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6190954G>A	uc010qzy.1	-	1	603	c.603C>T	c.(601-603)GGC>GGT	p.G201G		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
APBB1	322	broad.mit.edu	37	11	6432181	6432181	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6432181G>A	uc001mdb.1	-	2	497	c.397C>T	c.(397-399)CGA>TGA	p.R133*	APBB1_uc001mdc.1_Nonsense_Mutation_p.R133*|APBB1_uc010rah.1_Intron	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	133					apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)														---	---	---	---
OR2AG2	338755	broad.mit.edu	37	11	6789930	6789930	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6789930G>A	uc001meq.1	-	1	259	c.259C>T	c.(259-261)CGC>TGC	p.R87C		NM_001004490	NP_001004490	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG,	87	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
ST5	6764	broad.mit.edu	37	11	8751662	8751662	+	Missense_Mutation	SNP	C	T	T	rs142799946		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8751662C>T	uc001mgt.2	-	3	1361	c.1175G>A	c.(1174-1176)CGC>CAC	p.R392H	ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Missense_Mutation_p.R392H|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Missense_Mutation_p.R392H	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	392	Pro-rich.				positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)														---	---	---	---
ST5	6764	broad.mit.edu	37	11	8752303	8752303	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8752303C>T	uc001mgt.2	-	3	720	c.534G>A	c.(532-534)TCG>TCA	p.S178S	ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Silent_p.S178S|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Silent_p.S178S	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	178					positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)														---	---	---	---
SWAP70	23075	broad.mit.edu	37	11	9750921	9750921	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9750921T>C	uc001mhw.2	+	6	920	c.821T>C	c.(820-822)CTT>CCT	p.L274P	SWAP70_uc001mhv.2_Missense_Mutation_p.L274P|SWAP70_uc001mhx.2_Missense_Mutation_p.L216P	NM_015055	NP_055870	Q9UH65	SWP70_HUMAN	SWAP-70 protein	274	PH.					cytoplasm|lamellipodium|nucleus|plasma membrane	calcium ion binding|DNA binding			ovary(2)|central_nervous_system(1)	3				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)														---	---	---	---
PARVA	55742	broad.mit.edu	37	11	12549459	12549459	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12549459G>A	uc001mki.2	+	13	1155	c.1106G>A	c.(1105-1107)CGT>CAT	p.R369H		NM_018222	NP_060692	Q9NVD7	PARVA_HUMAN	parvin, alpha	369	CH 2.				cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)														---	---	---	---
KCNC1	3746	broad.mit.edu	37	11	17757725	17757725	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17757725G>A	uc001mnk.3	+	1	231	c.176G>A	c.(175-177)CGC>CAC	p.R59H	KCNC1_uc009yhc.1_Missense_Mutation_p.R59H	NM_004976	NP_004967	P48547	KCNC1_HUMAN	Shaw-related voltage-gated potassium channel	59	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18316699	18316699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18316699C>T	uc001mod.1	-	14	1930	c.1652G>A	c.(1651-1653)CGT>CAT	p.R551H	HPS5_uc001moe.1_Missense_Mutation_p.R437H|HPS5_uc001mof.1_Missense_Mutation_p.R437H	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	551						cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
IGSF22	283284	broad.mit.edu	37	11	18736152	18736152	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18736152C>T	uc009yht.2	-	12	1741	c.1551G>A	c.(1549-1551)AAG>AAA	p.K517K	IGSF22_uc001mpa.2_RNA	NM_173588	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	517										ovary(4)|large_intestine(2)|kidney(1)	7																		---	---	---	---
QSER1	79832	broad.mit.edu	37	11	32954631	32954631	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32954631G>T	uc001mty.2	+	4	1707	c.1440G>T	c.(1438-1440)CGG>CGT	p.R480R	QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_5'Flank	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	480	Ser-rich.									ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)																	---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35338975	35338975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35338975G>A	uc001mwd.2	-	2	698	c.106C>T	c.(106-108)CGC>TGC	p.R36C	SLC1A2_uc001mwe.2_Missense_Mutation_p.R27C|SLC1A2_uc010rev.1_Missense_Mutation_p.R36C	NM_004171	NP_004162	P43004	EAA2_HUMAN	excitatory amino acid transporter 2	36	Cytoplasmic (Potential).				D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)													---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35515735	35515735	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35515735G>A	uc001mwg.2	-	2	202	c.159C>T	c.(157-159)TGC>TGT	p.C53C	PAMR1_uc001mwf.2_Silent_p.C53C|PAMR1_uc010rew.1_Silent_p.C53C|PAMR1_uc010rex.1_Silent_p.C13C	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	53	Cys-rich.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
TRIM44	54765	broad.mit.edu	37	11	35684938	35684938	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35684938C>T	uc001mwi.2	+	1	586	c.279C>T	c.(277-279)AGC>AGT	p.S93S		NM_017583	NP_060053	Q96DX7	TRI44_HUMAN	DIPB protein	93	Glu-rich.					intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)																---	---	---	---
TRIM44	54765	broad.mit.edu	37	11	35685117	35685117	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35685117C>T	uc001mwi.2	+	1	765	c.458C>T	c.(457-459)GCG>GTG	p.A153V		NM_017583	NP_060053	Q96DX7	TRI44_HUMAN	DIPB protein	153	Glu-rich.					intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)																---	---	---	---
TRAF6	7189	broad.mit.edu	37	11	36518742	36518742	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36518742A>G	uc001mwr.1	-	5	862	c.522T>C	c.(520-522)ATT>ATC	p.I174I	TRAF6_uc001mws.1_Silent_p.I174I	NM_145803	NP_665802	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6	174	Interaction with TAX1BP1.|TRAF-type 1.				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|ossification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell cytokine production|protein autoubiquitination|protein K63-linked ubiquitination|response to interleukin-1|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cell cortex|cytosol|endosome membrane|internal side of plasma membrane|nuclear membrane	histone deacetylase binding|mitogen-activated protein kinase kinase kinase binding|protein kinase B binding|protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)																---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36596366	36596366	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36596366T>C	uc001mwu.3	+	2	1636	c.1512T>C	c.(1510-1512)CAT>CAC	p.H504H	RAG1_uc001mwt.2_RNA	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	504					histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)												Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
RAG2	5897	broad.mit.edu	37	11	36615447	36615447	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36615447T>C	uc001mwv.3	-	2	460	c.272A>G	c.(271-273)TAC>TGC	p.Y91C	C11orf74_uc010rfd.1_5'Flank|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank|C11orf74_uc010rfe.1_5'Flank	NM_000536	NP_000527	P55895	RAG2_HUMAN	recombination activating gene 2	91					chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding			skin(3)|ovary(1)|pancreas(1)	5	all_lung(20;0.226)	all_hematologic(20;0.00756)												Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43465021	43465021	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43465021C>T	uc001mxi.2	+	17	2412	c.2398C>T	c.(2398-2400)CGG>TGG	p.R800W	TTC17_uc001mxh.2_Missense_Mutation_p.R857W|TTC17_uc010rfj.1_Missense_Mutation_p.R800W|TTC17_uc001mxj.2_Missense_Mutation_p.R627W	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	800							binding			ovary(5)	5																		---	---	---	---
CD82	3732	broad.mit.edu	37	11	44626728	44626728	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44626728G>T	uc001myc.2	+	5	505	c.257G>T	c.(256-258)GGG>GTG	p.G86V	CD82_uc001myd.2_Missense_Mutation_p.G86V	NM_002231	NP_002222	P27701	CD82_HUMAN	CD82 antigen isoform 1	86	Helical; (Potential).					integral to plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671393	45671393	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671393G>A	uc001mys.1	-	4	1752	c.1081C>T	c.(1081-1083)CGC>TGC	p.R361C		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	361	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
HARBI1	283254	broad.mit.edu	37	11	46637429	46637429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46637429C>T	uc001ncy.2	-	2	607	c.359G>A	c.(358-360)CGC>CAC	p.R120H	KIAA0652_uc009yld.2_5'Flank|KIAA0652_uc001nda.2_5'Flank|KIAA0652_uc001ndb.2_5'Flank|KIAA0652_uc001ncz.2_5'Flank|KIAA0652_uc001ndc.2_5'Flank|KIAA0652_uc010rgv.1_5'Flank	NM_173811	NP_776172	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	120						cytoplasm|nucleus	metal ion binding|nuclease activity				0																		---	---	---	---
MADD	8567	broad.mit.edu	37	11	47304062	47304062	+	Missense_Mutation	SNP	C	T	T	rs138360989		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47304062C>T	uc001ner.1	+	9	1791	c.1600C>T	c.(1600-1602)CGG>TGG	p.R534W	MADD_uc001neq.2_Missense_Mutation_p.R534W|MADD_uc001nev.1_Missense_Mutation_p.R534W|MADD_uc001nes.1_Missense_Mutation_p.R534W|MADD_uc001net.1_Missense_Mutation_p.R534W|MADD_uc009yln.1_Missense_Mutation_p.R534W|MADD_uc001neu.1_Missense_Mutation_p.R534W|MADD_uc001nex.2_Missense_Mutation_p.R534W|MADD_uc001nez.2_Missense_Mutation_p.R534W|MADD_uc001new.2_Missense_Mutation_p.R534W	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	534	dDENN.				activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48185175	48185175	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48185175G>A	uc001ngp.3	+							NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
FOLH1	2346	broad.mit.edu	37	11	49204780	49204780	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49204780G>A	uc001ngy.2	-	7	1102	c.841C>T	c.(841-843)CGT>TGT	p.R281C	FOLH1_uc001ngz.2_Missense_Mutation_p.R281C|FOLH1_uc009yly.2_Missense_Mutation_p.R266C|FOLH1_uc009ylz.2_Missense_Mutation_p.R266C|FOLH1_uc009yma.2_5'UTR	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1	281	NAALADase.|Extracellular (Probable).				proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)													---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035844T>C	uc010rid.1	+	4	660	c.574T>C	c.(574-576)TAC>CAC	p.Y192H		NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48	176						intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035854	55035854	+	Intron	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035854T>A	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035855	55035855	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035855A>G	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
OR9G9	504191	broad.mit.edu	37	11	56467999	56467999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56467999G>A	uc010rjn.1	+	1	136	c.136G>A	c.(136-138)GTG>ATG	p.V46M		NM_001013358	NP_001013376	P0C7N8	OR9G9_HUMAN	olfactory receptor, family 9, subfamily G,	46	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
OR9G9	504191	broad.mit.edu	37	11	56468513	56468513	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56468513A>G	uc010rjn.1	+	1	650	c.650A>G	c.(649-651)TAC>TGC	p.Y217C		NM_001013358	NP_001013376	P0C7N8	OR9G9_HUMAN	olfactory receptor, family 9, subfamily G,	217	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
OR9Q1	219956	broad.mit.edu	37	11	57947373	57947373	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57947373C>G	uc001nmj.2	+	3	773	c.457C>G	c.(457-459)CTC>GTC	p.L153V		NM_001005212	NP_001005212	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q,	153	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)																---	---	---	---
OR9Q1	219956	broad.mit.edu	37	11	57947660	57947660	+	Silent	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57947660A>C	uc001nmj.2	+	3	1060	c.744A>C	c.(742-744)TCA>TCC	p.S248S		NM_001005212	NP_001005212	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q,	248	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)																---	---	---	---
OR5A1	219982	broad.mit.edu	37	11	59211077	59211077	+	Missense_Mutation	SNP	C	T	T	rs140540035	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59211077C>T	uc001nnx.1	+	1	436	c.436C>T	c.(436-438)CGC>TGC	p.R146C		NM_001004728	NP_001004728	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A,	146	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SDHAF2	54949	broad.mit.edu	37	11	61197637	61197637	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61197637T>C	uc001nrt.2	+	1	41	c.19T>C	c.(19-21)TTC>CTC	p.F7L	CPSF7_uc001nro.2_5'Flank|CPSF7_uc001nrp.2_5'Flank|CPSF7_uc001nrq.2_5'Flank|CPSF7_uc001nrr.2_5'Flank|CPSF7_uc001nrs.1_5'Flank|CPSF7_uc009ynp.2_5'Flank	NM_017841	NP_060311	Q9NX18	SDHF2_HUMAN	succinate dehydrogenase complex assembly factor	7					mitochondrial electron transport, succinate to ubiquinone|protein-FAD linkage	mitochondrion	protein binding			ovary(2)	2														Familial_Paragangliomas				---	---	---	---
DAGLA	747	broad.mit.edu	37	11	61502473	61502473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61502473C>T	uc001nsa.2	+	10	1238	c.1127C>T	c.(1126-1128)GCG>GTG	p.A376V		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	376	Cytoplasmic (Potential).				cell death|lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3				READ - Rectum adenocarcinoma(4;0.219)														---	---	---	---
C11orf9	745	broad.mit.edu	37	11	61553276	61553276	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61553276C>A	uc001nsc.1	+	26	3401	c.3305C>A	c.(3304-3306)ACC>AAC	p.T1102N	C11orf9_uc001nse.1_Missense_Mutation_p.T1062N|C11orf9_uc010rll.1_Missense_Mutation_p.T488N	NM_001127392	NP_001120864	Q9Y2G1	MRF_HUMAN	myelin gene regulatory factor isoform 2	1102					central nervous system myelination|positive regulation of myelination|positive regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62299845	62299845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62299845C>T	uc001ntl.2	-	5	2344	c.2044G>A	c.(2044-2046)GGC>AGC	p.G682S	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	682					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
INTS5	80789	broad.mit.edu	37	11	62417296	62417296	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62417296G>A	uc001nud.2	-	2	309	c.256C>T	c.(256-258)CGG>TGG	p.R86W		NM_030628	NP_085131	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	86					snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2																		---	---	---	---
BSCL2	26580	broad.mit.edu	37	11	62457861	62457861	+	Missense_Mutation	SNP	C	T	T	rs149466797		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62457861C>T	uc001nuo.1	-	11	1599	c.1175G>A	c.(1174-1176)CGC>CAC	p.R392H	LRRN4CL_uc001nun.2_5'Flank|BSCL2_uc009yoc.1_3'UTR|BSCL2_uc001nup.2_Missense_Mutation_p.R392H|BSCL2_uc001nuq.1_Missense_Mutation_p.R392H|BSCL2_uc001nur.3_Missense_Mutation_p.R456H|BSCL2_uc009yod.2_Missense_Mutation_p.R456H|BSCL2_uc001nut.3_Missense_Mutation_p.R458H|HNRNPUL2_uc001nuu.1_RNA	NM_032667	NP_116056	Q96G97	BSCL2_HUMAN	seipin isoform 2	392	Cytoplasmic (Potential).				cell death	integral to endoplasmic reticulum membrane					0																		---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64402870	64402870	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64402870G>T	uc001oap.2	-	3	831	c.320C>A	c.(319-321)CCC>CAC	p.P107H	NRXN2_uc001oar.2_Missense_Mutation_p.P1153H|NRXN2_uc001oas.2_Missense_Mutation_p.P1113H|NRXN2_uc001oaq.2_Missense_Mutation_p.P820H	NM_138734	NP_620063	P58401	NRX2B_HUMAN	neurexin 2 isoform beta precursor	107	Extracellular (Potential).|Laminin G-like.				cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64435006	64435006	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64435006G>A	uc001oar.2	-	10	1953	c.1514C>T	c.(1513-1515)GCG>GTG	p.A505V	NRXN2_uc001oas.2_Missense_Mutation_p.A474V|NRXN2_uc001oaq.2_Missense_Mutation_p.A172V	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	Error:Variant_position_missing_in_P58401_after_alignment					cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
SAC3D1	29901	broad.mit.edu	37	11	64812082	64812082	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64812082G>A	uc001ocm.2	+	2	1349	c.960G>A	c.(958-960)CCG>CCA	p.P320P	SAC3D1_uc010rnv.1_Silent_p.P307P	NM_013299	NP_037431			SAC3 domain containing 1												0																		---	---	---	---
C11orf2	738	broad.mit.edu	37	11	64876788	64876788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64876788A>G	uc001ocr.1	+	6	1520	c.1480A>G	c.(1480-1482)ATC>GTC	p.I494V	TM7SF2_uc001oct.2_5'Flank|TM7SF2_uc010rny.1_5'Flank|TM7SF2_uc001ocu.2_5'Flank|TM7SF2_uc001ocv.2_5'Flank|C11orf2_uc001ocs.1_Missense_Mutation_p.I370V	NM_013265	NP_037397	Q9UID3	FFR_HUMAN	chromosome 11 open reading frame 2	494					lipid transport|protein transport	Golgi apparatus|integral to membrane					0																		---	---	---	---
MAP3K11	4296	broad.mit.edu	37	11	65375812	65375812	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65375812C>T	uc001oew.2	-	2	1340	c.847G>A	c.(847-849)GCG>ACG	p.A283T	MAP3K11_uc001oev.2_5'Flank|MAP3K11_uc010rol.1_Missense_Mutation_p.A26T|MAP3K11_uc001oex.1_5'UTR	NM_002419	NP_002410	Q16584	M3K11_HUMAN	mitogen-activated protein kinase kinase kinase	283	Protein kinase.				activation of JUN kinase activity|cell proliferation|G1 phase of mitotic cell cycle|microtubule-based process|positive regulation of JNK cascade|protein autophosphorylation	centrosome|microtubule	ATP binding|JUN kinase kinase kinase activity|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity			breast(3)|lung(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
MUS81	80198	broad.mit.edu	37	11	65631997	65631997	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65631997C>T	uc001ofv.3	+	11	1442	c.1089C>T	c.(1087-1089)CGC>CGT	p.R363R	MUS81_uc001ofw.3_RNA|MUS81_uc001ofx.3_5'UTR	NM_025128	NP_079404	Q96NY9	MUS81_HUMAN	MUS81 endonuclease homolog	363	ERCC4.				DNA recombination|DNA repair	nucleolus	3'-flap endonuclease activity|DNA binding|metal ion binding|protein binding				0				READ - Rectum adenocarcinoma(159;0.166)									Homologous_recombination					---	---	---	---
CATSPER1	117144	broad.mit.edu	37	11	65789062	65789062	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65789062G>T	uc001ogt.2	-	4	1734	c.1596C>A	c.(1594-1596)CAC>CAA	p.H532Q		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	532	Helical; Name=Segment S3; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2																		---	---	---	---
CCS	9973	broad.mit.edu	37	11	66373297	66373297	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66373297G>T	uc001oir.2	+	8	839	c.796G>T	c.(796-798)GAG>TAG	p.E266*	CCS_uc001ois.2_RNA	NM_005125	NP_005116	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	266					intracellular copper ion transport|oxidation-reduction process|removal of superoxide radicals	cytosol|mitochondrial inner membrane|nucleus|soluble fraction	copper ion transmembrane transporter activity|protein binding|superoxide dismutase copper chaperone activity|zinc ion binding				0																		---	---	---	---
SPTBN2	6712	broad.mit.edu	37	11	66466214	66466214	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66466214C>T	uc001ojd.2	-	19	3982	c.3910G>A	c.(3910-3912)GTG>ATG	p.V1304M		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1304	Spectrin 10.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PC	5091	broad.mit.edu	37	11	66638551	66638551	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66638551C>T	uc001ojn.1	-	5	654	c.605G>A	c.(604-606)CGT>CAT	p.R202H	PC_uc001ojo.1_Missense_Mutation_p.R202H|PC_uc001ojp.1_Missense_Mutation_p.R202H	NM_022172	NP_071504	P11498	PYC_HUMAN	pyruvate carboxylase precursor	202	ATP-grasp.|Biotin carboxylation.				gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)													---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71715793	71715793	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71715793G>A	uc001orl.1	-	24	6071	c.5899C>T	c.(5899-5901)CGA>TGA	p.R1967*	IL18BP_uc009ysu.1_Intron|NUMA1_uc001orj.2_Nonsense_Mutation_p.R149*|NUMA1_uc009ysw.1_Nonsense_Mutation_p.R1534*|NUMA1_uc001ork.1_Nonsense_Mutation_p.R831*|NUMA1_uc001orm.1_Nonsense_Mutation_p.R1953*	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1967					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72083970	72083970	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72083970G>A	uc001osj.2	-	5	785	c.735C>T	c.(733-735)GGC>GGT	p.G245G	CLPB_uc010rqx.1_Silent_p.G200G|CLPB_uc010rqy.1_Intron|CLPB_uc001osk.2_Intron|CLPB_uc009ytg.2_Intron|CLPB_uc010rqz.1_Intron	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	245					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1																		---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72422130	72422130	+	Silent	SNP	G	A	A	rs143899624		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72422130G>A	uc001osu.2	-	9	1338	c.1149C>T	c.(1147-1149)ATC>ATT	p.I383I	ARAP1_uc001osv.2_Silent_p.I383I|ARAP1_uc001osr.2_Silent_p.I143I|ARAP1_uc001oss.2_Silent_p.I138I|ARAP1_uc009yth.2_Silent_p.I138I|ARAP1_uc010rre.1_Silent_p.I138I	NM_001040118	NP_001035207	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	383	PH 1.				actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73020656	73020656	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73020656G>T	uc001otu.2	+	1	994	c.973G>T	c.(973-975)GGG>TGG	p.G325W		NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	325					actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
UCP3	7352	broad.mit.edu	37	11	73716937	73716937	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73716937C>A	uc001our.2	-	4	734	c.379G>T	c.(379-381)GGA>TGA	p.G127*	UCP3_uc001ous.2_Nonsense_Mutation_p.G127*	NM_003356	NP_003347	P55916	UCP3_HUMAN	uncoupling protein 3 isoform UCP3L	127	Solcar 2.|Helical; Name=3; (Potential).				mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			pancreas(1)	1	Breast(11;2.08e-05)																	---	---	---	---
OR2AT4	341152	broad.mit.edu	37	11	74800314	74800314	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74800314A>C	uc010rro.1	-	1	445	c.445T>G	c.(445-447)TTG>GTG	p.L149V		NM_001005285	NP_001005285	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76174915	76174915	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76174915A>G	uc001oxl.2	+	7	765	c.622A>G	c.(622-624)AAC>GAC	p.N208D	C11orf30_uc009yuj.1_Missense_Mutation_p.N223D|C11orf30_uc010rsa.1_Missense_Mutation_p.N158D|C11orf30_uc001oxm.2_Missense_Mutation_p.N209D|C11orf30_uc010rsb.1_Missense_Mutation_p.N223D|C11orf30_uc010rsc.1_Missense_Mutation_p.N223D|C11orf30_uc001oxn.2_Missense_Mutation_p.N209D|C11orf30_uc010rsd.1_Missense_Mutation_p.N222D	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein	208	Interaction with BRCA2.				chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
MYO7A	4647	broad.mit.edu	37	11	76872067	76872067	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76872067G>A	uc001oyb.2	+	12	1521	c.1249G>A	c.(1249-1251)GCA>ACA	p.A417T	MYO7A_uc010rsl.1_Missense_Mutation_p.A417T|MYO7A_uc010rsm.1_Missense_Mutation_p.A406T|MYO7A_uc001oyc.2_Missense_Mutation_p.A417T	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1	417	Myosin head-like.				actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4																		---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85459463	85459463	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85459463A>C	uc010rth.1	-	2	381	c.105T>G	c.(103-105)CAT>CAG	p.H35Q	SYTL2_uc010rtg.1_Missense_Mutation_p.H35Q|SYTL2_uc010rti.1_Missense_Mutation_p.H35Q|SYTL2_uc010rtj.1_5'UTR|SYTL2_uc001pbf.3_Missense_Mutation_p.H35Q	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	35	RabBD.				intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
EED	8726	broad.mit.edu	37	11	85989444	85989444	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85989444T>G	uc001pbp.2	+	12	1660	c.1203T>G	c.(1201-1203)TGT>TGG	p.C401W	EED_uc001pbq.2_3'UTR|EED_uc001pbr.2_Missense_Mutation_p.C426W|EED_uc001pbs.2_Missense_Mutation_p.C321W	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a	401	Interaction with EZH2 (By similarity).|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)																---	---	---	---
PRSS23	11098	broad.mit.edu	37	11	86519031	86519031	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86519031C>T	uc001pcb.2	+	2	562	c.346C>T	c.(346-348)CGA>TGA	p.R116*	PRSS23_uc001pcc.1_Intron|PRSS23_uc010rts.1_Nonsense_Mutation_p.R84*	NM_007173	NP_009104	O95084	PRS23_HUMAN	protease, serine, 23 precursor	116					proteolysis	extracellular region|nucleus	serine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92088376	92088376	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92088376A>T	uc001pdj.3	+	1	3115	c.3098A>T	c.(3097-3099)GAT>GTT	p.D1033V		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1033	Cadherin 9.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
CWC15	51503	broad.mit.edu	37	11	94704174	94704174	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94704174G>A	uc001pfd.3	-	4	423	c.300C>T	c.(298-300)GCC>GCT	p.A100A	CWC15_uc009ywl.1_3'UTR|KDM4D_uc001pfe.2_5'Flank	NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog	100					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95718765	95718765	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95718765T>C	uc001pfw.1	-	4	3670	c.2385A>G	c.(2383-2385)TCA>TCG	p.S795S		NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2	795					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)						T	MECT1|CRTC3	salivary gland mucoepidermoid								---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103092866	103092866	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103092866G>A	uc001pho.2	+	58	9359	c.9215G>A	c.(9214-9216)GGC>GAC	p.G3072D	DYNC2H1_uc001phn.1_Missense_Mutation_p.G3072D|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3072	Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
CARD17	440068	broad.mit.edu	37	11	104971474	104971474	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104971474T>C	uc001pir.1	-	2	57	c.40A>G	c.(40-42)ATC>GTC	p.I14V	CASP1_uc010rve.1_Intron|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron	NM_001007232	NP_001007233	Q5XLA6	CAR17_HUMAN	caspase recruitment domain family, member 17	14	CARD.				proteolysis|regulation of apoptosis	cytoplasm	cysteine-type endopeptidase activity|cysteine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105836666	105836666	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105836666G>A	uc001pix.2	+						GRIA4_uc001piw.2_Intron|GRIA4_uc010rvm.1_Intron|GRIA4_uc009yxl.1_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
KBTBD3	143879	broad.mit.edu	37	11	105924368	105924368	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105924368A>G	uc001pja.2	-	4	1688	c.1048T>C	c.(1048-1050)TGC>CGC	p.C350R	KBTBD3_uc001pjb.2_Missense_Mutation_p.C350R|KBTBD3_uc009yxm.2_Missense_Mutation_p.C271R	NM_198439	NP_940841	Q8NAB2	KBTB3_HUMAN	BTB and kelch domain containing 3	346	Kelch 2.									ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)														---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106558447	106558447	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106558447G>A	uc001pjg.1	-	8	2417	c.2027C>T	c.(2026-2028)CCG>CTG	p.P676L	GUCY1A2_uc010rvo.1_Missense_Mutation_p.P697L|GUCY1A2_uc009yxn.1_Missense_Mutation_p.P707L	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	676					intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)														---	---	---	---
ELMOD1	55531	broad.mit.edu	37	11	107526758	107526758	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107526758A>C	uc010rvs.1	+	11	1202	c.798A>C	c.(796-798)GAA>GAC	p.E266D	ELMOD1_uc001pjm.2_Missense_Mutation_p.E258D|ELMOD1_uc010rvt.1_Missense_Mutation_p.E260D	NM_018712	NP_061182	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1 isoform 1	266	ELMO.				phagocytosis	cytoskeleton	GTPase activator activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)														---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107682466	107682466	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107682466A>C	uc001pjq.2	-	3	762	c.341T>G	c.(340-342)CTG>CGG	p.L114R	SLC35F2_uc010rvu.1_5'UTR|SLC35F2_uc001pjs.2_Missense_Mutation_p.L114R	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	114	Helical; (Potential).				transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108123621	108123621	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108123621T>C	uc001pkb.1	+	12	2265	c.1880T>C	c.(1879-1881)TTC>TCC	p.F627S	ATM_uc009yxr.1_Missense_Mutation_p.F627S	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	627					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)				D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108385147	108385147	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108385147G>A	uc001pkk.2	-	6	1198	c.1087C>T	c.(1087-1089)CCA>TCA	p.P363S	EXPH5_uc010rvy.1_Missense_Mutation_p.P175S|EXPH5_uc010rvz.1_Missense_Mutation_p.P207S|EXPH5_uc010rwa.1_Missense_Mutation_p.P287S	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	363					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108549087	108549087	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108549087G>A	uc001pkm.2	+	5	648	c.583G>A	c.(583-585)GTG>ATG	p.V195M	DDX10_uc001pkl.1_Missense_Mutation_p.V195M	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	195	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
HSPB2	3316	broad.mit.edu	37	11	111784410	111784410	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111784410T>C	uc001pmg.2	+	2	434	c.340T>C	c.(340-342)TCC>CCC	p.S114P	CRYAB_uc001pmf.1_5'Flank|CRYAB_uc010rwp.1_5'Flank|HSPB2_uc009yyj.2_RNA|C11orf52_uc001pmh.2_Intron	NM_001541	NP_001532	Q16082	HSPB2_HUMAN	heat shock 27kDa protein 2	114					response to heat|response to unfolded protein	cytosol|nucleus	enzyme activator activity|protein binding	p.S114S(1)		ovary(2)|skin(1)	3		all_cancers(61;3.75e-11)|all_epithelial(67;2.33e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)														---	---	---	---
DRD2	1813	broad.mit.edu	37	11	113295192	113295192	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113295192C>T	uc001pnz.2	-	1	503	c.182G>A	c.(181-183)CGC>CAC	p.R61H	DRD2_uc010rwv.1_Missense_Mutation_p.R61H|DRD2_uc001poa.3_Missense_Mutation_p.R61H|DRD2_uc001pob.3_Missense_Mutation_p.R61H|DRD2_uc009yyr.1_Missense_Mutation_p.R61H	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long	61	Cytoplasmic (By similarity).				activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)|skin(1)	2		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)													---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113610048	113610048	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113610048T>C	uc001poe.2	-	12	1677	c.1640A>G	c.(1639-1641)TAC>TGC	p.Y547C	ZW10_uc009yyv.2_RNA	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10	547					cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)														---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113629370	113629370	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113629370C>T	uc001poe.2	-	6	676	c.639G>A	c.(637-639)TCG>TCA	p.S213S	ZW10_uc009yyv.2_RNA	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10	213	Interaction with RINT1.				cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115102166	115102166	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115102166C>T	uc001ppi.3	-	4	598	c.469G>A	c.(469-471)GTG>ATG	p.V157M	CADM1_uc001ppf.3_Missense_Mutation_p.V157M|CADM1_uc001ppk.3_Missense_Mutation_p.V157M|CADM1_uc001ppj.3_Missense_Mutation_p.V157M|CADM1_uc001ppl.2_Missense_Mutation_p.V157M	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	157	Ig-like C2-type 1.|Extracellular (Potential).				adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115102170	115102170	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115102170A>G	uc001ppi.3	-	4	594	c.465T>C	c.(463-465)ACT>ACC	p.T155T	CADM1_uc001ppf.3_Silent_p.T155T|CADM1_uc001ppk.3_Silent_p.T155T|CADM1_uc001ppj.3_Silent_p.T155T|CADM1_uc001ppl.2_Silent_p.T155T	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	155	Ig-like C2-type 1.|Extracellular (Potential).				adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117391948	117391948	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117391948C>T	uc001prh.1	-	6	1292	c.1290G>A	c.(1288-1290)ACG>ACA	p.T430T	DSCAML1_uc001pri.1_Silent_p.T234T	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	370	Extracellular (Potential).|Ig-like C2-type 4.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117403187	117403187	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117403187G>A	uc001prh.1	-	4	744	c.742C>T	c.(742-744)CAG>TAG	p.Q248*	DSCAML1_uc001pri.1_Nonsense_Mutation_p.Q52*	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	188	Extracellular (Potential).|Ig-like C2-type 2.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
IL10RA	3587	broad.mit.edu	37	11	117870021	117870021	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117870021C>T	uc001prv.2	+	7	1479	c.1402C>T	c.(1402-1404)CCC>TCC	p.P468S	IL10RA_uc010rxl.1_Missense_Mutation_p.P448S|IL10RA_uc010rxm.1_Missense_Mutation_p.P448S|IL10RA_uc010rxn.1_Missense_Mutation_p.P319S|IL10RA_uc001prw.2_Missense_Mutation_p.P319S	NM_001558	NP_001549	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha precursor	468	Cytoplasmic (Potential).					integral to membrane|plasma membrane	interleukin-10 receptor activity			ovary(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)														---	---	---	---
DDX6	1656	broad.mit.edu	37	11	118656881	118656881	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118656881G>A	uc001pub.2	-	2	441	c.80C>T	c.(79-81)CCC>CTC	p.P27L	DDX6_uc001puc.2_Missense_Mutation_p.P27L	NM_004397	NP_004388	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	27					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)				T	IGH@	B-NHL								---	---	---	---
BCL9L	283149	broad.mit.edu	37	11	118770784	118770784	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118770784G>T	uc001pug.2	-	7	4213	c.3248C>A	c.(3247-3249)CCC>CAC	p.P1083H	BCL9L_uc009zal.2_Missense_Mutation_p.P1078H	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1083	Pro-rich.				negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)														---	---	---	---
BCL9L	283149	broad.mit.edu	37	11	118772446	118772446	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118772446A>T	uc001pug.2	-	6	2971	c.2006T>A	c.(2005-2007)TTC>TAC	p.F669Y	BCL9L_uc009zal.2_Missense_Mutation_p.F664Y	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	669					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)														---	---	---	---
CCDC153	283152	broad.mit.edu	37	11	119061525	119061525	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119061525G>A	uc010rze.1	-	6	462	c.374C>T	c.(373-375)GCT>GTT	p.A125V		NM_001145018	NP_001138490	Q494R4	CC153_HUMAN	coiled-coil domain containing 153	125	Potential.										0																		---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120169029	120169029	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120169029G>A	uc001pxc.2	+	4	290	c.188G>A	c.(187-189)TGC>TAC	p.C63Y	POU2F3_uc010rzk.1_Missense_Mutation_p.M1I|POU2F3_uc010rzl.1_5'UTR	NM_014352	NP_055167	Q9UKI9	PO2F3_HUMAN	POU transcription factor	63					negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	121000865	121000865	+	Silent	SNP	C	T	T	rs138065050		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121000865C>T	uc010rzo.1	+	9	2886	c.2886C>T	c.(2884-2886)AGC>AGT	p.S962S		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	962					cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
C11orf63	79864	broad.mit.edu	37	11	122805658	122805658	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122805658C>T	uc001pym.2	+	5	1806	c.1509C>T	c.(1507-1509)CAC>CAT	p.H503H		NM_024806	NP_079082	Q6NUN7	CK063_HUMAN	hypothetical protein LOC79864 isoform 1	503										ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)														---	---	---	---
ASAM	79827	broad.mit.edu	37	11	122944278	122944278	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122944278A>G	uc001pyt.2	-	7	1385	c.1026T>C	c.(1024-1026)GGT>GGC	p.G342G		NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor	342	Cytoplasmic (Potential).					integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)														---	---	---	---
TMEM225	338661	broad.mit.edu	37	11	123754864	123754864	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123754864A>G	uc001pzi.2	-	3	589	c.381T>C	c.(379-381)GGT>GGC	p.G127G		NM_001013743	NP_001013765	Q6GV28	TM225_HUMAN	transmembrane protein 225	127						integral to membrane				upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	3																		---	---	---	---
OR10G7	390265	broad.mit.edu	37	11	123909249	123909249	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909249G>A	uc001pzq.1	-	1	460	c.460C>T	c.(460-462)CAC>TAC	p.H154Y		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	154	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)														---	---	---	---
VWA5A	4013	broad.mit.edu	37	11	123989717	123989717	+	Silent	SNP	C	T	T	rs140579492	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123989717C>T	uc001pzu.2	+	7	890	c.681C>T	c.(679-681)GAC>GAT	p.D227D	VWA5A_uc001pzr.2_Silent_p.D227D|VWA5A_uc001pzs.2_Silent_p.D227D|VWA5A_uc010sae.1_Silent_p.D243D|VWA5A_uc001pzt.2_Silent_p.D227D	NM_001130142	NP_001123614	O00534	VMA5A_HUMAN	BCSC-1 isoform 1	227										upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
ROBO4	54538	broad.mit.edu	37	11	124756580	124756580	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124756580G>A	uc001qbg.2	-	16	2714	c.2574C>T	c.(2572-2574)TGC>TGT	p.C858C	ROBO4_uc010sas.1_Silent_p.C713C|ROBO4_uc001qbh.2_3'UTR|ROBO4_uc001qbi.2_Silent_p.C416C	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	858					angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)														---	---	---	---
SLC37A2	219855	broad.mit.edu	37	11	124947377	124947377	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124947377C>T	uc001qbn.2	+	4	518	c.267C>T	c.(265-267)GGC>GGT	p.G89G	SLC37A2_uc010sau.1_Silent_p.G89G	NM_001145290	NP_001138762	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glycerol-3-phosphate	89	Helical; (Potential).				carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)														---	---	---	---
EI24	9538	broad.mit.edu	37	11	125450084	125450084	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125450084T>C	uc001qca.2	+	8	899	c.657T>C	c.(655-657)TAT>TAC	p.Y219Y	EI24_uc001qcb.2_Silent_p.Y219Y|EI24_uc010sbd.1_RNA|EI24_uc009zbl.2_Silent_p.Y219Y|EI24_uc001qcc.2_RNA|EI24_uc010sbe.1_Silent_p.Y205Y|EI24_uc010sbf.1_RNA	NM_004879	NP_004870	O14681	EI24_HUMAN	etoposide induced 2.4 isoform 1	219					apoptosis|autophagy|induction of apoptosis|negative regulation of cell growth	endoplasmic reticulum membrane|integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)														---	---	---	---
EI24	9538	broad.mit.edu	37	11	125451163	125451163	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125451163G>T	uc001qca.2	+	9	972	c.730G>T	c.(730-732)GGG>TGG	p.G244W	EI24_uc001qcb.2_Intron|EI24_uc010sbd.1_RNA|EI24_uc009zbl.2_Missense_Mutation_p.G244W|EI24_uc001qcc.2_RNA|EI24_uc010sbe.1_Missense_Mutation_p.G230W|EI24_uc010sbf.1_RNA	NM_004879	NP_004870	O14681	EI24_HUMAN	etoposide induced 2.4 isoform 1	244	Helical; (Potential).				apoptosis|autophagy|induction of apoptosis|negative regulation of cell growth	endoplasmic reticulum membrane|integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)														---	---	---	---
CHEK1	1111	broad.mit.edu	37	11	125503102	125503102	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125503102T>C	uc009zbo.2	+	6	1361	c.469T>C	c.(469-471)TAT>CAT	p.Y157H	CHEK1_uc010sbh.1_Missense_Mutation_p.Y173H|CHEK1_uc010sbi.1_Missense_Mutation_p.Y157H|CHEK1_uc001qcf.3_Missense_Mutation_p.Y157H|CHEK1_uc009zbp.2_Missense_Mutation_p.Y157H|CHEK1_uc001qcg.3_Missense_Mutation_p.Y157H|CHEK1_uc009zbq.2_Missense_Mutation_p.Y157H|CHEK1_uc001qci.1_RNA	NM_001114122	NP_001107594	O14757	CHK1_HUMAN	checkpoint kinase 1	157	Protein kinase.				cellular response to mechanical stimulus|DNA repair|DNA replication|gamete generation|negative regulation of cell proliferation|reciprocal meiotic recombination|regulation of cyclin-dependent protein kinase activity|replicative senescence	condensed nuclear chromosome|microtubule organizing center|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(3)|lung(2)|skin(1)	6	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)									Other_conserved_DNA_damage_response_genes					---	---	---	---
HYLS1	219844	broad.mit.edu	37	11	125769773	125769773	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125769773C>T	uc009zbv.2	+	4	1044	c.510C>T	c.(508-510)TGC>TGT	p.C170C	HYLS1_uc001qcx.3_Silent_p.C170C|PUS3_uc001qcy.2_Intron	NM_145014	NP_659451	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	170						centrosome|nucleus				upper_aerodigestive_tract(1)	1	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)														---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129784838	129784838	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129784838T>C	uc001qfm.2	-	18	2846	c.2614A>G	c.(2614-2616)ACG>GCG	p.T872A	PRDM10_uc001qfj.2_Missense_Mutation_p.T786A|PRDM10_uc001qfk.2_Missense_Mutation_p.T782A|PRDM10_uc001qfl.2_Missense_Mutation_p.T786A|PRDM10_uc010sbx.1_Missense_Mutation_p.T782A|PRDM10_uc001qfn.2_Missense_Mutation_p.T868A|PRDM10_uc009zcs.1_Missense_Mutation_p.T55A	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	872	Thr-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132307170	132307170	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132307170C>T	uc001qgs.2	-	4	660	c.610G>A	c.(610-612)GCG>ACG	p.A204T	OPCML_uc001qgu.2_Missense_Mutation_p.A197T|OPCML_uc010sck.1_Missense_Mutation_p.A204T|OPCML_uc001qgt.2_Missense_Mutation_p.A203T|OPCML_uc010scl.1_Missense_Mutation_p.A163T	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	204	Ig-like C2-type 2.				cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity	p.A204A(1)		ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132399051	132399051	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132399051C>A	uc001qgs.2	-	3	480	c.430G>T	c.(430-432)GAC>TAC	p.D144Y	OPCML_uc001qgu.2_Missense_Mutation_p.D137Y|OPCML_uc010sck.1_Missense_Mutation_p.D144Y|OPCML_uc001qgt.2_Missense_Mutation_p.D144Y|OPCML_uc010scl.1_Missense_Mutation_p.D103Y	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	144	Ig-like C2-type 2.				cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133801988	133801988	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133801988C>T	uc001qgx.3	-	8	1319	c.1088G>A	c.(1087-1089)GGC>GAC	p.G363D	IGSF9B_uc001qgy.1_Missense_Mutation_p.G205D	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	363	Extracellular (Potential).|Ig-like 4.					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134177026	134177026	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134177026G>A	uc009zdf.2	+	10	1245	c.885G>A	c.(883-885)AAG>AAA	p.K295K	GLB1L3_uc010scu.1_5'UTR|GLB1L3_uc001qho.3_RNA	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3	295					carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
WNK1	65125	broad.mit.edu	37	12	994834	994834	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:994834C>A	uc001qio.3	+	19	5371	c.4864C>A	c.(4864-4866)CCT>ACT	p.P1622T	WNK1_uc001qip.3_Missense_Mutation_p.P1375T|WNK1_uc001qir.3_Missense_Mutation_p.P795T	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1622					intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2719725	2719725	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2719725G>A	uc009zdu.1	+	29	3950	c.3637G>A	c.(3637-3639)GCC>ACC	p.A1213T	CACNA1C_uc009zdv.1_Missense_Mutation_p.A1190T|CACNA1C_uc001qkb.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkc.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qke.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkf.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qjz.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkd.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkg.2_Missense_Mutation_p.A1193T|CACNA1C_uc009zdw.1_Missense_Mutation_p.A1193T|CACNA1C_uc001qkh.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkl.2_Missense_Mutation_p.A1213T|CACNA1C_uc001qkn.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qko.2_Missense_Mutation_p.A1213T|CACNA1C_uc001qkp.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkr.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qku.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkq.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qks.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qkt.2_Missense_Mutation_p.A1193T|CACNA1C_uc001qka.1_Missense_Mutation_p.A728T|CACNA1C_uc001qki.1_Missense_Mutation_p.A929T|CACNA1C_uc001qkj.1_Missense_Mutation_p.A929T|CACNA1C_uc001qkk.1_Missense_Mutation_p.A929T|CACNA1C_uc001qkm.1_Missense_Mutation_p.A929T	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1213	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
FOXM1	2305	broad.mit.edu	37	12	2983625	2983625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2983625C>T	uc001qlf.2	-	2	285	c.20G>A	c.(19-21)CGG>CAG	p.R7Q	TULP3_uc010sef.1_5'Flank|FOXM1_uc001qle.2_Missense_Mutation_p.R7Q|FOXM1_uc001qlg.2_Missense_Mutation_p.R7Q|FOXM1_uc009zea.2_Missense_Mutation_p.R7Q|FOXM1_uc009zeb.2_Missense_Mutation_p.R7Q|C12orf32_uc001qlh.2_5'Flank|C12orf32_uc010see.1_5'Flank|C12orf32_uc001qli.2_5'Flank	NM_021953	NP_068772	Q08050	FOXM1_HUMAN	forkhead box M1 isoform 2	7					cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.000622)															---	---	---	---
TEAD4	7004	broad.mit.edu	37	12	3126610	3126610	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3126610C>T	uc010sej.1	+	6	675	c.398C>T	c.(397-399)TCG>TTG	p.S133L	TEAD4_uc010sek.1_Intron|TEAD4_uc001qln.2_Missense_Mutation_p.S5L	NM_003213	NP_003204	Q15561	TEAD4_HUMAN	TEA domain family member 4 isoform 1	134					hippo signaling cascade|muscle organ development|skeletal system development		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
NDUFA9	4704	broad.mit.edu	37	12	4763447	4763447	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4763447T>C	uc001qnc.2	+						NDUFA9_uc009zei.1_Intron	NM_005002	NP_004993			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|sodium ion transport	mitochondrial matrix|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
NDUFA9	4704	broad.mit.edu	37	12	4796283	4796283	+	3'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4796283G>A	uc001qnc.2	+	11					NDUFA9_uc010ses.1_3'UTR	NM_005002	NP_004993			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|sodium ion transport	mitochondrial matrix|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
VWF	7450	broad.mit.edu	37	12	6077330	6077330	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6077330C>T	uc001qnn.1	-	46	7983	c.7733G>A	c.(7732-7734)CGC>CAC	p.R2578H	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	2578					blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
TNFRSF1A	7132	broad.mit.edu	37	12	6438657	6438657	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6438657G>A	uc001qnu.2	-	10	1470	c.1189C>T	c.(1189-1191)CGC>TGC	p.R397C	TNFRSF1A_uc001qnt.2_Missense_Mutation_p.R289C|TNFRSF1A_uc010sey.1_Missense_Mutation_p.R165C|TNFRSF1A_uc010sez.1_Missense_Mutation_p.R289C|TNFRSF1A_uc009zek.2_Missense_Mutation_p.R354C	NM_001065	NP_001056	P19438	TNR1A_HUMAN	tumor necrosis factor receptor 1 precursor	397	Death.|Cytoplasmic (Potential).				apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity			lung(2)|skin(1)	3																		---	---	---	---
LTBR	4055	broad.mit.edu	37	12	6495247	6495247	+	Missense_Mutation	SNP	G	T	T	rs149981490	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6495247G>T	uc001qny.1	+	5	656	c.488G>T	c.(487-489)GGT>GTT	p.G163V	LTBR_uc010sfc.1_Missense_Mutation_p.G144V|LTBR_uc001qnz.1_Missense_Mutation_p.G158V	NM_002342	NP_002333	P36941	TNR3_HUMAN	lymphotoxin beta receptor precursor	163	Extracellular (Potential).|TNFR-Cys 3.				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity			lung(2)	2																		---	---	---	---
NCAPD2	9918	broad.mit.edu	37	12	6620296	6620296	+	Missense_Mutation	SNP	G	T	T	rs149220411		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6620296G>T	uc001qoo.2	+	6	511	c.465G>T	c.(463-465)AAG>AAT	p.K155N	NCAPD2_uc009zen.1_Intron|NCAPD2_uc010sfd.1_Missense_Mutation_p.K110N	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	155	Interactions with SMC2 and SMC4.				cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5																		---	---	---	---
GNB3	2784	broad.mit.edu	37	12	6953139	6953139	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6953139C>A	uc001qrd.2	+	9	1101	c.696C>A	c.(694-696)ATC>ATA	p.I232I	GNB3_uc001qrc.2_Silent_p.I188I|GNB3_uc009zfe.2_Silent_p.I231I	NM_002075	NP_002066	P16520	GBB3_HUMAN	guanine nucleotide-binding protein, beta-3	232	WD 5.				cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of blood pressure|synaptic transmission	plasma membrane	GTPase activity|GTPase binding|signal transducer activity				0																		---	---	---	---
ENO2	2026	broad.mit.edu	37	12	7031575	7031575	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7031575C>A	uc001qru.1	+						ENO2_uc009zfi.1_Intron|ENO2_uc010sfq.1_Intron|ENO2_uc001qrv.1_Intron|ATN1_uc001qrw.1_5'Flank	NM_001975	NP_001966			enolase 2						gluconeogenesis|glycolysis	phosphopyruvate hydratase complex|plasma membrane	magnesium ion binding|phosphopyruvate hydratase activity				0																		---	---	---	---
A2M	2	broad.mit.edu	37	12	9229497	9229497	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9229497C>T	uc001qvk.1	-	28	3500	c.3387G>A	c.(3385-3387)GAG>GAA	p.E1129E	A2M_uc001qvj.1_Silent_p.E171E|A2M_uc009zgk.1_Silent_p.E979E	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1129					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)													---	---	---	---
TAS2R50	259296	broad.mit.edu	37	12	11139087	11139087	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11139087C>T	uc001qzl.2	-	1	425	c.373G>A	c.(373-375)GTT>ATT	p.V125I	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176890	NP_795371	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	125	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(2)	2																		---	---	---	---
KCNJ8	3764	broad.mit.edu	37	12	21926343	21926343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21926343G>A	uc001rff.2	-	2	546	c.208C>T	c.(208-210)CGC>TGC	p.R70C		NM_004982	NP_004973	Q15842	IRK8_HUMAN	potassium inwardly-rectifying channel J8	70	Helical; Name=M1; (By similarity).					voltage-gated potassium channel complex					0					Levosimendan(DB00922)											OREG0021704	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ST8SIA1	6489	broad.mit.edu	37	12	22408244	22408244	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22408244C>T	uc001rfo.3	-	3	943	c.461G>A	c.(460-462)CGT>CAT	p.R154H	ST8SIA1_uc009zix.2_Intron	NM_003034	NP_003025	Q92185	SIA8A_HUMAN	alpha-2,8-sialyltransferase 1	154	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23687190	23687190	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23687190C>G	uc001rfw.2	-	15	2357	c.2255G>C	c.(2254-2256)AGT>ACT	p.S752T	SOX5_uc001rfx.2_Missense_Mutation_p.S739T|SOX5_uc001rfy.2_Missense_Mutation_p.S631T|SOX5_uc001rfv.2_Missense_Mutation_p.S366T|SOX5_uc010siv.1_Missense_Mutation_p.S739T	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	752					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
KLHDC5	57542	broad.mit.edu	37	12	27950973	27950973	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27950973G>T	uc001rij.2	+	3	1469	c.1392G>T	c.(1390-1392)TTG>TTT	p.L464F	KLHDC5_uc009zjj.2_RNA	NM_020782	NP_065833	Q9P2K6	KLDC5_HUMAN	kelch domain containing 5	464	Kelch 6.									ovary(1)|central_nervous_system(1)	2	Lung SC(9;0.0873)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31632613	31632613	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31632613G>A	uc001rki.1	-	3	1000	c.814C>T	c.(814-816)CGG>TGG	p.R272W	DENND5B_uc001rkh.1_Missense_Mutation_p.R307W|DENND5B_uc009zjq.1_Missense_Mutation_p.R191W|DENND5B_uc001rkj.2_Missense_Mutation_p.R294W|DENND5B_uc001rkk.1_Missense_Mutation_p.R194W	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	272	DENN.					integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C12orf35	55196	broad.mit.edu	37	12	32135664	32135664	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32135664G>A	uc001rks.2	+	4	2189	c.1775G>A	c.(1774-1776)CGT>CAT	p.R592H		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	592										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)															---	---	---	---
C12orf35	55196	broad.mit.edu	37	12	32135791	32135791	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32135791T>C	uc001rks.2	+	4	2316	c.1902T>C	c.(1900-1902)ACT>ACC	p.T634T		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	634										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)															---	---	---	---
ABCD2	225	broad.mit.edu	37	12	39980001	39980001	+	Missense_Mutation	SNP	C	T	T	rs151149571	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39980001C>T	uc001rmb.2	-	7	2171	c.1745G>A	c.(1744-1746)CGT>CAT	p.R582H		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	582	ABC transporter.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40076706	40076706	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40076706T>C	uc001rmc.2	+	8	1147	c.980T>C	c.(979-981)ATG>ACG	p.M327T	C12orf40_uc009zjv.1_RNA	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	327										ovary(6)	6																		---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40734097	40734097	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40734097T>A	uc001rmg.3	+	41	6071	c.5950T>A	c.(5950-5952)TAC>AAC	p.Y1984N	LRRK2_uc009zjw.2_Missense_Mutation_p.Y822N|LRRK2_uc001rmi.2_Missense_Mutation_p.Y817N	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1984	Protein kinase.				activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)																---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41323660	41323660	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41323660C>T	uc001rmm.1	+	7	672	c.559C>T	c.(559-561)CGA>TGA	p.R187*	CNTN1_uc009zjy.1_Nonsense_Mutation_p.R187*|CNTN1_uc001rmn.1_Nonsense_Mutation_p.R176*|CNTN1_uc001rmo.2_Nonsense_Mutation_p.R187*	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	187	Ig-like C2-type 2.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45781974	45781974	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45781974G>T	uc001roo.2	+	11	1531	c.1196G>T	c.(1195-1197)CGC>CTC	p.R399L	ANO6_uc010sld.1_Missense_Mutation_p.R399L|ANO6_uc010sle.1_Missense_Mutation_p.R399L|ANO6_uc010slf.1_Missense_Mutation_p.R420L|ANO6_uc010slg.1_Missense_Mutation_p.R381L	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	399	Cytoplasmic (Potential).				activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46211624	46211624	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46211624C>G	uc001ros.1	+	5	590	c.590C>G	c.(589-591)CCT>CGT	p.P197R	ARID2_uc001ror.2_Missense_Mutation_p.P197R	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	197					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)														---	---	---	---
VDR	7421	broad.mit.edu	37	12	48251288	48251288	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48251288C>T	uc001rqm.2	-	6	743	c.461G>A	c.(460-462)CGG>CAG	p.R154Q	VDR_uc001rql.2_Missense_Mutation_p.R204Q|VDR_uc001rqn.2_Missense_Mutation_p.R154Q|VDR_uc010slq.1_Missense_Mutation_p.R122Q	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor	154	Hinge.				decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)													---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49438647	49438647	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49438647G>A	uc001rta.3	-	19	4843	c.4843C>T	c.(4843-4845)CGA>TGA	p.R1615*		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1615					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
METTL7A	25840	broad.mit.edu	37	12	51318975	51318975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51318975G>A	uc001rxb.2	+	1	442	c.154G>A	c.(154-156)GCA>ACA	p.A52T	METTL7A_uc010smv.1_Missense_Mutation_p.A52T	NM_014033	NP_054752	Q9H8H3	MET7A_HUMAN	methyltransferase like 7A precursor	52						endoplasmic reticulum|lipid particle|membrane	methyltransferase activity				0																		---	---	---	---
KRT5	3852	broad.mit.edu	37	12	52913971	52913971	+	Missense_Mutation	SNP	C	T	T	rs61747181		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52913971C>T	uc001san.2	-	1	273	c.110G>A	c.(109-111)CGG>CAG	p.R37Q	KRT5_uc009zmh.2_Missense_Mutation_p.R37Q	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5	37	Head.				epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT74	121391	broad.mit.edu	37	12	52962081	52962081	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52962081G>A	uc001sap.1	-	7	1275	c.1227C>T	c.(1225-1227)GGC>GGT	p.G409G		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	409	Rod.|Coil 2.					keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)														---	---	---	---
KRT72	140807	broad.mit.edu	37	12	52981452	52981452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52981452C>T	uc001sar.2	-	7	1359	c.1273G>A	c.(1273-1275)GCC>ACC	p.A425T	KRT72_uc001saq.2_Missense_Mutation_p.A425T|KRT72_uc010sns.1_Missense_Mutation_p.A383T|KRT72_uc010snt.1_Missense_Mutation_p.A237T	NM_001146225	NP_001139697	Q14CN4	K2C72_HUMAN	keratin 72 isoform 1	425	Coil 2.|Rod.					keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)														---	---	---	---
KRT76	51350	broad.mit.edu	37	12	53164811	53164811	+	Missense_Mutation	SNP	G	A	A	rs144079786	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53164811G>A	uc001sax.2	-	7	1510	c.1456C>T	c.(1456-1458)CGC>TGC	p.R486C		NM_015848	NP_056932	Q01546	K22O_HUMAN	keratin 76	486	Rod.|Coil 2.				cytoskeleton organization	keratin filament	structural molecule activity			breast(1)|skin(1)	2																		---	---	---	---
KRT3	3850	broad.mit.edu	37	12	53187985	53187985	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53187985C>T	uc001say.2	-	2	842	c.776G>A	c.(775-777)CGG>CAG	p.R259Q		NM_057088	NP_476429	P12035	K2C3_HUMAN	keratin 3	259	Rod.|Coil 1B.				epithelial cell differentiation|intermediate filament cytoskeleton organization	keratin filament	structural molecule activity				0																		---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53291404	53291404	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53291404T>C	uc001sbd.2	-						KRT8_uc009zmj.2_Intron|KRT8_uc009zmk.1_Intron|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_002273	NP_002264			keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
KIAA0748	9840	broad.mit.edu	37	12	55356889	55356889	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55356889G>A	uc001sgn.3	-	9	903	c.793C>T	c.(793-795)CCA>TCA	p.P265S	KIAA0748_uc001sgl.3_Missense_Mutation_p.P127S|KIAA0748_uc001sgm.3_Missense_Mutation_p.P12S|KIAA0748_uc010spb.1_Missense_Mutation_p.P12S|KIAA0748_uc010spc.1_Missense_Mutation_p.P127S|KIAA0748_uc010spd.1_Missense_Mutation_p.P265S|KIAA0748_uc001sgo.3_RNA	NM_001098815	NP_001092285	A2RU30	K0748_HUMAN	hypothetical protein LOC9840	265										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SILV	6490	broad.mit.edu	37	12	56349117	56349117	+	Silent	SNP	C	T	T	rs3741503		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56349117C>T	uc001sip.2	-	10	1822	c.1791G>A	c.(1789-1791)CCG>CCA	p.P597P	SILV_uc001siq.2_Silent_p.P604P|SILV_uc010spx.1_Silent_p.P511P|SILV_uc001sir.2_Silent_p.P597P	NM_006928	NP_008859	P40967	PMEL_HUMAN	silver homolog	597	Helical; (Potential).			P -> R (in Ref. 1; AAA60121).	melanin biosynthetic process|melanosome organization	endoplasmic reticulum membrane|extracellular region|Golgi apparatus|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding				0																		---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56489516	56489516	+	Missense_Mutation	SNP	G	A	A	rs139022684		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56489516G>A	uc001sjh.2	+	17	2174	c.1981G>A	c.(1981-1983)GGC>AGC	p.G661S	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Missense_Mutation_p.G18S|ERBB3_uc010sqc.1_Missense_Mutation_p.G602S|ERBB3_uc009zok.2_Missense_Mutation_p.G103S|ERBB3_uc001sjk.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	661	Helical; (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56572188	56572188	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56572188C>T	uc001skb.2	-	14	1416	c.1310G>A	c.(1309-1311)AGT>AAT	p.S437N	SMARCC2_uc001skd.2_Missense_Mutation_p.S437N|SMARCC2_uc001ska.2_Missense_Mutation_p.S437N|SMARCC2_uc001skc.2_Missense_Mutation_p.S437N|SMARCC2_uc010sqf.1_Missense_Mutation_p.S326N	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	437	SWIRM.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
SLC39A5	283375	broad.mit.edu	37	12	56625138	56625138	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56625138C>A	uc010sqj.1	+	4	337	c.80C>A	c.(79-81)CCC>CAC	p.P27H	SLC39A5_uc010sqi.1_Intron|SLC39A5_uc010sqk.1_Missense_Mutation_p.P27H	NM_173596	NP_775867	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (metal ion	27	Extracellular (By similarity).				zinc ion transport	basolateral plasma membrane|integral to membrane	metal ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
APOF	319	broad.mit.edu	37	12	56755032	56755032	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56755032C>A	uc001sle.1	-	2	1012	c.958G>T	c.(958-960)GGG>TGG	p.G320W		NM_001638	NP_001629	Q13790	APOF_HUMAN	apolipoprotein F precursor	320					cholesterol metabolic process	high-density lipoprotein particle|low-density lipoprotein particle	cholesterol binding|lipid transporter activity|receptor binding				0																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57574533	57574533	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57574533C>T	uc001snd.2	+	33	5936	c.5470C>T	c.(5470-5472)CGG>TGG	p.R1824W		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	1824	Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57920006	57920006	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57920006C>T	uc001soj.1	+	6	1479	c.1255C>T	c.(1255-1257)CCC>TCC	p.P419S	MBD6_uc001sok.1_Missense_Mutation_p.P286S|MBD6_uc001sol.1_5'Flank	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	419	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
LEMD3	23592	broad.mit.edu	37	12	65633991	65633991	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65633991G>A	uc001ssl.1	+	8	2105	c.2099G>A	c.(2098-2100)CGC>CAC	p.R700H	LEMD3_uc009zqo.1_Missense_Mutation_p.R699H	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	700	Interaction with SMAD1, SMAD2, SMAD3 and SMAD5.				negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	66502395	66502395	+	IGR	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66502395C>T								HMGA2 (142327 upstream) : LLPH (14455 downstream)																																			---	---	---	---
HELB	92797	broad.mit.edu	37	12	66725101	66725101	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66725101T>C	uc001sti.2	+	12	2866	c.2838T>C	c.(2836-2838)CGT>CGC	p.R946R	HELB_uc010ssz.1_RNA|HELB_uc009zqt.1_RNA	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	946					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66839252	66839252	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66839252T>C	uc001stk.2	-	11	1476	c.1235A>G	c.(1234-1236)CAG>CGG	p.Q412R	GRIP1_uc010sta.1_Missense_Mutation_p.Q356R|GRIP1_uc001stj.2_Missense_Mutation_p.Q194R|GRIP1_uc001stl.1_Missense_Mutation_p.Q304R|GRIP1_uc001stm.2_Missense_Mutation_p.Q412R	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	464					androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
BBS10	79738	broad.mit.edu	37	12	76740596	76740596	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76740596C>T	uc001syd.1	-	2	1253	c.1169G>A	c.(1168-1170)TGT>TAT	p.C390Y		NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	390					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2														Bardet-Biedl_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	12	80665545	80665545	+	IGR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80665545G>A								PPP1R12A (336310 upstream) : PTPRQ (172581 downstream)																																			---	---	---	---
MYF6	4618	broad.mit.edu	37	12	81101695	81101695	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81101695C>T	uc001szf.1	+	1	250	c.197C>T	c.(196-198)CCG>CTG	p.P66L		NM_002469	NP_002460	P23409	MYF6_HUMAN	myogenic factor 6	66					muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
ACSS3	79611	broad.mit.edu	37	12	81610701	81610701	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81610701C>T	uc001szl.1	+	10	1467	c.1376C>T	c.(1375-1377)GCG>GTG	p.A459V	ACSS3_uc001szm.1_Missense_Mutation_p.A458V|ACSS3_uc001szn.1_Missense_Mutation_p.A141V	NM_024560	NP_078836	Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	459						mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85518300	85518300	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85518300A>G	uc001tac.2	+						LRRIQ1_uc001tab.1_Silent_p.*1337*	NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88496712	88496712	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88496712G>T	uc001tar.2	-	26	3238	c.2894C>A	c.(2893-2895)GCT>GAT	p.A965D	CEP290_uc001taq.2_Missense_Mutation_p.A25D|CEP290_uc001tat.2_Missense_Mutation_p.A758D	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	965	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
TMTC3	160418	broad.mit.edu	37	12	88566411	88566411	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88566411C>T	uc001tau.2	+	8	1308	c.1088C>T	c.(1087-1089)TCG>TTG	p.S363L	TMTC3_uc009zsm.2_RNA	NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat	363	Helical; (Potential).					integral to membrane	binding			skin(1)	1																		---	---	---	---
LUM	4060	broad.mit.edu	37	12	91502288	91502288	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91502288C>A	uc001tbm.2	-	2	858	c.469G>T	c.(469-471)GGA>TGA	p.G157*	LUM_uc001tbn.2_Intron	NM_002345	NP_002336	P51884	LUM_HUMAN	lumican precursor	157	LRR 4.				collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent			central_nervous_system(2)	2																		---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94654559	94654559	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94654559C>T	uc001tdc.2	+	20	3642	c.3393C>T	c.(3391-3393)TCC>TCT	p.S1131S	PLXNC1_uc010sut.1_Silent_p.S178S|PLXNC1_uc009zsv.2_5'Flank	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	1131	Cytoplasmic (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101723026	101723026	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101723026C>T	uc001tia.1	+	27	3372	c.3216C>T	c.(3214-3216)TGC>TGT	p.C1072C		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	1072					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102025452	102025452	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102025452C>T	uc001tii.2	+	5	420	c.318C>T	c.(316-318)GCC>GCT	p.A106A	MYBPC1_uc001tif.1_Silent_p.A119A|MYBPC1_uc001tig.2_Silent_p.A131A|MYBPC1_uc010svq.1_Silent_p.A93A|MYBPC1_uc001tih.2_Silent_p.A131A|MYBPC1_uc001tij.2_Silent_p.A106A|MYBPC1_uc010svr.1_Silent_p.A106A|MYBPC1_uc010svs.1_Silent_p.A106A|MYBPC1_uc010svt.1_Silent_p.A94A|MYBPC1_uc010svu.1_Silent_p.A106A|MYBPC1_uc001tik.2_Silent_p.A80A	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	106	Ig-like C2-type 1.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102057273	102057273	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102057273G>A	uc001tii.2	+	20	2318	c.2216G>A	c.(2215-2217)CGC>CAC	p.R739H	MYBPC1_uc001tig.2_Missense_Mutation_p.R764H|MYBPC1_uc010svq.1_Missense_Mutation_p.R726H|MYBPC1_uc001tih.2_Missense_Mutation_p.R764H|MYBPC1_uc001tij.2_Missense_Mutation_p.R739H|MYBPC1_uc010svr.1_Missense_Mutation_p.R739H|MYBPC1_uc010svs.1_Missense_Mutation_p.R739H|MYBPC1_uc010svt.1_Missense_Mutation_p.R727H|MYBPC1_uc010svu.1_Missense_Mutation_p.R720H|MYBPC1_uc001tik.2_Missense_Mutation_p.R713H|MYBPC1_uc001til.2_5'Flank|MYBPC1_uc001tim.2_5'Flank	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	739	Fibronectin type-III 2.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104139027	104139027	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104139027G>A	uc001tjw.2	+	57	6294	c.6108G>A	c.(6106-6108)TGG>TGA	p.W2036*	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	2036	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
HSP90B1	7184	broad.mit.edu	37	12	104333281	104333281	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104333281C>A	uc001tkb.1	+						HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Intron	NM_003299	NP_003290			heat shock protein 90kDa beta, member 1						actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)													---	---	---	---
USP30	84749	broad.mit.edu	37	12	109520678	109520678	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109520678C>T	uc010sxi.1	+	11	1083	c.979C>T	c.(979-981)CGG>TGG	p.R327W	USP30_uc001tnu.3_Missense_Mutation_p.R296W|USP30_uc001tnw.3_Missense_Mutation_p.R44W	NM_032663	NP_116052	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	327	Cytoplasmic (Potential).				ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1																		---	---	---	---
C12orf34	84915	broad.mit.edu	37	12	110205883	110205883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110205883C>T	uc001tpd.1	+	3	708	c.149C>T	c.(148-150)GCC>GTC	p.A50V	MGC14436_uc010sxs.1_Intron|MGC14436_uc001tpe.2_Intron|C12orf34_uc001tpf.1_Missense_Mutation_p.A50V	NM_032829	NP_116218	Q5U5X8	CL034_HUMAN	hypothetical protein LOC84915	50										ovary(1)	1																		---	---	---	---
TCHP	84260	broad.mit.edu	37	12	110352326	110352326	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110352326G>T	uc001tpn.2	+	11	1367	c.1214G>T	c.(1213-1215)AGG>ATG	p.R405M	TCHP_uc001tpo.1_RNA|TCHP_uc001tpp.2_Missense_Mutation_p.R405M	NM_001143852	NP_001137324	Q9BT92	TCHP_HUMAN	trichoplein	405	Trichohyalin/plectin homology domain.|Glu-rich.|Potential.|Interaction with keratin proteins.				apoptosis|negative regulation of cell growth	apical cortex|centrosome|keratin filament|mitochondrion|plasma membrane	protein binding			skin(1)	1																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111923522	111923522	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111923522C>T	uc001tsj.2	-	17	3094	c.2932G>A	c.(2932-2934)GTG>ATG	p.V978M	ATXN2_uc001tsh.2_Missense_Mutation_p.V713M|ATXN2_uc001tsi.2_Missense_Mutation_p.V689M|ATXN2_uc001tsk.2_RNA|ATXN2_uc001tsg.2_Missense_Mutation_p.V164M	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2	978	Pro-rich.				cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111924565	111924565	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111924565C>A	uc001tsj.2	-	16	2946	c.2784G>T	c.(2782-2784)CAG>CAT	p.Q928H	ATXN2_uc001tsh.2_Missense_Mutation_p.Q663H|ATXN2_uc001tsi.2_Missense_Mutation_p.Q639H|ATXN2_uc001tsk.2_RNA|ATXN2_uc001tsg.2_Missense_Mutation_p.Q114H	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2	928					cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112509731	112509731	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112509731C>T	uc001ttm.2	-	10	1024	c.1004G>A	c.(1003-1005)CGA>CAA	p.R335Q	NAA25_uc001ttn.3_RNA|NAA25_uc009zvz.1_Missense_Mutation_p.R307Q|NAA25_uc009zwa.1_Missense_Mutation_p.R335Q	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	335						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112610652	112610652	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112610652C>T	uc009zwc.2	-	60	10360	c.10342G>A	c.(10342-10344)GAT>AAT	p.D3448N		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115117422	115117422	+	Missense_Mutation	SNP	C	T	T	rs151047347		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115117422C>T	uc001tvt.1	-	4	1716	c.752G>A	c.(751-753)CGG>CAG	p.R251Q	TBX3_uc001tvu.1_Missense_Mutation_p.R231Q	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	251	T-box; second part.				anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding	p.R251Q(1)		ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)														---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120575470	120575470	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120575470C>T	uc001txo.2	-	49	6555	c.6542G>A	c.(6541-6543)CGC>CAC	p.R2181H		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	2181					regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
MLEC	9761	broad.mit.edu	37	12	121134168	121134168	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121134168A>G	uc001tyy.1	+	5	850	c.699A>G	c.(697-699)GAA>GAG	p.E233E		NM_014730	NP_055545	Q14165	MLEC_HUMAN	malectin precursor	233	Poly-Glu.|Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	carbohydrate binding			ovary(1)	1																		---	---	---	---
WDR66	144406	broad.mit.edu	37	12	122441592	122441592	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122441592C>T	uc009zxk.2	+	22	3514	c.3372C>T	c.(3370-3372)GAC>GAT	p.D1124D		NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	1124							calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)														---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123262123	123262123	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123262123A>T	uc001udc.2	+	2	267	c.122A>T	c.(121-123)GAT>GTT	p.D41V	CCDC62_uc010tah.1_RNA|CCDC62_uc001udf.2_Missense_Mutation_p.D41V|CCDC62_uc001ude.2_5'UTR	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b	41	Potential.					cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)														---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123285897	123285897	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123285897G>T	uc001udc.2	+	9	1349	c.1204G>T	c.(1204-1206)GAC>TAC	p.D402Y	CCDC62_uc010tah.1_RNA|CCDC62_uc001udf.2_Missense_Mutation_p.D402Y|CCDC62_uc001ude.2_Missense_Mutation_p.D163Y	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b	402						cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)														---	---	---	---
VPS37B	79720	broad.mit.edu	37	12	123351996	123351996	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123351996C>T	uc001udl.2	-	4	628	c.525G>A	c.(523-525)CCG>CCA	p.P175P		NM_024667	NP_078943	Q9H9H4	VP37B_HUMAN	vacuolar protein sorting 37B	175	Pro-rich.				cellular membrane organization|endosome transport|protein transport	late endosome membrane					0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.08e-05)|Epithelial(86;0.000197)|BRCA - Breast invasive adenocarcinoma(302;0.205)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124401250	124401250	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124401250G>A	uc001uft.3	+	62	10640	c.10615G>A	c.(10615-10617)GTG>ATG	p.V3539M		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3539	AAA 5 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
AACS	65985	broad.mit.edu	37	12	125561153	125561153	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125561153T>C	uc001uhc.2	+	3	560	c.354T>C	c.(352-354)ATT>ATC	p.I118I	AACS_uc009zyg.2_RNA|AACS_uc001uhd.2_Silent_p.I118I|AACS_uc009zyh.2_RNA	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	118					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)														---	---	---	---
PIWIL1	9271	broad.mit.edu	37	12	130827601	130827601	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130827601C>T	uc001uik.2	+	3	235	c.145C>T	c.(145-147)CGT>TGT	p.R49C	PIWIL1_uc001uij.1_Missense_Mutation_p.R49C	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	49					gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)														---	---	---	---
ULK1	8408	broad.mit.edu	37	12	132396511	132396511	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132396511C>T	uc001uje.2	+	13	1241	c.973C>T	c.(973-975)CAG>TAG	p.Q325*		NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1	325	Interaction with GABARAP and GABARAPL2.				autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)														---	---	---	---
ULK1	8408	broad.mit.edu	37	12	132399892	132399892	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132399892C>A	uc001uje.2	+	18	1803	c.1535C>A	c.(1534-1536)CCT>CAT	p.P512H		NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1	512					autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132512622	132512622	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132512622C>T	uc001ujn.2	+	26	5205	c.5170C>T	c.(5170-5172)CGC>TGC	p.R1724C	EP400_uc001ujl.2_Missense_Mutation_p.R1723C|EP400_uc001ujm.2_Missense_Mutation_p.R1643C	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1760					histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
POLE	5426	broad.mit.edu	37	12	133234004	133234004	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133234004C>A	uc001uks.1	-	28	3434	c.3390G>T	c.(3388-3390)TGG>TGT	p.W1130C	POLE_uc001ukr.1_5'UTR|POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Missense_Mutation_p.W1103C	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	1130					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20580605	20580605	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20580605T>C	uc001umr.2	+	7	1689	c.1391T>C	c.(1390-1392)ATG>ACG	p.M464T	ZMYM2_uc001umq.2_Missense_Mutation_p.M377T|ZMYM2_uc001ums.2_Missense_Mutation_p.M464T|ZMYM2_uc001umt.2_Missense_Mutation_p.M464T|ZMYM2_uc010tco.1_Intron	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	464	MYM-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21361745	21361745	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21361745T>C	uc001unq.3	-							NM_022459	NP_071904			exportin 4						protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
EFHA1	221154	broad.mit.edu	37	13	22095397	22095397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22095397C>T	uc001uof.2	-	6	606	c.584G>A	c.(583-585)AGG>AAG	p.R195K		NM_152726	NP_689939	Q8IYU8	EFHA1_HUMAN	EF-hand domain family, member A1	195	EF-hand 1.						calcium ion binding				0		all_cancers(29;1.24e-15)|all_epithelial(30;5.4e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000171)|Epithelial(112;0.000398)|OV - Ovarian serous cystadenocarcinoma(117;0.00641)|Lung(94;0.189)														---	---	---	---
MIPEP	4285	broad.mit.edu	37	13	24444222	24444222	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24444222C>T	uc001uox.3	-	6	816	c.716G>A	c.(715-717)CGT>CAT	p.R239H		NM_005932	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase precursor	239					protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
CENPJ	55835	broad.mit.edu	37	13	25482264	25482264	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25482264C>A	uc001upt.3	-	5	1119	c.866G>T	c.(865-867)GGA>GTA	p.G289V	CENPJ_uc010tdf.1_RNA|CENPJ_uc010aae.2_RNA|CENPJ_uc010aaf.2_RNA	NM_018451	NP_060921	Q9HC77	CENPJ_HUMAN	centromere protein J	289					cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)														---	---	---	---
RNF6	6049	broad.mit.edu	37	13	26792747	26792747	+	Intron	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26792747A>C	uc001uqo.2	-						RNF6_uc001uqn.1_Intron|RNF6_uc010aak.2_Intron|RNF6_uc001uqp.2_Intron|RNF6_uc001uqq.2_Intron|RNF6_uc010tdk.1_Intron	NM_183044	NP_898865			ring finger protein 6						negative regulation of axon extension|positive regulation of transcription, DNA-dependent|protein K27-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|regulation of androgen receptor signaling pathway|ubiquitin-dependent protein catabolic process	axon|cytoplasm|PML body	androgen receptor binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)														---	---	---	---
LNX2	222484	broad.mit.edu	37	13	28155587	28155587	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28155587G>A	uc001url.3	-	2	563	c.254C>T	c.(253-255)CCG>CTG	p.P85L	LNX2_uc001urm.1_Missense_Mutation_p.P85L	NM_153371	NP_699202	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	85	RING-type.						zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	6		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)														---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28589369	28589369	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28589369G>A	uc001urw.2	-	22	2760	c.2678C>T	c.(2677-2679)CCG>CTG	p.P893L	FLT3_uc010aao.2_RNA|FLT3_uc010tdn.1_Missense_Mutation_p.P852L	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor	893	Protein kinase.|Cytoplasmic (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity	p.G885fs*4(1)		haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28854577	28854577	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28854577C>T	uc001urz.2	+	15	1788	c.1780C>T	c.(1780-1782)CGA>TGA	p.R594*	PAN3_uc001ury.2_Nonsense_Mutation_p.R428*|PAN3_uc001urx.2_Nonsense_Mutation_p.R540*	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	740	Protein kinase.|Interaction with PAN2.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32836519	32836519	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32836519C>T	uc001utx.2	+	53	8182	c.7686C>T	c.(7684-7686)ACC>ACT	p.T2562T	FRY_uc010tdw.1_RNA|FRY_uc001uty.2_Silent_p.T117T|FRY_uc001utz.2_Silent_p.T87T|FRY_uc010tdx.1_5'Flank	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	2562					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32914163	32914163	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32914163G>T	uc001uub.1	+	11	5898	c.5671G>T	c.(5671-5673)GCA>TCA	p.A1891S		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	1891					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
SPG20	23111	broad.mit.edu	37	13	36903638	36903638	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36903638G>T	uc001uvn.2	-	5	1295	c.1025C>A	c.(1024-1026)GCA>GAA	p.A342E	SPG20_uc010ten.1_Missense_Mutation_p.A342E|SPG20_uc001uvm.2_Missense_Mutation_p.A342E|SPG20_uc001uvo.2_Missense_Mutation_p.A342E|SPG20_uc001uvq.2_Missense_Mutation_p.A342E|SPG20_uc001uvp.2_Missense_Mutation_p.A342E	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	342					cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)														---	---	---	---
AKAP11	11215	broad.mit.edu	37	13	42872697	42872697	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42872697T>C	uc001uys.1	+	7	555	c.380T>C	c.(379-381)ATG>ACG	p.M127T		NM_016248	NP_057332	Q9UKA4	AKA11_HUMAN	A-kinase anchor protein 11	127					intracellular protein kinase cascade	microtubule organizing center	protein kinase A binding|protein phosphatase 1 binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43872566	43872566	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43872566T>C	uc001uza.3	-	12	1662	c.1362A>G	c.(1360-1362)AAA>AAG	p.K454K	ENOX1_uc001uzb.3_Silent_p.K454K|ENOX1_uc001uzc.3_Silent_p.K454K|ENOX1_uc001uyz.3_Silent_p.K63K	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	454	Potential.				electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
SPERT	220082	broad.mit.edu	37	13	46287859	46287859	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46287859C>T	uc001van.1	+	3	779	c.699C>T	c.(697-699)CAC>CAT	p.H233H	SPERT_uc001vao.2_Silent_p.H197H	NM_152719	NP_689932	Q8NA61	SPERT_HUMAN	spermatid associated	233						cytoplasmic membrane-bounded vesicle				central_nervous_system(1)|pancreas(1)	2		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)														---	---	---	---
SIAH3	283514	broad.mit.edu	37	13	46358134	46358134	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46358134G>T	uc001vap.2	-	2	276	c.194C>A	c.(193-195)CCT>CAT	p.P65H		NM_198849	NP_942146	Q8IW03	SIAH3_HUMAN	seven in absentia homolog 3	65	SIAH-type; degenerate.|His-rich.				multicellular organismal development|ubiquitin-dependent protein catabolic process	nucleus	metal ion binding			ovary(1)|skin(1)	2																		---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46701731	46701731	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46701731C>T	uc001vaz.3	-	16	2005	c.1879G>A	c.(1879-1881)GTG>ATG	p.V627M	LCP1_uc010ack.2_Missense_Mutation_p.V196M|LCP1_uc001vay.3_Missense_Mutation_p.V224M|LCP1_uc001vba.3_Missense_Mutation_p.V627M	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin	627					regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58207510	58207510	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58207510A>G	uc001vhq.1	+	1	1722	c.830A>G	c.(829-831)GAA>GGA	p.E277G	PCDH17_uc010aec.1_Missense_Mutation_p.E277G	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	277	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61102778	61102778	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61102778G>A	uc001via.2	+	11	1928	c.1140G>A	c.(1138-1140)CCG>CCA	p.P380P	TDRD3_uc010aef.2_Silent_p.P205P|TDRD3_uc001vhz.3_Silent_p.P380P|TDRD3_uc010aeg.2_Silent_p.P473P|TDRD3_uc001vib.3_Silent_p.P379P	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2	380					chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67801018	67801018	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67801018G>A	uc001vik.2	-	2	2247	c.1555C>T	c.(1555-1557)CGA>TGA	p.R519*	PCDH9_uc001vil.2_Nonsense_Mutation_p.R519*|PCDH9_uc010thl.1_Nonsense_Mutation_p.R519*|PCDH9_uc001vin.3_Nonsense_Mutation_p.R519*	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	519	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
RNF219	79596	broad.mit.edu	37	13	79190223	79190223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79190223C>T	uc001vkw.1	-	6	1732	c.1673G>A	c.(1672-1674)GGT>GAT	p.G558D	uc001vku.1_RNA|RNF219_uc010afb.1_Missense_Mutation_p.G368D|RNF219_uc010afc.2_Intron	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219	558	Ser-rich.						zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)														---	---	---	---
SLITRK6	84189	broad.mit.edu	37	13	86368556	86368556	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86368556A>G	uc001vll.1	-	2	2547	c.2088T>C	c.(2086-2088)GGT>GGC	p.G696G	SLITRK6_uc010afe.1_Silent_p.G149G	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6 precursor	696	Cytoplasmic (Potential).					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)														---	---	---	---
DZIP1	22873	broad.mit.edu	37	13	96239926	96239926	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96239926G>A	uc001vmk.2	-	20	2937	c.2085C>T	c.(2083-2085)TAC>TAT	p.Y695Y	DZIP1_uc001vmi.2_Translation_Start_Site|DZIP1_uc001vmj.2_Silent_p.Y171Y|DZIP1_uc001vml.2_Silent_p.Y676Y	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	695					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)															---	---	---	---
STK24	8428	broad.mit.edu	37	13	99171609	99171609	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99171609A>G	uc001vnm.1	-	2	432	c.197T>C	c.(196-198)ATC>ACC	p.I66T	STK24_uc001vnn.1_Missense_Mutation_p.I54T|STK24_uc010tim.1_Missense_Mutation_p.I54T	NM_003576	NP_003567	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24 isoform a	66	Protein kinase.				cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	100037585	100037585	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100037585A>G	uc001voa.3	+	9	1515	c.1031A>G	c.(1030-1032)CAC>CGC	p.H344R	UBAC2_uc010tiu.1_Missense_Mutation_p.H366R|UBAC2_uc001vob.3_Missense_Mutation_p.H317R|UBAC2_uc010tiv.1_RNA|UBAC2_uc001vod.2_Missense_Mutation_p.H231R|UBAC2_uc001voc.2_Missense_Mutation_p.H309R|UBAC2_uc010tiw.1_RNA|UBAC2_uc001voh.2_Missense_Mutation_p.H148R	NM_001144072	NP_001137544	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2 isoform 1	344	UBA.|Cytoplasmic (Potential).					integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101733910	101733910	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101733910C>T	uc001vox.1	-	34	4042	c.3853G>A	c.(3853-3855)GTT>ATT	p.V1285I		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1285	Helical; Name=S3 of repeat IV; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101833582	101833582	+	Intron	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101833582A>C	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Missense_Mutation_p.L624R|NALCN_uc001vpa.2_Missense_Mutation_p.L624R	NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110828999	110828999	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110828999C>A	uc001vqw.3	-	35	3064	c.2942G>T	c.(2941-2943)GGG>GTG	p.G981V	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	981	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111155588	111155588	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111155588C>A	uc001vqx.2	+	42	4287	c.3998C>A	c.(3997-3999)CCC>CAC	p.P1333H		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	1333	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111870098	111870098	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111870098G>A	uc001vrs.2	+	6	854	c.604G>A	c.(604-606)GAG>AAG	p.E202K	ARHGEF7_uc001vrr.2_Missense_Mutation_p.E181K|ARHGEF7_uc001vrt.2_Missense_Mutation_p.E152K|ARHGEF7_uc010tjn.1_RNA|ARHGEF7_uc001vru.1_Missense_Mutation_p.E24K|ARHGEF7_uc001vrv.3_Missense_Mutation_p.E24K|ARHGEF7_uc001vrw.3_Missense_Mutation_p.E24K|ARHGEF7_uc001vrx.3_Missense_Mutation_p.E24K|ARHGEF7_uc010tjo.1_Missense_Mutation_p.E99K	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	202	SH3.				apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113728869	113728869	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113728869A>C	uc001vsu.2	+	10	1301	c.1279A>C	c.(1279-1281)AAA>CAA	p.K427Q	MCF2L_uc001vsq.2_Missense_Mutation_p.K427Q|MCF2L_uc010tjr.1_Missense_Mutation_p.K370Q|MCF2L_uc001vsr.2_Missense_Mutation_p.K374Q|MCF2L_uc001vss.3_Missense_Mutation_p.K368Q|MCF2L_uc010tjs.1_Missense_Mutation_p.K368Q|MCF2L_uc001vst.1_Missense_Mutation_p.K332Q	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming	400	Spectrin.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
FAM70B	348013	broad.mit.edu	37	13	114514832	114514832	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114514832A>G	uc001vuh.2	+	9	964	c.937A>G	c.(937-939)ACC>GCC	p.T313A		NM_182614	NP_872420	Q8WV15	FA70B_HUMAN	family with sequence similarity 70, member B	313	Pro-rich.					integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)	all cancers(43;0.181)															---	---	---	---
OR4K1	79544	broad.mit.edu	37	14	20404371	20404371	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20404371C>A	uc001vwj.1	+	1	546	c.546C>A	c.(544-546)CCC>CCA	p.P182P		NM_001004063	NP_001004063	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)														---	---	---	---
OR4K17	390436	broad.mit.edu	37	14	20585703	20585703	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20585703G>T	uc001vwo.1	+	1	138	c.138G>T	c.(136-138)CTG>CTT	p.L46L		NM_001004715	NP_001004715	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20841549	20841549	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20841549G>T	uc001vxe.2	-	47	6734	c.6694C>A	c.(6694-6696)CAC>AAC	p.H2232N	TEP1_uc010ahj.1_5'Flank|TEP1_uc010ahk.2_Missense_Mutation_p.H1575N|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Missense_Mutation_p.H2124N|TEP1_uc010tlh.1_Missense_Mutation_p.H570N	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2232	WD 14.				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
METT11D1	64745	broad.mit.edu	37	14	21464427	21464427	+	Silent	SNP	G	A	A	rs138028455		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21464427G>A	uc001vyn.2	+	12	1253	c.1056G>A	c.(1054-1056)GCG>GCA	p.A352A	METT11D1_uc001vym.2_Silent_p.A352A|METT11D1_uc001vyo.2_Silent_p.A352A|METT11D1_uc001vyp.2_Silent_p.A194A|METT11D1_uc001vyq.2_Silent_p.A194A|SLC39A2_uc001vyr.2_5'Flank|SLC39A2_uc001vys.2_5'Flank	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform	352					translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
METT11D1	64745	broad.mit.edu	37	14	21464433	21464433	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21464433T>A	uc001vyn.2	+	12	1259	c.1062T>A	c.(1060-1062)CAT>CAA	p.H354Q	METT11D1_uc001vym.2_Missense_Mutation_p.H354Q|METT11D1_uc001vyo.2_Missense_Mutation_p.H354Q|METT11D1_uc001vyp.2_Missense_Mutation_p.H196Q|METT11D1_uc001vyq.2_Missense_Mutation_p.H196Q|SLC39A2_uc001vyr.2_5'Flank|SLC39A2_uc001vys.2_5'Flank	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform	354					translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
CHD8	57680	broad.mit.edu	37	14	21868149	21868149	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21868149G>A	uc001was.1	-	25	4065	c.3971C>T	c.(3970-3972)GCG>GTG	p.A1324V	CHD8_uc001war.1_Missense_Mutation_p.A1220V|SNORD8_uc001wau.1_5'Flank	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1603					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22409639	22409639	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22409639G>A	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010ajb.1_RNA|uc001wck.2_Silent_p.T43T					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22600777	22600777	+	Intron	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22600777A>C	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc010tmq.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23853673	23853673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23853673C>T	uc001wjv.2	-	36	5610	c.5543G>A	c.(5542-5544)CGC>CAC	p.R1848H		NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	1848	Potential.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23869921	23869921	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23869921G>A	uc001wjv.2	-	13	1474	c.1407C>T	c.(1405-1407)TTC>TTT	p.F469F	MYH6_uc010akp.1_Silent_p.F469F	NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	469	Myosin head-like.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24529366	24529366	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24529366A>G	uc001wlj.2	+	24	2120	c.1963A>G	c.(1963-1965)ATC>GTC	p.I655V	LRRC16B_uc001wlk.2_5'Flank	NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	655										ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24532375	24532375	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24532375C>T	uc001wlj.2	+	30	2910	c.2753C>T	c.(2752-2754)CCG>CTG	p.P918L	LRRC16B_uc001wlk.2_Missense_Mutation_p.P14L	NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	918										ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
PSME2	5721	broad.mit.edu	37	14	24614302	24614302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24614302G>A	uc001wmj.2	-	6	390	c.325C>T	c.(325-327)CCA>TCA	p.P109S	PSME2_uc001wmk.2_Missense_Mutation_p.P32S|RNF31_uc001wml.1_5'Flank|RNF31_uc001wmm.1_5'Flank|RNF31_uc001wmn.1_5'Flank|RNF31_uc010alg.1_5'Flank	NM_002818	NP_002809	Q9UL46	PSME2_HUMAN	proteasome activator subunit 2	109					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome activator complex					0				GBM - Glioblastoma multiforme(265;0.00839)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24731311	24731311	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24731311C>T	uc001wod.2	-	2	372	c.248G>A	c.(247-249)CGG>CAG	p.R83Q	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	83	Membrane anchorage region.				cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)													---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	26949260	26949260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26949260G>A	uc001wpy.2	-	3	688	c.370C>T	c.(370-372)CCC>TCC	p.P124S	NOVA1_uc001wpz.2_Missense_Mutation_p.P124S|NOVA1_uc001wqa.2_Missense_Mutation_p.P2S|NOVA1_uc001wqb.2_Missense_Mutation_p.P124S	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1	127					locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31792947	31792947	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31792947G>A	uc001wrf.3	-	18	2809	c.2732C>T	c.(2731-2733)GCC>GTC	p.A911V	HEATR5A_uc010ami.2_Missense_Mutation_p.A809V|HEATR5A_uc001wrg.1_Missense_Mutation_p.A793V	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1198							binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35078948	35078948	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35078948G>A	uc001wsf.1	-	3	99	c.91C>T	c.(91-93)CTT>TTT	p.L31F	SNX6_uc001wse.1_5'UTR|SNX6_uc010tpm.1_5'UTR|SNX6_uc010amm.1_5'UTR	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b	19					cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)														---	---	---	---
INSM2	84684	broad.mit.edu	37	14	36004830	36004830	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36004830C>T	uc001wth.1	+	1	1583	c.1372C>T	c.(1372-1374)CCG>TCG	p.P458S		NM_032594	NP_115983	Q96T92	INSM2_HUMAN	insulinoma-associated protein IA-6	458					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)|skin(1)	2	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)														---	---	---	---
C14orf106	55320	broad.mit.edu	37	14	45679579	45679579	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45679579T>C	uc001wwf.2	-							NM_018353	NP_060823			chromosome 14 open reading frame 106						cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0																		---	---	---	---
RPL10L	140801	broad.mit.edu	37	14	47120933	47120933	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47120933G>A	uc001wwg.2	-	1	96	c.7C>T	c.(7-9)CGC>TGC	p.R3C		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	3					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
POLE2	5427	broad.mit.edu	37	14	50120913	50120913	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50120913G>A	uc001wwu.2	-	14	1107	c.1093C>T	c.(1093-1095)CCT>TCT	p.P365S	SDCCAG1_uc010anj.1_Intron|POLE2_uc010ann.2_Missense_Mutation_p.P79S|POLE2_uc001wwv.2_RNA|POLE2_uc010ano.2_Missense_Mutation_p.P80S	NM_002692	NP_002683	P56282	DPOE2_HUMAN	DNA-directed DNA polymerase epsilon 2	365					DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity			ovary(1)|skin(1)	2	all_epithelial(31;0.0021)|Breast(41;0.0124)																	---	---	---	---
C14orf138	79609	broad.mit.edu	37	14	50582612	50582612	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50582612C>T	uc001wxo.1	-	3	422	c.395G>A	c.(394-396)GGC>GAC	p.G132D	C14orf138_uc001wxn.1_RNA|C14orf138_uc001wxp.1_Missense_Mutation_p.G132D|C14orf138_uc001wxq.1_RNA	NM_024558	NP_078834	Q9H867	MT21D_HUMAN	hypothetical protein LOC79609 isoform a	132							methyltransferase activity				0	all_epithelial(31;0.000822)|Breast(41;0.0065)																	---	---	---	---
CDKL1	8814	broad.mit.edu	37	14	50805675	50805675	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50805675G>T	uc010anu.1	-	19	2744	c.2744C>A	c.(2743-2745)CCT>CAT	p.P915H	CDKL1_uc001wxz.2_Missense_Mutation_p.P244H	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	243	Protein kinase.					cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)																	---	---	---	---
PYGL	5836	broad.mit.edu	37	14	51383683	51383683	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51383683A>T	uc001wyu.2	-	8	1123	c.996T>A	c.(994-996)GAT>GAA	p.D332E	PYGL_uc010tqq.1_Missense_Mutation_p.D298E|PYGL_uc001wyv.2_Missense_Mutation_p.I5N|PYGL_uc010anz.1_Missense_Mutation_p.D135E	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	332					glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding			skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)													---	---	---	---
ARID4A	5926	broad.mit.edu	37	14	58814561	58814561	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58814561A>C	uc001xdp.2	+	15	1623	c.1369A>C	c.(1369-1371)AGT>CGT	p.S457R	ARID4A_uc001xdo.2_Missense_Mutation_p.S457R|ARID4A_uc001xdq.2_Missense_Mutation_p.S457R|ARID4A_uc010apg.1_Missense_Mutation_p.S135R	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	457					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64669642	64669642	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64669642C>T	uc001xgm.2	+	100	18392	c.18162C>T	c.(18160-18162)TGC>TGT	p.C6054C	SYNE2_uc001xgl.2_Silent_p.C6054C|SYNE2_uc010apy.2_Silent_p.C2439C|SYNE2_uc001xgn.2_Silent_p.C1016C|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Silent_p.C24C|SYNE2_uc001xgq.2_Silent_p.C419C	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6054	Cytoplasmic (Potential).|Spectrin 6.				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
ESR2	2100	broad.mit.edu	37	14	64701832	64701832	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64701832T>C	uc001xha.1	-	8	1730	c.1262A>G	c.(1261-1263)GAC>GGC	p.D421G	ESR2_uc001xgu.2_Missense_Mutation_p.D421G|ESR2_uc001xgv.2_Missense_Mutation_p.D421G|ESR2_uc001xgw.2_RNA|ESR2_uc001xgx.2_Missense_Mutation_p.D421G|ESR2_uc001xgy.1_Missense_Mutation_p.D421G|ESR2_uc001xgz.1_Missense_Mutation_p.D421G|ESR2_uc010aqb.1_RNA|ESR2_uc010aqc.1_Missense_Mutation_p.D330G|ESR2_uc010aqd.1_RNA	NM_001437	NP_001428	Q92731	ESR2_HUMAN	estrogen receptor beta isoform 1	421	Steroid-binding.				cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)													---	---	---	---
ZBTB25	7597	broad.mit.edu	37	14	64954639	64954639	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64954639C>T	uc001xhf.2	-	3	493	c.310G>A	c.(310-312)GCC>ACC	p.A104T	ZBTB25_uc001xhc.2_Intron|ZBTB25_uc001xhg.2_Missense_Mutation_p.A104T	NM_006977	NP_008908	P24278	ZBT25_HUMAN	zinc finger protein 46	104	BTB.					cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2				all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)														---	---	---	---
SFRS5	6430	broad.mit.edu	37	14	70237238	70237238	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70237238C>T	uc001xll.2	+	7	1872	c.421C>T	c.(421-423)CGA>TGA	p.R141*	SFRS5_uc001xlm.2_RNA|SFRS5_uc001xln.1_3'UTR|SFRS5_uc001xlo.2_Nonsense_Mutation_p.R141*|SFRS5_uc001xlp.2_Nonsense_Mutation_p.R141*|SFRS5_uc001xlq.2_Nonsense_Mutation_p.R138*	NM_006925	NP_008856	Q13243	SRSF5_HUMAN	splicing factor, arginine/serine-rich 5	141	RRM 2.				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding				0				all cancers(60;0.00144)|BRCA - Breast invasive adenocarcinoma(234;0.0132)|OV - Ovarian serous cystadenocarcinoma(108;0.0154)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75277033	75277033	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75277033G>A	uc001xqj.3	+	9	5262	c.5138G>A	c.(5137-5139)CGT>CAT	p.R1713H	YLPM1_uc001xql.3_RNA|YLPM1_uc001xqm.1_Missense_Mutation_p.R196H	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	1518	Arg-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
PROX2	283571	broad.mit.edu	37	14	75330257	75330257	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75330257C>T	uc001xqr.1	-	1	281	c.281G>A	c.(280-282)CGC>CAC	p.R94H	PROX2_uc001xqq.1_Missense_Mutation_p.R20H	NM_001080408	NP_001073877	Q3B8N5	PROX2_HUMAN	prospero homeobox 2	94					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)														---	---	---	---
PGF	5228	broad.mit.edu	37	14	75416195	75416195	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75416195G>A	uc010ase.1	-	3	526	c.180C>T	c.(178-180)GAC>GAT	p.D60D	PGF_uc001xqz.2_Silent_p.D60D|PGF_uc001xra.2_Silent_p.D59D|PGF_uc001xrb.2_Silent_p.D60D|PGF_uc010asf.1_Missense_Mutation_p.T46M	NM_002632	NP_002623	P49763	PLGF_HUMAN	placental growth factor, vascular endothelial	60					angiogenesis|cell differentiation|cell-cell signaling|positive regulation of cell division|positive regulation of cell proliferation|vascular endothelial growth factor receptor signaling pathway	extracellular region|membrane	growth factor activity|heparin binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00668)														---	---	---	---
MLH3	27030	broad.mit.edu	37	14	75515975	75515975	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75515975T>C	uc001xrd.1	-	2	600	c.384A>G	c.(382-384)AAA>AAG	p.K128K	MLH3_uc001xre.1_Silent_p.K128K|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	128					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)									MMR					---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	78063607	78063607	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78063607G>T	uc001xub.2	-	2	437	c.249C>A	c.(247-249)CTC>CTA	p.L83L		NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base	83	Helical; (Potential).					integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79432612	79432612	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79432612C>T	uc001xun.2	+	9	2012	c.1521C>T	c.(1519-1521)AGC>AGT	p.S507S	NRXN3_uc001xum.1_RNA|NRXN3_uc010asv.1_Silent_p.S632S	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	880	Extracellular (Potential).|Laminin G-like 5.				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
KCNK10	54207	broad.mit.edu	37	14	88658729	88658729	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88658729A>T	uc001xwo.2	-	5	1149	c.692T>A	c.(691-693)ATC>AAC	p.I231N	KCNK10_uc001xwm.2_Missense_Mutation_p.I236N|KCNK10_uc001xwn.2_Missense_Mutation_p.I236N	NM_021161	NP_066984	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	231	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(2)|pancreas(1)	5																		---	---	---	---
IFI27	3429	broad.mit.edu	37	14	94582214	94582214	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94582214C>T	uc010tws.1	+	4	397	c.276C>T	c.(274-276)CGC>CGT	p.R92R	IFI27_uc001ycn.1_RNA|IFI27_uc001yco.2_Missense_Mutation_p.A73V	NM_005532	NP_005523	P40305	IFI27_HUMAN	interferon, alpha-inducible protein 27 isoform	Error:Variant_position_missing_in_P40305_after_alignment					activation of caspase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|type I interferon-mediated signaling pathway	integral to membrane|mitochondrion					0				Epithelial(152;0.112)|all cancers(159;0.187)|COAD - Colon adenocarcinoma(157;0.206)														---	---	---	---
SERPINA6	866	broad.mit.edu	37	14	94780394	94780394	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94780394C>A	uc001ycv.2	-	2	696	c.592G>T	c.(592-594)GTC>TTC	p.V198F	SERPINA6_uc010auv.2_RNA	NM_001756	NP_001747	P08185	CBG_HUMAN	corticosteroid binding globulin precursor	198					regulation of proteolysis|transport	extracellular space	serine-type endopeptidase inhibitor activity|steroid binding			skin(3)|ovary(1)|central_nervous_system(1)	5		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)													---	---	---	---
TRAF3	7187	broad.mit.edu	37	14	103336736	103336736	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103336736C>A	uc001ymc.1	+	3	551	c.198C>A	c.(196-198)ACC>ACA	p.T66T	TRAF3_uc001yme.1_Silent_p.T66T|TRAF3_uc001ymd.1_Silent_p.T66T|TRAF3_uc010txy.1_Silent_p.T66T	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1	66					apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)														---	---	---	---
PPP1R13B	23368	broad.mit.edu	37	14	104208439	104208439	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104208439G>A	uc001yof.1	-	11	1793	c.1510C>T	c.(1510-1512)CCC>TCC	p.P504S	PPP1R13B_uc010awv.1_RNA|PPP1R13B_uc001yog.1_Missense_Mutation_p.P371S	NM_015316	NP_056131	Q96KQ4	ASPP1_HUMAN	apoptosis-stimulating protein of p53, 1	504	Pro-rich.				apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)																---	---	---	---
MTA1	9112	broad.mit.edu	37	14	105936469	105936469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105936469G>A	uc001yqx.2	+	21	2252	c.2065G>A	c.(2065-2067)GCC>ACC	p.A689T	MTA1_uc001yqy.2_RNA|MTA1_uc001yrb.2_Missense_Mutation_p.A454T|CRIP2_uc010tyr.1_5'Flank|CRIP2_uc001yrc.2_5'Flank	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein	689					signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106068029	106068029	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106068029G>A	uc010tyt.1	-	3649		c.62628C>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Missense_Mutation_p.R27C|uc001yrx.1_5'UTR|uc001yrv.1_5'Flank|uc001yru.2_5'Flank|uc010axq.1_5'Flank					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106306991	106306991	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106306991G>A	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Silent_p.L294L|uc001ysk.1_Silent_p.L294L|uc001ysl.1_Silent_p.L294L|uc001ysm.1_Silent_p.L237L|uc001ysn.1_Silent_p.L237L|uc001yso.1_Silent_p.L237L					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
MAGEL2	54551	broad.mit.edu	37	15	23889416	23889416	+	Silent	SNP	G	A	A	rs112299217	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23889416G>A	uc001ywj.3	-	1	1760	c.1665C>T	c.(1663-1665)ACC>ACT	p.T555T		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)														---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28260085	28260085	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28260085G>A	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				---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28369299	28369299	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28369299C>T	uc001zbj.2	-	85	13178	c.13072G>A	c.(13072-13074)GAG>AAG	p.E4358K		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	4358					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28519467	28519467	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28519467G>A	uc001zbj.2	-	7	876	c.770C>T	c.(769-771)GCG>GTG	p.A257V	HERC2_uc001zbl.1_5'UTR	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	257					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30020191	30020191	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30020191G>A	uc001zcr.2	-	16	2525	c.2050C>T	c.(2050-2052)CGT>TGT	p.R684C	TJP1_uc010azl.2_Missense_Mutation_p.R672C|TJP1_uc001zcq.2_Missense_Mutation_p.R688C|TJP1_uc001zcs.2_Missense_Mutation_p.R684C	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a	684	Guanylate kinase-like.				cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31334373	31334373	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31334373T>A	uc001zfm.2	-	16	1930	c.1802A>T	c.(1801-1803)GAC>GTC	p.D601V	TRPM1_uc010azy.2_Missense_Mutation_p.D508V|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	601	Cytoplasmic (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
CHRM5	1133	broad.mit.edu	37	15	34356497	34356497	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34356497G>A	uc001zhk.1	+	3	2249	c.1579G>A	c.(1579-1581)GGG>AGG	p.G527R	CHRM5_uc001zhl.1_Missense_Mutation_p.G527R	NM_012125	NP_036257	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	527	Cytoplasmic (By similarity).				cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)													---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34546658	34546658	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34546658C>T	uc001zhw.2	-	8	1173	c.1009G>A	c.(1009-1011)GTA>ATA	p.V337I	SLC12A6_uc001zhv.2_Missense_Mutation_p.V286I|SLC12A6_uc001zhx.2_Missense_Mutation_p.V322I|SLC12A6_uc001zhy.2_RNA|SLC12A6_uc001zhz.2_RNA|SLC12A6_uc001zia.2_Missense_Mutation_p.V278I|SLC12A6_uc001zib.2_Missense_Mutation_p.V328I|SLC12A6_uc001zic.2_Missense_Mutation_p.V337I|SLC12A6_uc010bau.2_Missense_Mutation_p.V337I|SLC12A6_uc001zid.2_Missense_Mutation_p.V278I|SLC12A6_uc001zhu.2_Missense_Mutation_p.V149I	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN	solute carrier family 12, member 6 isoform a	337	Helical; (Potential).				angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)													---	---	---	---
LPCAT4	254531	broad.mit.edu	37	15	34657357	34657357	+	Silent	SNP	G	A	A	rs148649438		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34657357G>A	uc001zig.2	-	3	424	c.330C>T	c.(328-330)CGC>CGT	p.R110R	LPCAT4_uc010bav.1_Silent_p.R110R	NM_153613	NP_705841	Q643R3	LPCT4_HUMAN	lysophosphatidylcholine acyltransferase 4	110					phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|calcium ion binding				0																		---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40093859	40093859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40093859C>T	uc001zkj.1	-	3	1888	c.1022G>A	c.(1021-1023)CGG>CAG	p.R341Q	GPR176_uc010uck.1_Missense_Mutation_p.R281Q	NM_007223	NP_009154	Q14439	GP176_HUMAN	G protein-coupled receptor 176	341	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)														---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40303476	40303476	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40303476C>T	uc001zkm.1	+						EIF2AK4_uc010bbj.1_Intron|EIF2AK4_uc001zkn.1_Intron|EIF2AK4_uc001zko.1_Intron|EIF2AK4_uc010bbk.1_Intron	NM_001013703	NP_001013725			eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)														---	---	---	---
IVD	3712	broad.mit.edu	37	15	40703542	40703542	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40703542G>A	uc001zls.3	+	5	883	c.549G>A	c.(547-549)GCG>GCA	p.A183A	IVD_uc001zlq.2_Silent_p.A153A	NM_002225	NP_002216	P26440	IVD_HUMAN	isovaleryl Coenzyme A dehydrogenase isoform 1	180					leucine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|isovaleryl-CoA dehydrogenase activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)														---	---	---	---
BAHD1	22893	broad.mit.edu	37	15	40754430	40754430	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40754430T>C	uc001zlu.2	+	3	1823	c.1752T>C	c.(1750-1752)CGT>CGC	p.R584R	BAHD1_uc001zlt.2_Silent_p.R583R|BAHD1_uc010bbp.1_Silent_p.R583R|BAHD1_uc001zlv.2_Silent_p.R584R	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	584	Arg-rich.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)														---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40914106	40914106	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40914106G>A	uc010bbs.1	+	11	1883	c.1722G>A	c.(1720-1722)CAG>CAA	p.Q574Q	CASC5_uc010ucq.1_Silent_p.Q398Q|CASC5_uc001zme.2_Silent_p.Q548Q|CASC5_uc010bbt.1_Silent_p.Q548Q	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	574	Interaction with BUB1 and BUB1B.				acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)														---	---	---	---
INO80	54617	broad.mit.edu	37	15	41372056	41372056	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41372056G>A	uc001zni.2	-	9	1187	c.974C>T	c.(973-975)GCC>GTC	p.A325V	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	325	Assembles INO80 complex module consisting of conserved components ACTR8, ACTL6A and YY1.|DBINO.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42127266	42127266	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42127266G>A	uc001zoo.3	+	3	357	c.317G>A	c.(316-318)CGC>CAC	p.R106H	JMJD7-PLA2G4B_uc001zom.2_Missense_Mutation_p.R6H|JMJD7-PLA2G4B_uc001zon.2_Missense_Mutation_p.R106H|JMJD7-PLA2G4B_uc010bcn.2_Missense_Mutation_p.R106H|JMJD7-PLA2G4B_uc001zop.1_Missense_Mutation_p.R6H|JMJD7-PLA2G4B_uc001zoq.3_5'Flank	NM_005090	NP_005081	P0C869	PA24B_HUMAN	JMJD7-PLA2G4B protein	Error:Variant_position_missing_in_P0C869_after_alignment					arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1																		---	---	---	---
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42136794	42136794	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42136794G>A	uc010bco.2	+	12	1106	c.1005G>A	c.(1003-1005)TCG>TCA	p.S335S	JMJD7-PLA2G4B_uc001zoo.3_Silent_p.S566S|JMJD7-PLA2G4B_uc010bcn.2_Silent_p.S566S|JMJD7-PLA2G4B_uc001zoq.3_Silent_p.S36S|JMJD7-PLA2G4B_uc001zor.1_Silent_p.S36S	NM_001114633	NP_001108105	P0C869	PA24B_HUMAN	phospholipase A2, group IVB	335	PLA2c.	Nucleophile (By similarity).		S->A: Abolishes enzyme activity.	arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1																		---	---	---	---
SPTBN5	51332	broad.mit.edu	37	15	42169448	42169448	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42169448G>T	uc001zos.2	-	18	3805	c.3472C>A	c.(3472-3474)CTG>ATG	p.L1158M		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1193	Spectrin 8.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)														---	---	---	---
GANC	2595	broad.mit.edu	37	15	42589866	42589866	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42589866T>C	uc001zpi.2	+						GANC_uc001zph.2_Intron|GANC_uc001zpj.1_Intron	NM_198141	NP_937784			glucosidase, alpha; neutral C						carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42720248	42720248	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42720248C>T	uc001zpw.2	-	12	5232	c.4897G>A	c.(4897-4899)GCA>ACA	p.A1633T	ZFP106_uc001zpu.2_Missense_Mutation_p.A731T|ZFP106_uc001zpv.2_Missense_Mutation_p.A818T|ZFP106_uc001zpx.2_Missense_Mutation_p.A861T	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	1633						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
MAP1A	4130	broad.mit.edu	37	15	43821959	43821959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43821959G>A	uc001zrt.2	+	5	8614	c.8147G>A	c.(8146-8148)CGT>CAT	p.R2716H		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2716						cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(3)|breast(3)|pancreas(2)|skin(1)	9		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)													---	---	---	---
MFAP1	4236	broad.mit.edu	37	15	44105457	44105457	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44105457T>C	uc001zth.1	-	5	900	c.716A>G	c.(715-717)TAC>TGC	p.Y239C		NM_005926	NP_005917	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	239						microfibril				skin(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)														---	---	---	---
WDR76	79968	broad.mit.edu	37	15	44143401	44143401	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44143401C>T	uc001zti.1	+	9	1172	c.1149C>T	c.(1147-1149)GGC>GGT	p.G383G		NM_024908	NP_079184	Q9H967	WDR76_HUMAN	WD repeat domain 76	383	WD 2.										0		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44951513	44951513	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44951513A>G	uc001ztx.2	-						SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Intron|SPG11_uc001zua.1_Intron	NM_025137	NP_079413			spatacsin isoform 1						cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56390302	56390302	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56390302C>T	uc010bfn.2	-	8	1084	c.1084G>A	c.(1084-1086)GCA>ACA	p.A362T	RFX7_uc010ugk.1_RNA|RFX7_uc002adn.1_Missense_Mutation_p.A176T	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	265					regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56390410	56390410	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56390410C>A	uc010bfn.2	-	8	976	c.976G>T	c.(976-978)GGA>TGA	p.G326*	RFX7_uc010ugk.1_RNA|RFX7_uc002adn.1_Nonsense_Mutation_p.G140*	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	229					regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
FAM63B	54629	broad.mit.edu	37	15	59102595	59102595	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59102595G>A	uc002afj.2	+						FAM63B_uc002afi.2_Intron|FAM63B_uc002afk.2_Intron|FAM63B_uc002afl.2_Intron	NM_001040450	NP_001035540			hypothetical protein LOC54629 isoform a											central_nervous_system(1)	1																		---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59175946	59175946	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59175946G>A	uc002afp.2	-	20	2963	c.2875C>T	c.(2875-2877)CGG>TGG	p.R959W	SLTM_uc002afn.2_Missense_Mutation_p.R501W|SLTM_uc002afo.2_Missense_Mutation_p.R941W|SLTM_uc002afq.2_Missense_Mutation_p.R528W|SLTM_uc010bgd.2_Missense_Mutation_p.R528W	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	959					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59182558	59182558	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59182558T>C	uc002afp.2	-	15	2089	c.2001A>G	c.(1999-2001)CTA>CTG	p.L667L	SLTM_uc002afn.2_Silent_p.L209L|SLTM_uc002afo.2_Silent_p.L649L|SLTM_uc002afq.2_Silent_p.L236L|SLTM_uc010bgd.2_Silent_p.L236L	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	667	Arg/Glu-rich.|Potential.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62939541	62939541	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62939541G>A	uc002alb.3	+	1	32	c.32G>A	c.(31-33)CGC>CAC	p.R11H	MGC15885_uc010uib.1_5'Flank|MGC15885_uc002ala.3_5'Flank	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	11					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
CA12	771	broad.mit.edu	37	15	63632630	63632630	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63632630C>T	uc002amc.2	-	7	760	c.604G>A	c.(604-606)GTC>ATC	p.V202I	CA12_uc002amd.2_Missense_Mutation_p.V202I|CA12_uc002ame.2_Missense_Mutation_p.V142I	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor	202	Extracellular (Potential).				one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)													---	---	---	---
FBXL22	283807	broad.mit.edu	37	15	63889730	63889730	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63889730G>A	uc002amn.2	+	1	135	c.121G>A	c.(121-123)GCA>ACA	p.A41T	uc002amj.2_Intron|uc002amk.2_Intron|uc002aml.2_Intron|FBXL22_uc002amm.1_Missense_Mutation_p.A41T	NM_203373	NP_976307	Q6P050	FXL22_HUMAN	F-box and leucine-rich repeat protein 22	41	F-box.										0																		---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63951951	63951951	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63951951C>A	uc002amp.2	-	47	9556	c.9408G>T	c.(9406-9408)GAG>GAT	p.E3136D		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	3136					protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
PIF1	80119	broad.mit.edu	37	15	65108789	65108789	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65108789C>T	uc002ant.2	-	12	1916	c.1850G>A	c.(1849-1851)GGC>GAC	p.G617D	PIF1_uc002anr.2_Missense_Mutation_p.G165D|PIF1_uc002ans.2_Missense_Mutation_p.G308D|PIF1_uc010uiq.1_Missense_Mutation_p.G617D	NM_025049	NP_079325	Q9H611	PIF1_HUMAN	DNA helicase homolog PIF1	617	Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity.				negative regulation of telomerase activity|regulation of telomere maintenance|viral genome replication	nuclear chromosome, telomeric region	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' DNA/RNA helicase activity|magnesium ion binding|single-stranded DNA-dependent ATP-dependent DNA helicase activity|telomeric DNA binding				0																		---	---	---	---
IGDCC3	9543	broad.mit.edu	37	15	65667514	65667514	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65667514C>T	uc002aos.2	-	2	582	c.330G>A	c.(328-330)TCG>TCA	p.S110S		NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule	110	Extracellular (Potential).|Ig-like C2-type 1.									ovary(3)	3																		---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68617466	68617466	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68617466T>C	uc002ari.2	-						ITGA11_uc010bib.2_Intron	NM_001004439	NP_001004439			integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)													---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69738650	69738650	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69738650G>A	uc002asb.2	+	21	2860	c.2743G>A	c.(2743-2745)GCA>ACA	p.A915T	KIF23_uc002asc.2_Missense_Mutation_p.A811T|KIF23_uc010bii.2_Missense_Mutation_p.A721T|KIF23_uc010ukc.1_Missense_Mutation_p.A628T	NM_138555	NP_612565	Q02241	KIF23_HUMAN	kinesin family member 23 isoform 1	915					blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72190775	72190775	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72190775G>A	uc002atl.3	-	25	4542	c.4069C>T	c.(4069-4071)CCA>TCA	p.P1357S	MYO9A_uc010biq.2_Missense_Mutation_p.P977S|MYO9A_uc002atn.1_Missense_Mutation_p.P1338S|MYO9A_uc002atk.2_Missense_Mutation_p.P81S|MYO9A_uc002atm.1_Missense_Mutation_p.P81S	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	1357	Tail.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
HCN4	10021	broad.mit.edu	37	15	73635991	73635991	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73635991C>T	uc002avp.2	-	2	1938	c.944G>A	c.(943-945)CGC>CAC	p.R315H		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	315	Cytoplasmic (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6				COAD - Colon adenocarcinoma(1;0.142)														---	---	---	---
CYP1A1	1543	broad.mit.edu	37	15	75015357	75015357	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75015357C>T	uc002ayp.3	-	2	204	c.82G>A	c.(82-84)GCC>ACC	p.A28T	CYP1A1_uc010bjv.2_RNA|CYP1A1_uc010bjw.2_RNA|CYP1A1_uc010bju.2_Intron|CYP1A1_uc010bjx.2_Intron|CYP1A1_uc002ayq.3_Missense_Mutation_p.A28T|CYP1A1_uc010bjy.2_Missense_Mutation_p.A28T|CYP1A1_uc010bjz.1_Intron	NM_000499	NP_000490	P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A,	28					cellular lipid metabolic process|drug metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|vitamin D 24-hydroxylase activity			ovary(2)|breast(2)|pancreas(1)	5					Arsenic trioxide(DB01169)|Benzphetamine(DB00865)|Bleomycin(DB00290)|Chlorzoxazone(DB00356)|Dacarbazine(DB00851)|Dactinomycin(DB00970)|Esomeprazole(DB00736)|Estrone(DB00655)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Ginseng(DB01404)|Granisetron(DB00889)|Ketoconazole(DB01026)|Menadione(DB00170)|Picrotoxin(DB00466)|Primaquine(DB01087)|Quinidine(DB00908)|Quinine(DB00468)|Thiabendazole(DB00730)									Endometrial_Cancer_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia				---	---	---	---
C15orf39	56905	broad.mit.edu	37	15	75503288	75503288	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75503288C>A	uc002azp.3	+	3	3295	c.2975C>A	c.(2974-2976)GCT>GAT	p.A992D	C15orf39_uc002azq.3_Missense_Mutation_p.A992D|C15orf39_uc002azr.3_3'UTR	NM_015492	NP_056307	Q6ZRI6	CO039_HUMAN	hypothetical protein LOC56905	992											0																		---	---	---	---
NEIL1	79661	broad.mit.edu	37	15	75644475	75644475	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75644475C>T	uc002bad.2	+	3	964	c.458C>T	c.(457-459)GCG>GTG	p.A153V	NEIL1_uc002bae.2_Missense_Mutation_p.A239V	NM_024608	NP_078884	Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1	153					base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress	cytoplasm|nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding			ovary(1)	1													BER_DNA_glycosylases					---	---	---	---
CSPG4	1464	broad.mit.edu	37	15	75975092	75975092	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75975092G>T	uc002baw.2	-							NM_001897	NP_001888			chondroitin sulfate proteoglycan 4 precursor						angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3																		---	---	---	---
LINGO1	84894	broad.mit.edu	37	15	77907179	77907179	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77907179G>A	uc002bct.1	-	2	1122	c.1070C>T	c.(1069-1071)TCG>TTG	p.S357L	LINGO1_uc002bcu.1_Missense_Mutation_p.S351L	NM_032808	NP_116197	Q96FE5	LIGO1_HUMAN	leucine-rich repeat neuronal 6A	357	Extracellular (Potential).|LRR 11.				negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2																		---	---	---	---
ADAMTS7	11173	broad.mit.edu	37	15	79090410	79090410	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79090410G>T	uc002bej.3	-	3	713	c.502C>A	c.(502-504)CTG>ATG	p.L168M	ADAMTS7_uc010und.1_Missense_Mutation_p.L168M|ADAMTS7_uc002bek.1_Missense_Mutation_p.L168M	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	168					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
TMC3	342125	broad.mit.edu	37	15	81650576	81650576	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81650576G>A	uc002bgo.1	-	7	657	c.657C>T	c.(655-657)ATC>ATT	p.I219I	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Silent_p.I219I	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	219	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2																		---	---	---	---
MEX3B	84206	broad.mit.edu	37	15	82335653	82335653	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82335653C>T	uc002bgq.1	-	2	1873	c.1558G>A	c.(1558-1560)GTG>ATG	p.V520M		NM_032246	NP_115622	Q6ZN04	MEX3B_HUMAN	mex-3 homolog B	520	RING-type.				protein autophosphorylation	cytoplasmic mRNA processing body|nucleus	calcium ion binding|RNA binding|zinc ion binding			breast(1)|kidney(1)	2																		---	---	---	---
EFTUD1	79631	broad.mit.edu	37	15	82444584	82444584	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82444584G>A	uc002bgt.1	-	18	2380	c.2211C>T	c.(2209-2211)GAC>GAT	p.D737D	EFTUD1_uc002bgs.1_Silent_p.D108D|EFTUD1_uc002bgu.1_Silent_p.D686D	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain	737					mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1																		---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83455946	83455946	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83455946T>C	uc002bjd.2	-	2	364	c.197A>G	c.(196-198)GAC>GGC	p.D66G	FSD2_uc010uol.1_Missense_Mutation_p.D66G|FSD2_uc010uom.1_Missense_Mutation_p.D66G	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing	66										central_nervous_system(1)	1																		---	---	---	---
BNC1	646	broad.mit.edu	37	15	83935659	83935659	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83935659C>A	uc002bjt.1	-	3	452	c.364G>T	c.(364-366)GAT>TAT	p.D122Y	BNC1_uc010uos.1_Missense_Mutation_p.D110Y	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	122					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
PDE8A	5151	broad.mit.edu	37	15	85661076	85661076	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85661076C>T	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron|PDE8A_uc002bll.2_5'Flank	NM_002605	NP_002596			phosphodiesterase 8A isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)															---	---	---	---
DET1	55070	broad.mit.edu	37	15	89074513	89074513	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89074513G>A	uc002bmr.2	-	2	576	c.424C>T	c.(424-426)CGG>TGG	p.R142W	DET1_uc002bmp.3_RNA|DET1_uc010bnk.2_RNA|DET1_uc002bmq.2_Missense_Mutation_p.R153W	NM_001144074	NP_001137546	Q7L5Y6	DET1_HUMAN	de-etiolated 1 isoform 2	142						nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)															---	---	---	---
ANPEP	290	broad.mit.edu	37	15	90349542	90349542	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90349542C>T	uc002bop.3	-	2	565	c.273G>A	c.(271-273)CCG>CCA	p.P91P		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	91	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)|skin(1)	4	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)													---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	94858845	94858845	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94858845C>T	uc002btj.2	+	3	681	c.616C>T	c.(616-618)CTG>TTG	p.L206L	MCTP2_uc010urg.1_Silent_p.L206L|MCTP2_uc002bti.2_Silent_p.L206L|MCTP2_uc010boj.2_5'UTR|MCTP2_uc010bok.2_Silent_p.L206L|MCTP2_uc002btg.3_Silent_p.L206L|MCTP2_uc002bth.3_Silent_p.L206L	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1	206	C2 1.				calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)															---	---	---	---
SYNM	23336	broad.mit.edu	37	15	99671104	99671104	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99671104G>A	uc002bup.2	+	6	2659	c.2539G>A	c.(2539-2541)GGC>AGC	p.G847S	SYNM_uc002buo.2_Missense_Mutation_p.G847S|SYNM_uc002buq.2_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	desmuslin isoform A	847	Tail.				intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100801677	100801677	+	Intron	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100801677A>T	uc002bvv.1	-						ADAMTS17_uc002bvx.1_Intron	NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101586294	101586294	+	Silent	SNP	C	T	T	rs143276193	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101586294C>T	uc002bwr.2	+	21	3391	c.3072C>T	c.(3070-3072)CCC>CCT	p.P1024P	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1024					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
PCSK6	5046	broad.mit.edu	37	15	101983793	101983793	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101983793C>A	uc002bwy.2	-	3	684	c.370G>T	c.(370-372)GGC>TGC	p.G124C	PCSK6_uc010bpd.2_Translation_Start_Site|PCSK6_uc010bpe.2_Missense_Mutation_p.G124C|PCSK6_uc002bxa.2_Missense_Mutation_p.G124C|PCSK6_uc002bxb.2_Missense_Mutation_p.G124C|PCSK6_uc002bxc.1_Missense_Mutation_p.G124C|PCSK6_uc002bxd.1_Missense_Mutation_p.G124C|PCSK6_uc002bxe.2_Missense_Mutation_p.G124C|PCSK6_uc002bxg.1_Missense_Mutation_p.G124C	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4	124					glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
MSLN	10232	broad.mit.edu	37	16	816331	816331	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:816331G>A	uc002cjw.1	+						MSLN_uc002cjt.1_Intron|MSLN_uc002cju.1_Intron|MSLN_uc010brd.1_Intron|MSLN_uc002cjv.1_Intron|MSLN_uc002cjx.1_Intron|MSLN_uc002cjy.1_Intron	NM_013404	NP_037536			mesothelin isoform 2 preproprotein						cell adhesion	anchored to membrane|extracellular region|Golgi apparatus|plasma membrane				pancreas(1)	1		Hepatocellular(780;0.00335)																---	---	---	---
MSLNL	401827	broad.mit.edu	37	16	823253	823253	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:823253T>C	uc002cjz.1	-	10	2015	c.2015A>G	c.(2014-2016)CAC>CGC	p.H672R		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	321	Extracellular (Potential).				cell adhesion	integral to membrane				breast(3)|ovary(1)	4																		---	---	---	---
MSLNL	401827	broad.mit.edu	37	16	830495	830495	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:830495C>T	uc002cjz.1	-	3	506	c.506G>A	c.(505-507)CGT>CAT	p.R169H		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	Error:Variant_position_missing_in_Q96KJ4_after_alignment					cell adhesion	integral to membrane				breast(3)|ovary(1)	4																		---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1261185	1261185	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1261185C>T	uc002cks.2	+	22	4489	c.4241C>T	c.(4240-4242)CCG>CTG	p.P1414L	CACNA1H_uc002ckt.2_Missense_Mutation_p.P1414L|CACNA1H_uc002cku.2_Missense_Mutation_p.P120L|CACNA1H_uc010brj.2_Missense_Mutation_p.P120L|CACNA1H_uc002ckv.2_Missense_Mutation_p.P120L	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1414	III.|Helical; Name=S4 of repeat III; (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1261517	1261517	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1261517G>A	uc002cks.2	+	23	4635	c.4387G>A	c.(4387-4389)GAC>AAC	p.D1463N	CACNA1H_uc002ckt.2_Missense_Mutation_p.D1463N|CACNA1H_uc002cku.2_Missense_Mutation_p.D169N|CACNA1H_uc010brj.2_Missense_Mutation_p.D169N|CACNA1H_uc002ckv.2_Missense_Mutation_p.D169N	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1463	Extracellular (Potential).|III.		D -> N (in IGE6).		aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1817646	1817646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1817646C>T	uc002cmk.2	+	27	3436	c.3316C>T	c.(3316-3318)CGC>TGC	p.R1106C	MAPK8IP3_uc002cml.2_Missense_Mutation_p.R1100C|MAPK8IP3_uc010uvl.1_Missense_Mutation_p.R1107C	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	1106					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1817684	1817684	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1817684G>A	uc002cmk.2	+	27	3474	c.3354G>A	c.(3352-3354)ACG>ACA	p.T1118T	MAPK8IP3_uc002cml.2_Silent_p.T1112T|MAPK8IP3_uc010uvl.1_Silent_p.T1119T	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	1118					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2025449	2025449	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2025449G>A	uc002cnu.1	+						TBL3_uc002cnv.1_Intron|TBL3_uc010bsb.1_Intron|TBL3_uc010bsc.1_Intron|TBL3_uc010uvt.1_Intron|TBL3_uc002cnw.1_5'Flank	NM_006453	NP_006444			transducin beta-like 3						G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
TSC2	7249	broad.mit.edu	37	16	2127732	2127732	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2127732C>T	uc002con.2	+						TSC2_uc010bsd.2_Intron|TSC2_uc002coo.2_Intron|TSC2_uc010uvv.1_Intron|TSC2_uc010uvw.1_Intron|TSC2_uc002cop.2_Intron	NM_000548	NP_000539			tuberous sclerosis 2 isoform 1						cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)						D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
E4F1	1877	broad.mit.edu	37	16	2283192	2283192	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2283192C>T	uc002cpm.2	+						E4F1_uc010bsi.2_Intron|E4F1_uc010bsj.2_Intron	NM_004424	NP_004415			p120E4F						cell division|cell proliferation|interspecies interaction between organisms|mitosis|regulation of growth	cytoplasm|nucleoplasm	DNA binding|ligase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
RNPS1	10921	broad.mit.edu	37	16	2312299	2312299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2312299G>A	uc002cpt.2	-	6	1202	c.656C>T	c.(655-657)GCG>GTG	p.A219V	RNPS1_uc002cpu.2_Missense_Mutation_p.A219V|RNPS1_uc002cpv.2_Missense_Mutation_p.A42V|RNPS1_uc002cpw.2_Missense_Mutation_p.A219V|RNPS1_uc002cpx.2_Missense_Mutation_p.A196V|RNPS1_uc010uwa.1_RNA	NM_080594	NP_542161	Q15287	RNPS1_HUMAN	RNA-binding protein S1, serine-rich domain	219	Necessary for interaction with PNN and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.|RRM.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|termination of RNA polymerase II transcription	cytosol|nuclear speck	mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(1)	1																		---	---	---	---
TBC1D24	57465	broad.mit.edu	37	16	2546318	2546318	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2546318C>T	uc002cql.2	+	2	309	c.169C>T	c.(169-171)CGC>TGC	p.R57C	TBC1D24_uc002cqk.2_Missense_Mutation_p.R57C|TBC1D24_uc002cqm.2_Missense_Mutation_p.R57C|TBC1D24_uc010bsm.2_5'Flank	NM_020705	NP_065756	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	57	Rab-GAP TBC.				neuron projection development	cytoplasm	protein binding|Rab GTPase activator activity				0																		---	---	---	---
AMDHD2	51005	broad.mit.edu	37	16	2580683	2580683	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2580683G>T	uc010uwc.1	+	11	1805	c.1708G>T	c.(1708-1710)GAT>TAT	p.D570Y	AMDHD2_uc010uwd.1_Missense_Mutation_p.D334Y|CEMP1_uc002cqr.2_Missense_Mutation_p.S131Y	NM_001145815	NP_001139287	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2 isoform 2	Error:Variant_position_missing_in_Q9Y303_after_alignment					N-acetylglucosamine metabolic process		N-acetylglucosamine-6-phosphate deacetylase activity			skin(2)|large_intestine(1)|breast(1)	4																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2809661	2809661	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2809661C>T	uc002crk.2	+	9	1381	c.832C>T	c.(832-834)CGG>TGG	p.R278W	SRRM2_uc002crj.1_Missense_Mutation_p.R182W|SRRM2_uc002crl.1_Missense_Mutation_p.R278W|SRRM2_uc010bsu.1_Missense_Mutation_p.R182W	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	278	Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MMP25	64386	broad.mit.edu	37	16	3100033	3100033	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3100033C>T	uc002cth.2	+	3	493	c.256C>T	c.(256-258)CGT>TGT	p.R86C	MMP25_uc002cti.1_Missense_Mutation_p.R22C	NM_022468	NP_071913	Q9NPA2	MMP25_HUMAN	matrix metalloproteinase 25 preproprotein	86					inflammatory response|proteolysis	anchored to membrane|cell surface|plasma membrane|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
ZNF205	7755	broad.mit.edu	37	16	3170166	3170166	+	Missense_Mutation	SNP	G	A	A	rs144250660		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3170166G>A	uc002cub.2	+	7	1640	c.1505G>A	c.(1504-1506)CGG>CAG	p.R502Q	ZNF205_uc002cua.2_Missense_Mutation_p.R502Q	NM_001042428	NP_001035893	O95201	ZN205_HUMAN	zinc finger protein 205	502					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding				0																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3642801	3642801	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3642801G>A	uc002cvp.2	-	11	2853	c.2226C>T	c.(2224-2226)GAC>GAT	p.D742D		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	742	BTB.|Interaction with PLK1 and TERF2-TERF2IP.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0													Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3828764	3828764	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3828764C>A	uc002cvv.2	-	9	2082	c.1878G>T	c.(1876-1878)ATG>ATT	p.M626I	CREBBP_uc002cvw.2_Missense_Mutation_p.M588I	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	626	KIX.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
DNAJA3	9093	broad.mit.edu	37	16	4494700	4494700	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4494700G>T	uc002cwk.2	+	7	992	c.967G>T	c.(967-969)GGA>TGA	p.G323*	DNAJA3_uc002cwl.2_Nonsense_Mutation_p.G323*|DNAJA3_uc010uxk.1_Nonsense_Mutation_p.G170*	NM_005147	NP_005138	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	323					activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4																		---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9943605	9943605	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9943605C>T	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
RRN3	54700	broad.mit.edu	37	16	15155703	15155703	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15155703G>A	uc002dde.2	-	18	1922	c.1854C>T	c.(1852-1854)ACC>ACT	p.T618T	PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Silent_p.T486T|RRN3_uc010uzq.1_Silent_p.T588T	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor	618	Interaction with EIF3L.|Interaction with TWISTNB.				regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18887616	18887616	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18887616A>G	uc002dfm.2	-	13	2083	c.1720T>C	c.(1720-1722)TGT>CGT	p.C574R	SMG1_uc010bwb.2_Missense_Mutation_p.C434R	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	574	Interaction with SMG8 and SMG9.				DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20996749	20996749	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20996749C>T	uc010vbe.1	-	48	7315	c.7315G>A	c.(7315-7317)GGG>AGG	p.G2439R	DNAH3_uc010vbd.1_5'Flank	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2439	ATP (Potential).|AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
HS3ST2	9956	broad.mit.edu	37	16	22926746	22926746	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22926746C>T	uc002dli.2	+	2	1039	c.967C>T	c.(967-969)CCT>TCT	p.P323S	HS3ST2_uc002dlj.2_RNA	NM_006043	NP_006034	Q9Y278	HS3S2_HUMAN	heparan sulfate D-glucosaminyl	323	Lumenal (Potential).					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(48;0.0299)														---	---	---	---
PLK1	5347	broad.mit.edu	37	16	23690504	23690504	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23690504T>C	uc002dlz.1	+	1	304	c.251T>C	c.(250-252)GTG>GCG	p.V84A		NM_005030	NP_005021	P53350	PLK1_HUMAN	polo-like kinase 1	84	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
RBBP6	5930	broad.mit.edu	37	16	24567130	24567130	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24567130T>C	uc002dmh.2	+						RBBP6_uc010vcb.1_Intron|RBBP6_uc002dmi.2_Intron|RBBP6_uc010bxr.2_Intron|RBBP6_uc002dmk.2_Intron	NM_006910	NP_008841			retinoblastoma-binding protein 6 isoform 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)														---	---	---	---
JMJD5	79831	broad.mit.edu	37	16	27231782	27231782	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27231782G>A	uc002doh.2	+	7	1244	c.1062G>A	c.(1060-1062)ACG>ACA	p.T354T	JMJD5_uc010vcn.1_Silent_p.T392T|JMJD5_uc010bxw.2_Intron|JMJD5_uc010bxx.2_RNA	NM_024773	NP_079049	Q8N371	KDM8_HUMAN	jumonji domain containing 5 isoform 2	354	JmjC.				G2/M transition of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|histone demethylase activity (H3-K36 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
INO80E	283899	broad.mit.edu	37	16	30008133	30008133	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30008133C>A	uc002dvg.1	+	3	258	c.157C>A	c.(157-159)CTC>ATC	p.L53I	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvh.1_RNA|INO80E_uc002dvi.1_Missense_Mutation_p.L53I|INO80E_uc002dvj.1_RNA|INO80E_uc002dvk.1_Missense_Mutation_p.L53I|HIRIP3_uc002dve.2_5'Flank|HIRIP3_uc002dvf.2_5'Flank	NM_173618	NP_775889	Q8NBZ0	IN80E_HUMAN	INO80 complex subunit E	53	Potential.				DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex				skin(1)	1																		---	---	---	---
PPP4C	5531	broad.mit.edu	37	16	30094985	30094985	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30094985G>A	uc002dwe.2	+	7	631	c.487G>A	c.(487-489)GTG>ATG	p.V163M	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|PPP4C_uc002dwf.2_Missense_Mutation_p.V163M|PPP4C_uc002dwg.2_RNA|PPP4C_uc002dwh.2_Missense_Mutation_p.V84M	NM_002720	NP_002711	P60510	PP4C_HUMAN	protein phosphatase 4, catalytic subunit	163					microtubule cytoskeleton organization|regulation of double-strand break repair via homologous recombination	centrosome|nucleus	metal ion binding|NF-kappaB-inducing kinase activity|protein binding|protein serine/threonine phosphatase activity			skin(1)	1																		---	---	---	---
TBX6	6911	broad.mit.edu	37	16	30100101	30100101	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30100101C>A	uc010veh.1	-	5	741	c.681G>T	c.(679-681)CAG>CAT	p.Q227H	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TBX6_uc002dwk.1_Missense_Mutation_p.Q227H	NM_004608	NP_004599	O95947	TBX6_HUMAN	T-box 6	227	T-box.				anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30750598	30750598	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30750598G>T	uc002dze.1	+	34	9622	c.9237G>T	c.(9235-9237)CGG>CGT	p.R3079R	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.R2874R	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	3079					interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30976273	30976273	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30976273C>T	uc002ead.1	+	7	1896	c.1210C>T	c.(1210-1212)CGC>TGC	p.R404C		NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	404	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30977164	30977164	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30977164G>A	uc002ead.1	+	8	2648	c.1962G>A	c.(1960-1962)CCG>CCA	p.P654P		NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	654	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
ZNF646	9726	broad.mit.edu	37	16	31091982	31091982	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31091982C>T	uc002eap.2	+	2	4626	c.4337C>T	c.(4336-4338)GCA>GTA	p.A1446V		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	1446					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2																		---	---	---	---
BCKDK	10295	broad.mit.edu	37	16	31121062	31121062	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31121062C>T	uc002eaw.3	+	4	649	c.333C>T	c.(331-333)TGC>TGT	p.C111C	BCKDK_uc002eav.3_Silent_p.C111C|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Silent_p.C111C	NM_005881	NP_005872	O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	111					branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation	mitochondrial alpha-ketoglutarate dehydrogenase complex	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity			stomach(1)|breast(1)	2																		---	---	---	---
MYST1	84148	broad.mit.edu	37	16	31131702	31131702	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31131702C>T	uc002eay.2	+	3	347	c.329C>T	c.(328-330)GCG>GTG	p.A110V	MYST1_uc002eax.2_Missense_Mutation_p.A110V	NM_032188	NP_115564	Q9H7Z6	MYST1_HUMAN	MYST histone acetyltransferase 1 isoform 1	110	Chromo.				histone H4-K16 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex|MSL complex	histone acetyltransferase activity|metal ion binding|methylated histone residue binding|transcription factor binding			ovary(1)	1																		---	---	---	---
ITGAM	3684	broad.mit.edu	37	16	31309099	31309099	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31309099G>A	uc002ebq.2	+	14	1629	c.1531G>A	c.(1531-1533)GGG>AGG	p.G511R	ITGAM_uc002ebr.2_Missense_Mutation_p.G512R|ITGAM_uc010cam.1_Intron|ITGAM_uc010can.2_Intron	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	511	FG-GAP 6.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1																		---	---	---	---
ARMC5	79798	broad.mit.edu	37	16	31473763	31473763	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31473763G>A	uc002ecc.2	+	3	1424	c.895G>A	c.(895-897)GAG>AAG	p.E299K	ARMC5_uc010vfn.1_Missense_Mutation_p.E394K|ARMC5_uc010vfo.1_Missense_Mutation_p.E331K|ARMC5_uc002eca.3_Missense_Mutation_p.E299K|ARMC5_uc010vfp.1_Intron|ARMC5_uc002ecb.2_Missense_Mutation_p.E299K	NM_001105247	NP_001098717	Q96C12	ARMC5_HUMAN	armadillo repeat containing 5 isoform a	299	ARM 4.						binding			pancreas(1)	1																		---	---	---	---
SLC5A2	6524	broad.mit.edu	37	16	31500224	31500224	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31500224T>C	uc002ecf.3	+	11	1323	c.1304T>C	c.(1303-1305)GTA>GCA	p.V435A	SLC5A2_uc010car.2_Intron|C16orf58_uc002ecg.2_RNA	NM_003041	NP_003032	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose	435	Helical; (Potential).				carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1																		---	---	---	---
GPT2	84706	broad.mit.edu	37	16	46943744	46943744	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46943744C>T	uc002eel.2	+	6	819	c.725C>T	c.(724-726)GCG>GTG	p.A242V	GPT2_uc002eem.2_Missense_Mutation_p.A142V	NM_133443	NP_597700	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase 2 isoform 1	242					2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47536902	47536902	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47536902G>T	uc002eev.3	+	4	358	c.306G>T	c.(304-306)AGG>AGT	p.R102S	PHKB_uc010vgi.1_Missense_Mutation_p.R95S|PHKB_uc002eeu.3_Missense_Mutation_p.R95S	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a	102					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48149412	48149412	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48149412C>T	uc002efc.1	-	13	2249	c.1903G>A	c.(1903-1905)GCC>ACC	p.A635T	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	635	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49525194	49525194	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49525194C>T	uc002efs.2	-	9	4145	c.3847G>A	c.(3847-3849)GCA>ACA	p.A1283T	ZNF423_uc010vgn.1_Missense_Mutation_p.A1166T	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	1283					cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49671593	49671593	+	Silent	SNP	G	A	A	rs34742420	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49671593G>A	uc002efs.2	-	5	1768	c.1470C>T	c.(1468-1470)GCC>GCT	p.A490A	ZNF423_uc010vgn.1_Silent_p.A373A	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	490	C2H2-type 11.				cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
BRD7	29117	broad.mit.edu	37	16	50357573	50357573	+	Silent	SNP	C	T	T	rs139109763	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50357573C>T	uc002egf.1	-	13	1435	c.1368G>A	c.(1366-1368)CCG>CCA	p.P456P	BRD7_uc002ege.1_Silent_p.P456P	NM_013263	NP_037395	Q9NPI1	BRD7_HUMAN	bromodomain containing 7	456					cell cycle|negative regulation of cell proliferation|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of histone acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|nucleus	histone acetyl-lysine binding|p53 binding|transcription coactivator activity|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding				0		all_cancers(37;0.0127)																---	---	---	---
CPNE2	221184	broad.mit.edu	37	16	57155016	57155016	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57155016C>T	uc002eks.1	+	8	922	c.693C>T	c.(691-693)TAC>TAT	p.Y231Y	CPNE2_uc010cct.1_Silent_p.Y257Y|CPNE2_uc010ccu.1_Silent_p.Y231Y	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II	231	C2 2.									central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)																---	---	---	---
CCDC135	84229	broad.mit.edu	37	16	57758652	57758652	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57758652C>T	uc002emi.2	+	12	1752	c.1663C>T	c.(1663-1665)CGC>TGC	p.R555C	CCDC135_uc002emj.2_Missense_Mutation_p.R555C|CCDC135_uc002emk.2_Missense_Mutation_p.R490C	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	555						cytoplasm				central_nervous_system(1)	1																		---	---	---	---
CCDC135	84229	broad.mit.edu	37	16	57760055	57760055	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57760055G>A	uc002emi.2	+	13	1923	c.1834G>A	c.(1834-1836)GCG>ACG	p.A612T	CCDC135_uc002emj.2_Missense_Mutation_p.A612T|CCDC135_uc002emk.2_Missense_Mutation_p.A547T	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	612						cytoplasm				central_nervous_system(1)	1																		---	---	---	---
CNGB1	1258	broad.mit.edu	37	16	57983310	57983310	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57983310A>C	uc002emt.2	-	14	1133	c.1068T>G	c.(1066-1068)GAT>GAG	p.D356E	CNGB1_uc010cdh.2_Missense_Mutation_p.D350E	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	356	Poly-Glu.|Cytoplasmic (Potential).				sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4																		---	---	---	---
MMP15	4324	broad.mit.edu	37	16	58076219	58076219	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58076219G>A	uc002ena.2	+	7	2222	c.1249G>A	c.(1249-1251)GGT>AGT	p.G417S		NM_002428	NP_002419	P51511	MMP15_HUMAN	matrix metalloproteinase 15 preproprotein	417	Hemopexin-like 1.|Extracellular (Potential).				protein modification process|proteolysis	extracellular matrix|integral to plasma membrane	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|protein binding|zinc ion binding			central_nervous_system(2)|breast(1)	3																		---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61687976	61687976	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61687976G>A	uc002eog.1	-	12	2188	c.1936C>T	c.(1936-1938)CGG>TGG	p.R646W		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	646	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	p.R646Q(1)		ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CMTM2	146225	broad.mit.edu	37	16	66613571	66613571	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66613571G>T	uc002ept.2	+	1	221	c.61G>T	c.(61-63)GGG>TGG	p.G21W	CMTM2_uc010cdu.2_Missense_Mutation_p.G21W	NM_144673	NP_653274	Q8TAZ6	CKLF2_HUMAN	chemokine-like factor superfamily 2	21					chemotaxis	extracellular space|integral to membrane	cytokine activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)														---	---	---	---
CES2	8824	broad.mit.edu	37	16	66972087	66972087	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66972087C>T	uc002eqr.2	+	2	1416	c.416C>T	c.(415-417)CCC>CTC	p.P139L	CES2_uc002eqq.2_Missense_Mutation_p.P139L|CES2_uc002eqs.2_5'UTR	NM_003869	NP_003860	O00748	EST2_HUMAN	carboxylesterase 2 isoform 1	75					catabolic process	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0663)|Epithelial(162;0.166)														---	---	---	---
EXOC3L	283849	broad.mit.edu	37	16	67219057	67219057	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67219057C>T	uc002erx.1	-	11	1972	c.1731G>A	c.(1729-1731)GTG>GTA	p.V577V	KIAA0895L_uc002ert.2_5'Flank|KIAA0895L_uc002eru.2_5'Flank|EXOC3L_uc002erv.1_RNA|EXOC3L_uc002erw.1_Silent_p.V228V|EXOC3L_uc002ery.1_Silent_p.V479V|EXOC3L_uc010vje.1_Silent_p.V474V	NM_178516	NP_848611	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like	577					exocytosis|peptide hormone secretion	exocyst|stored secretory granule|transport vesicle					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0021)|Epithelial(162;0.0073)|all cancers(182;0.0616)														---	---	---	---
EXOC3L	283849	broad.mit.edu	37	16	67220729	67220729	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67220729C>T	uc002erx.1	-	7	1458	c.1217G>A	c.(1216-1218)CGG>CAG	p.R406Q	KIAA0895L_uc002ert.2_5'Flank|KIAA0895L_uc002eru.2_5'Flank|EXOC3L_uc002erv.1_RNA|EXOC3L_uc002erw.1_Missense_Mutation_p.R57Q|EXOC3L_uc002ery.1_Intron|EXOC3L_uc010vje.1_Intron	NM_178516	NP_848611	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like	406					exocytosis|peptide hormone secretion	exocyst|stored secretory granule|transport vesicle					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0021)|Epithelial(162;0.0073)|all cancers(182;0.0616)														---	---	---	---
RLTPR	146206	broad.mit.edu	37	16	67681439	67681439	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67681439C>A	uc002etn.2	+	11	925	c.805C>A	c.(805-807)CTG>ATG	p.L269M	RLTPR_uc010cel.1_Missense_Mutation_p.L269M|RLTPR_uc010vjr.1_Missense_Mutation_p.L269M	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	269	LRR 3.									breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)														---	---	---	---
RLTPR	146206	broad.mit.edu	37	16	67683404	67683404	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67683404C>T	uc002etn.2	+	20	1921	c.1801C>T	c.(1801-1803)CTA>TTA	p.L601L	RLTPR_uc010cel.1_Silent_p.L594L|RLTPR_uc010vjr.1_Silent_p.L565L	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	601	Tropomodulin-like.|LRR 13.									breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)														---	---	---	---
PSMB10	5699	broad.mit.edu	37	16	67968771	67968771	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67968771G>A	uc002eux.1	-	7	740	c.639C>T	c.(637-639)GAC>GAT	p.D213D		NM_002801	NP_002792	P40306	PSB10_HUMAN	proteasome beta 10 subunit proprotein	213					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|humoral immune response|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)														---	---	---	---
SLC12A4	6560	broad.mit.edu	37	16	67978781	67978781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67978781G>A	uc002euz.2	-	24	3361	c.3220C>T	c.(3220-3222)CGC>TGC	p.R1074C	LCAT_uc002euy.1_5'Flank|SLC12A4_uc010ceu.2_Missense_Mutation_p.R1068C|SLC12A4_uc010vkh.1_Missense_Mutation_p.R1043C|SLC12A4_uc010vki.1_Missense_Mutation_p.R1068C|SLC12A4_uc010vkj.1_Missense_Mutation_p.R1076C|SLC12A4_uc002eva.2_3'UTR	NM_005072	NP_005063	Q9UP95	S12A4_HUMAN	solute carrier family 12, member 4 isoform a	1074	Cytoplasmic (Potential).				cell volume homeostasis|potassium ion transport|sodium ion transport	integral to plasma membrane|membrane fraction	potassium:chloride symporter activity			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68716291	68716291	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68716291G>A	uc002ewf.2	+	9	2215	c.1083G>A	c.(1081-1083)GCG>GCA	p.A361A	CDH3_uc010vli.1_Silent_p.A306A	NM_001793	NP_001784	P22223	CADH3_HUMAN	cadherin 3, type 1 preproprotein	361	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)|breast(1)|skin(1)	5		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68943249	68943249	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68943249C>T	uc002ewi.3	+	11	1948	c.1936C>T	c.(1936-1938)CTG>TTG	p.L646L		NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	646						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
HAS3	3038	broad.mit.edu	37	16	69143752	69143752	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69143752C>T	uc010cfh.2	+	2	678	c.454C>T	c.(454-456)CGC>TGC	p.R152C	HAS3_uc002ewk.2_Missense_Mutation_p.R152C|HAS3_uc010vlk.1_Missense_Mutation_p.R152C|HAS3_uc002ewl.2_Missense_Mutation_p.R152C	NM_005329	NP_005320	O00219	HAS3_HUMAN	hyaluronan synthase 3 isoform a	152	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	hyaluronan synthase activity				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)														---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70955005	70955005	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70955005C>T	uc002ezr.2	-	46	7399	c.7271G>A	c.(7270-7272)GGC>GAC	p.G2424D		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2425										ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
KIAA0174	9798	broad.mit.edu	37	16	71950427	71950427	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71950427C>T	uc002fbj.1	+	5	473	c.190C>T	c.(190-192)CGA>TGA	p.R64*	KIAA0174_uc010cgh.1_Nonsense_Mutation_p.R64*|KIAA0174_uc002fbk.1_Nonsense_Mutation_p.R51*|KIAA0174_uc002fbm.1_Nonsense_Mutation_p.R51*|KIAA0174_uc002fbl.1_Nonsense_Mutation_p.R51*|KIAA0174_uc002fbn.1_Intron|KIAA0174_uc010cgi.1_Intron|KIAA0174_uc010cgj.1_Translation_Start_Site|KIAA0174_uc010vmk.1_Intron			P53990	IST1_HUMAN	SubName: Full=cDNA FLJ32696 fis, clone TESTI2000358; SubName: Full=cDNA FLJ77725;	51	Interaction with CHMP1A and CHMP1B.				cell cycle|cell division	cytoplasmic membrane-bounded vesicle|ER-Golgi intermediate compartment	protein binding			ovary(1)	1																		---	---	---	---
HP	3240	broad.mit.edu	37	16	72090100	72090100	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72090100C>T	uc002fbr.3	+	2	90	c.46C>T	c.(46-48)CTT>TTT	p.L16F	TXNL4B_uc010cgl.2_Intron|HP_uc010cgm.2_Missense_Mutation_p.L16F|HP_uc002fbt.3_Missense_Mutation_p.L16F|HP_uc002fbu.1_5'UTR|HP_uc002fbv.3_5'UTR|HP_uc002fbw.3_5'UTR|HP_uc002fbx.3_5'Flank	NM_005143	NP_005134	P00738	HPT_HUMAN	haptoglobin isoform 1 preproprotein	16					cellular iron ion homeostasis|defense response|negative regulation of hydrogen peroxide catabolic process|negative regulation of oxidoreductase activity|positive regulation of cell death|proteolysis|response to hydrogen peroxide	extracellular region|haptoglobin-hemoglobin complex	hemoglobin binding|serine-type endopeptidase activity				0		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)														---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72828622	72828622	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72828622T>C	uc002fck.2	-	9	8632	c.7959A>G	c.(7957-7959)CTA>CTG	p.L2653L	ZFHX3_uc002fcl.2_Silent_p.L1739L	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2653	Homeobox 3.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)																---	---	---	---
CHST6	4166	broad.mit.edu	37	16	75513373	75513373	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75513373G>A	uc002fef.2	-	3	534	c.354C>T	c.(352-354)TCC>TCT	p.S118S	CHST6_uc002feg.1_RNA|CHST6_uc002feh.1_Silent_p.S118S	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	118	Lumenal (Potential).				keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0																		---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76482796	76482796	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76482796G>T	uc002feu.1	+	8	1260	c.875G>T	c.(874-876)AGG>ATG	p.R292M	CNTNAP4_uc002fev.1_Missense_Mutation_p.R204M|CNTNAP4_uc010chb.1_Missense_Mutation_p.R267M|CNTNAP4_uc002fex.1_Missense_Mutation_p.R295M|CNTNAP4_uc002few.2_Missense_Mutation_p.R267M	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	292	Extracellular (Potential).|Laminin G-like 1.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
MON1B	22879	broad.mit.edu	37	16	77228528	77228528	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77228528C>T	uc002fez.2	+	4	1102	c.772C>T	c.(772-774)CGA>TGA	p.R258*	MON1B_uc010vnf.1_Nonsense_Mutation_p.R149*|MON1B_uc010vng.1_Nonsense_Mutation_p.R112*|MON1B_uc002ffa.2_Nonsense_Mutation_p.R138*	NM_014940	NP_055755	Q7L1V2	MON1B_HUMAN	MON1 homolog B	258							protein binding				0																		---	---	---	---
GAN	8139	broad.mit.edu	37	16	81411121	81411121	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81411121G>A	uc002fgo.2	+	11	1862	c.1714G>A	c.(1714-1716)GCC>ACC	p.A572T		NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin	572	Kelch 6.				cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)																---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84108269	84108269	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84108269C>A	uc002fhi.2	-	12	2028	c.1526G>T	c.(1525-1527)GGA>GTA	p.G509V	MBTPS1_uc002fhh.2_Missense_Mutation_p.G13V	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	509	Lumenal (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
KLHDC4	54758	broad.mit.edu	37	16	87745031	87745031	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87745031C>T	uc002fki.2	-	9	900	c.854G>A	c.(853-855)CGG>CAG	p.R285Q	KLHDC4_uc002fkh.1_5'Flank|KLHDC4_uc010cht.1_Missense_Mutation_p.R104Q|KLHDC4_uc002fkj.2_Missense_Mutation_p.R254Q|KLHDC4_uc002fkk.2_Missense_Mutation_p.R104Q|KLHDC4_uc002fkl.2_Missense_Mutation_p.R228Q|KLHDC4_uc010chu.1_Missense_Mutation_p.R104Q	NM_017566	NP_060036	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	285	Kelch 4.									pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0283)														---	---	---	---
SLC7A5	8140	broad.mit.edu	37	16	87902644	87902644	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87902644C>T	uc002fkm.2	-	1	457	c.385G>A	c.(385-387)GCC>ACC	p.A129T		NM_003486	NP_003477	Q01650	LAT1_HUMAN	solute carrier family 7 (cationic amino acid	129	Helical; (Potential).				blood coagulation|cell differentiation|cellular amino acid metabolic process|ion transport|leukocyte migration|nervous system development	apical plasma membrane|cytosol|integral to membrane	neutral amino acid transmembrane transporter activity|peptide antigen binding				0				BRCA - Breast invasive adenocarcinoma(80;0.049)														---	---	---	---
CTU2	348180	broad.mit.edu	37	16	88781004	88781004	+	Missense_Mutation	SNP	C	T	T	rs148822873		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88781004C>T	uc002flm.2	+	12	1259	c.1211C>T	c.(1210-1212)ACG>ATG	p.T404M	CTU2_uc002fln.2_Missense_Mutation_p.T404M|CTU2_uc010chz.2_Missense_Mutation_p.T475M|CTU2_uc010cia.2_Missense_Mutation_p.T317M	NM_001012759	NP_001012777	Q2VPK5	CTU2_HUMAN	cytoplasmic tRNA 2-thiolation protein 2 isoform	404					tRNA thio-modification|tRNA wobble uridine modification	cytoplasm|protein complex|soluble fraction	protein binding			skin(1)	1																		---	---	---	---
ACSF3	197322	broad.mit.edu	37	16	89178585	89178585	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89178585A>G	uc002fmp.2	+	5	1248	c.908A>G	c.(907-909)TAC>TGC	p.Y303C	ACSF3_uc010cig.1_Missense_Mutation_p.Y303C|ACSF3_uc010cih.1_Missense_Mutation_p.Y38C|ACSF3_uc002fmq.1_RNA|ACSF3_uc010cii.1_RNA|ACSF3_uc002fmr.1_Missense_Mutation_p.Y38C	NM_174917	NP_777577	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3 precursor	303					fatty acid metabolic process	mitochondrion	acid-thiol ligase activity|ATP binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0281)														---	---	---	---
ZNF778	197320	broad.mit.edu	37	16	89291968	89291968	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89291968C>T	uc002fmv.2	+	5	589	c.250C>T	c.(250-252)CGA>TGA	p.R84*	ZNF778_uc010vpf.1_RNA|ZNF778_uc002fmw.1_Nonsense_Mutation_p.R42*|ZNF778_uc010vpg.1_5'UTR	NM_182531	NP_872337	Q96MU6	ZN778_HUMAN	zinc finger protein 778	84	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89346504	89346504	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89346504G>A	uc002fmx.1	-	9	6907	c.6446C>T	c.(6445-6447)GCA>GTA	p.A2149V	ANKRD11_uc002fmy.1_Missense_Mutation_p.A2149V|ANKRD11_uc002fnc.1_Missense_Mutation_p.A2149V|ANKRD11_uc002fna.1_5'Flank|ANKRD11_uc002fnb.1_Missense_Mutation_p.A2106V	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2149	Pro-rich.					nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
SPG7	6687	broad.mit.edu	37	16	89595935	89595935	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89595935A>G	uc002fnj.2	+	6	830	c.809A>G	c.(808-810)TAT>TGT	p.Y270C	SPG7_uc002fni.2_Missense_Mutation_p.Y270C	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	270	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)														---	---	---	---
RPL13	6137	broad.mit.edu	37	16	89628783	89628783	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89628783T>C	uc002fnm.1	+	5	512	c.461T>C	c.(460-462)GTC>GCC	p.V154A	RPL13_uc010vpj.1_Missense_Mutation_p.V107A|RPL13_uc002fnn.1_Missense_Mutation_p.V154A|RPL13_uc002fno.1_3'UTR	NM_000977	NP_000968	P26373	RL13_HUMAN	ribosomal protein L13	154					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic ribosome	protein binding|RNA binding|structural constituent of ribosome				0		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)														---	---	---	---
CPNE7	27132	broad.mit.edu	37	16	89651201	89651201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89651201A>G	uc002fnp.2	+	7	882	c.752A>G	c.(751-753)GAC>GGC	p.D251G	CPNE7_uc002fnq.2_Missense_Mutation_p.D176G	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	251	C2 2.				lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)														---	---	---	---
SPIRE2	84501	broad.mit.edu	37	16	89936085	89936085	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89936085C>A	uc002foz.1	+	14	1969	c.1917C>A	c.(1915-1917)ATC>ATA	p.I639I	SPIRE2_uc010ciw.1_Intron|SPIRE2_uc002fpa.1_Silent_p.I591I|SPIRE2_uc010cix.1_Silent_p.I506I	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	spire homolog 2	639					transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)														---	---	---	---
GEMIN4	50628	broad.mit.edu	37	17	650567	650567	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:650567G>A	uc002frs.1	-	2	835	c.716C>T	c.(715-717)GCG>GTG	p.A239V	GEMIN4_uc010vqa.1_Intron	NM_015721	NP_056536	P57678	GEMI4_HUMAN	gemin 4	239					rRNA processing|spliceosomal snRNP assembly	Cajal body|cytosol|nucleolus|small nuclear ribonucleoprotein complex|spliceosomal complex	protein binding			ovary(2)|kidney(1)|skin(1)	4		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)														---	---	---	---
INPP5K	51763	broad.mit.edu	37	17	1401248	1401248	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1401248G>A	uc002fsr.2	-	8	1334	c.945C>T	c.(943-945)TCC>TCT	p.S315S	INPP5K_uc002fss.2_Silent_p.S239S|INPP5K_uc002fsq.2_Silent_p.S239S|INPP5K_uc010cjr.2_Silent_p.S239S|INPP5K_uc010vql.1_Silent_p.S223S|INPP5K_uc010vqm.1_Silent_p.S219S	NM_016532	NP_057616	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K isoform	315	Catalytic (Potential).		S -> F (in a breast cancer sample; somatic mutation).		actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0																		---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1840618	1840618	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1840618G>A	uc002ftp.2	-	2	517	c.498C>T	c.(496-498)GAC>GAT	p.D166D		NM_178568	NP_848663	Q86UN2	R4RL1_HUMAN	reticulon 4 receptor-like 1 precursor	166	LRR 5.				axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
DPH1	1801	broad.mit.edu	37	17	1943624	1943624	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1943624A>G	uc002fts.2	+	8	895	c.877A>G	c.(877-879)ATT>GTT	p.I293V	DPH1_uc002ftr.1_RNA|DPH1_uc002ftt.2_Missense_Mutation_p.I277V|DPH1_uc010cjx.2_Missense_Mutation_p.I153V|DPH1_uc010vqs.1_Missense_Mutation_p.I303V|DPH1_uc002ftu.2_Missense_Mutation_p.I49V|DPH1_uc002ftv.2_Missense_Mutation_p.I49V|DPH1_uc002ftw.2_Missense_Mutation_p.I21V|OVCA2_uc002ftx.2_5'Flank	NM_001383	NP_001374	Q9BZG8	DPH1_HUMAN	diptheria toxin resistance protein required for	293					peptidyl-diphthamide biosynthetic process from peptidyl-histidine|translation	cytoplasm|nucleus				pancreas(1)	1																		---	---	---	---
KIAA0664	23277	broad.mit.edu	37	17	2604715	2604715	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2604715C>T	uc002fuy.1	-	6	816	c.730G>A	c.(730-732)GCC>ACC	p.A244T	KIAA0664_uc002fux.1_Missense_Mutation_p.A176T	NM_015229	NP_056044	O75153	K0664_HUMAN	hypothetical protein LOC23277	244							binding			breast(2)	2																		---	---	---	---
CTNS	1497	broad.mit.edu	37	17	3563925	3563925	+	3'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3563925G>A	uc002fwb.2	+	12					CTNS_uc002fwa.2_Missense_Mutation_p.R367H|CTNS_uc010ckj.2_Missense_Mutation_p.R367H|CTNS_uc010vrv.1_3'UTR|CTNS_uc010vrw.1_Missense_Mutation_p.R259H	NM_004937	NP_004928			cystinosin isoform 2						ATP metabolic process|brain development|cognition|glutathione metabolic process	integral to membrane|late endosome|lysosomal membrane	L-cystine transmembrane transporter activity				0				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)													---	---	---	---
GP1BA	2811	broad.mit.edu	37	17	4836049	4836049	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4836049C>T	uc010vsq.1	+	2	225	c.150C>T	c.(148-150)ACC>ACT	p.T50T	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	50											0																		---	---	---	---
ENO3	2027	broad.mit.edu	37	17	4860157	4860157	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4860157G>A	uc002gab.3	+	11	1302	c.1208G>A	c.(1207-1209)CGT>CAT	p.R403H	ENO3_uc002gac.3_Missense_Mutation_p.R403H|ENO3_uc010vss.1_Missense_Mutation_p.R360H|ENO3_uc010vst.1_Missense_Mutation_p.R230H	NM_053013	NP_443739	P13929	ENOB_HUMAN	enolase 3	403					gluconeogenesis|glycolysis	phosphopyruvate hydratase complex	magnesium ion binding|phosphopyruvate hydratase activity			ovary(1)	1																OREG0024110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AIPL1	23746	broad.mit.edu	37	17	6328807	6328807	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6328807C>T	uc002gcp.2	-	6	1223	c.1128G>A	c.(1126-1128)CCG>CCA	p.P376P	AIPL1_uc002gcq.2_Silent_p.P316P|AIPL1_uc002gcr.2_Silent_p.P313P|AIPL1_uc010clk.2_Silent_p.P354P|AIPL1_uc010cll.2_Silent_p.P352P|AIPL1_uc002gcs.2_3'UTR	NM_014336	NP_055151	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting	376					protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
PITPNM3	83394	broad.mit.edu	37	17	6374530	6374530	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6374530G>A	uc002gdd.3	-	12	1726	c.1575C>T	c.(1573-1575)AGC>AGT	p.S525S	PITPNM3_uc010cln.2_Silent_p.S489S|PITPNM3_uc010clm.2_Silent_p.S8S|PITPNM3_uc002gdc.3_Silent_p.S116S	NM_031220	NP_112497	Q9BZ71	PITM3_HUMAN	PITPNM family member 3 isoform 1	525	DDHD.				phosphatidylinositol metabolic process	endomembrane system|integral to membrane	calcium ion binding|lipid binding|phosphatidylinositol transporter activity|receptor tyrosine kinase binding			ovary(2)|central_nervous_system(2)	4				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)														---	---	---	---
ALOX12	239	broad.mit.edu	37	17	6900144	6900144	+	Splice_Site	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6900144G>T	uc002gdx.3	+	2	189	c.136_splice	c.e2-1	p.E46_splice		NM_000697	NP_000688			arachidonate 12-lipoxygenase						anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
CLDN7	1366	broad.mit.edu	37	17	7163686	7163686	+	3'UTR	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7163686T>A	uc002gfm.3	-	4					CLDN7_uc010cmc.2_3'UTR|CLDN7_uc002gfn.3_3'UTR	NM_001307	NP_001298			claudin 7						calcium-independent cell-cell adhesion	integral to membrane|lateral plasma membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1																		---	---	---	---
NEURL4	84461	broad.mit.edu	37	17	7226362	7226362	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7226362C>T	uc002gga.1	-	15	2505	c.2498G>A	c.(2497-2499)CGC>CAC	p.R833H	NEURL4_uc002ggb.1_Missense_Mutation_p.R833H|NEURL4_uc002ggc.1_Missense_Mutation_p.R179H	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	833	NHR 4.						protein binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
NEURL4	84461	broad.mit.edu	37	17	7230149	7230149	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7230149C>T	uc002gga.1	-	4	980	c.973G>A	c.(973-975)GGG>AGG	p.G325R	NEURL4_uc002ggb.1_Missense_Mutation_p.G325R|NEURL4_uc002ggc.1_5'UTR	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	325	NHR 2.						protein binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
C17orf61	254863	broad.mit.edu	37	17	7306516	7306516	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7306516G>A	uc002ggs.2	-	4	226	c.211C>T	c.(211-213)CTA>TTA	p.L71L	PLSCR3_uc002ggr.1_Intron|PLSCR3_uc010cmg.1_Intron	NM_152766	NP_689979	Q8N2U0	CQ061_HUMAN	hypothetical protein LOC254863 precursor	71	Helical; (Potential).					integral to membrane				ovary(1)	1		Prostate(122;0.173)																---	---	---	---
SOX15	6665	broad.mit.edu	37	17	7492633	7492633	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7492633C>T	uc002ghy.1	-	2	510	c.362G>A	c.(361-363)CGG>CAG	p.R121Q	MPDU1_uc010vuc.1_Intron|SOX15_uc002ghz.1_Missense_Mutation_p.R121Q	NM_006942	NP_008873	O60248	SOX15_HUMAN	SRY-box 15	121					chromatin organization|male gonad development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1																OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7696146	7696146	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7696146G>A	uc002giu.1	+	46	7331	c.7317G>A	c.(7315-7317)TCG>TCA	p.S2439S		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	2439	AAA 3 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
CNTROB	116840	broad.mit.edu	37	17	7842978	7842978	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7842978C>T	uc002gjq.2	+	9	1994	c.1075C>T	c.(1075-1077)CGG>TGG	p.R359W	CNTROB_uc002gjp.2_Missense_Mutation_p.R359W|CNTROB_uc002gjr.2_Missense_Mutation_p.R261W|CNTROB_uc010vum.1_Missense_Mutation_p.R71W	NM_053051	NP_444279	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	359	Potential.				centriole replication|centrosome separation|cytokinesis	centriole	protein domain specific binding			breast(1)|central_nervous_system(1)	2		Prostate(122;0.173)																---	---	---	---
GUCY2D	3000	broad.mit.edu	37	17	7918376	7918376	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7918376T>C	uc002gjt.2	+							NM_000180	NP_000171			guanylate cyclase 2D, membrane (retina-specific)						intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			skin(1)	1		Prostate(122;0.157)																---	---	---	---
PFAS	5198	broad.mit.edu	37	17	8158437	8158437	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8158437G>A	uc002gkr.2	+	4	512	c.371G>A	c.(370-372)CGC>CAC	p.R124H	PFAS_uc010vuv.1_5'UTR	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	124					'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
PFAS	5198	broad.mit.edu	37	17	8168866	8168866	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8168866C>T	uc002gkr.2	+						PFAS_uc010vuv.1_Intron|PFAS_uc002gks.2_5'Flank	NM_012393	NP_036525			phosphoribosylformylglycinamidine synthase						'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
CCDC42	146849	broad.mit.edu	37	17	8638817	8638817	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8638817C>T	uc002gln.2	-	5	832	c.605G>A	c.(604-606)CGG>CAG	p.R202Q	CCDC42_uc002glo.2_Intron	NM_144681	NP_653282	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42 isoform 1	202	Potential.			Missing (in Ref. 2; AAH29224).						ovary(1)	1																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9460797	9460797	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9460797C>T	uc002glx.2	-	3	316	c.166G>A	c.(166-168)GCC>ACC	p.A56T		NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8	56	Cytoplasmic (Potential).|Potential.				transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
USP43	124739	broad.mit.edu	37	17	9632312	9632312	+	3'UTR	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9632312G>T	uc010cod.2	+	15					USP43_uc002gma.3_3'UTR|USP43_uc010vva.1_3'UTR|USP43_uc010coe.2_3'UTR|USP43_uc002gmc.3_3'UTR	NM_153210	NP_694942			ubiquitin specific protease 43						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																OREG0024168	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GLP2R	9340	broad.mit.edu	37	17	9791276	9791276	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9791276T>G	uc002gmd.1	+	12	1312	c.1312T>G	c.(1312-1314)TTT>GTT	p.F438V		NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor	438	Helical; Name=7; (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				lung(2)|ovary(1)	3					Glucagon recombinant(DB00040)													---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10209899	10209899	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10209899G>T	uc002gmk.1	-	37	5433	c.5343C>A	c.(5341-5343)GCC>GCA	p.A1781A		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1781	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6																		---	---	---	---
MYH1	4619	broad.mit.edu	37	17	10397659	10397659	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10397659T>C	uc002gmo.2	-						uc002gml.1_Intron	NM_005963	NP_005954			myosin, heavy chain 1, skeletal muscle, adult							muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21																		---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10432326	10432326	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10432326C>T	uc010coi.2	-	27	3553	c.3425G>A	c.(3424-3426)CGC>CAC	p.R1142H	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.R1142H|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1142	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11603195	11603195	+	Missense_Mutation	SNP	G	A	A	rs140721719		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11603195G>A	uc002gne.2	+	23	5088	c.5020G>A	c.(5020-5022)GGG>AGG	p.G1674R	DNAH9_uc010coo.2_Missense_Mutation_p.G968R	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1674	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	p.G1674W(1)		skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
HS3ST3B1	9953	broad.mit.edu	37	17	14204958	14204958	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14204958C>T	uc002goh.1	+	1	453	c.123C>T	c.(121-123)TGC>TGT	p.C41C	MGC12916_uc010vvv.1_5'Flank	NM_006041	NP_006032	Q9Y662	HS3SB_HUMAN	heparan sulfate D-glucosaminyl	41	Helical; Signal-anchor for type II membrane protein; (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	Golgi membrane|integral to plasma membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)														---	---	---	---
TEKT3	64518	broad.mit.edu	37	17	15207315	15207315	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15207315C>T	uc002gon.2	-	9	1598	c.1411G>A	c.(1411-1413)GAA>AAA	p.E471K		NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3	471					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)														---	---	---	---
FAM83G	644815	broad.mit.edu	37	17	18880964	18880964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18880964C>T	uc002guw.2	-	5	2182	c.2015G>A	c.(2014-2016)CGG>CAG	p.R672Q	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	672										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MAPK7	5598	broad.mit.edu	37	17	19284208	19284208	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19284208C>T	uc002gvn.2	+	4	1072	c.686C>T	c.(685-687)GCG>GTG	p.A229V	B9D1_uc010cqm.1_5'Flank|B9D1_uc002gvl.3_5'Flank|MAPK7_uc002gvo.2_Missense_Mutation_p.A90V|MAPK7_uc002gvq.2_Missense_Mutation_p.A229V|MAPK7_uc002gvp.2_Missense_Mutation_p.A229V	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	229	Necessary for oligomerization (By similarity).|Protein kinase.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)																	---	---	---	---
SLC47A1	55244	broad.mit.edu	37	17	19470501	19470501	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19470501C>T	uc002gvy.1	+	14	1355	c.1269C>T	c.(1267-1269)ATC>ATT	p.I423I	SLC47A1_uc002gvx.2_Silent_p.I423I|SLC47A1_uc010vyz.1_Silent_p.I400I|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Silent_p.I228I|SLC47A1_uc010vza.1_Silent_p.I135I|SLC47A1_uc010vzb.1_Silent_p.I157I|SLC47A1_uc010vzc.1_Silent_p.I95I	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1	423	Helical; (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)																	---	---	---	---
ALDH3A2	224	broad.mit.edu	37	17	19561065	19561065	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19561065A>G	uc002gwb.1	+	5	909	c.688A>G	c.(688-690)ACC>GCC	p.T230A	ALDH3A2_uc002gwa.1_Missense_Mutation_p.T230A|ALDH3A2_uc010cqr.1_Missense_Mutation_p.T37A|ALDH3A2_uc002gwc.1_Missense_Mutation_p.T230A|ALDH3A2_uc002gwd.1_Missense_Mutation_p.T37A	NM_000382	NP_000373	P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3A2 isoform 2	230	Cytoplasmic.				cellular aldehyde metabolic process|central nervous system development|epidermis development|lipid metabolic process|peripheral nervous system development	endoplasmic reticulum membrane|integral to membrane	3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(2)	2	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)				NADH(DB00157)													---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21319798	21319798	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319798G>A	uc002gyv.1	+	3	1849	c.1144G>A	c.(1144-1146)GCC>ACC	p.A382T		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	382	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25919610	25919610	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25919610C>T	uc010crg.2	+	9	1291	c.846C>T	c.(844-846)GCC>GCT	p.A282A	KSR1_uc002gzj.1_RNA|KSR1_uc002gzm.2_Silent_p.A83A	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras	417					Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
TNFAIP1	7126	broad.mit.edu	37	17	26667419	26667419	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26667419A>G	uc002hax.1	+	3	309	c.290A>G	c.(289-291)AAC>AGC	p.N97S	TNFAIP1_uc002hay.2_Missense_Mutation_p.N97S|TNFAIP1_uc010waf.1_5'UTR	NM_021137	NP_066960	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1	97					apoptosis|cell migration|DNA replication|embryo development|immune response|negative regulation of Rho protein signal transduction|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|endosome|nucleus|voltage-gated potassium channel complex	GTP-Rho binding|voltage-gated potassium channel activity				0	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)														---	---	---	---
PIPOX	51268	broad.mit.edu	37	17	27382105	27382105	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27382105G>A	uc002hdr.1	+	6	1158	c.832G>A	c.(832-834)GCA>ACA	p.A278T		NM_016518	NP_057602	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	278					tetrahydrofolate metabolic process	peroxisome	L-pipecolate oxidase activity|sarcosine oxidase activity				0	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)													---	---	---	---
SSH2	85464	broad.mit.edu	37	17	27959504	27959504	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27959504C>T	uc002heo.1	-	15	2627	c.2627G>A	c.(2626-2628)CGC>CAC	p.R876H	SSH2_uc010wbh.1_Missense_Mutation_p.R903H	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	876					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	30986201	30986201	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30986201G>A	uc002hho.1	-	17	2289	c.2277C>T	c.(2275-2277)CAC>CAT	p.H759H	MYO1D_uc002hhp.1_Silent_p.H759H	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	759						myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)													OREG0024311	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZNF830	91603	broad.mit.edu	37	17	33289637	33289637	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33289637G>T	uc002hih.3	+	1	1089	c.1052G>T	c.(1051-1053)AGC>ATC	p.S351I	CCT6B_uc002hig.2_5'Flank|CCT6B_uc010ctg.2_5'Flank|CCT6B_uc010wcc.1_5'Flank	NM_052857	NP_443089	Q96NB3	ZN830_HUMAN	coiled-coil domain containing 16	351					cell division|mitosis	cytoplasm|nucleus	metal ion binding			breast(1)	1		Ovarian(249;0.17)																---	---	---	---
SLFN5	162394	broad.mit.edu	37	17	33591663	33591663	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33591663G>A	uc002hjf.3	+	4	1717	c.1600G>A	c.(1600-1602)GTG>ATG	p.V534M	SLFN5_uc010wcg.1_Intron	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5	534					cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)														---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34858967	34858967	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34858967C>T	uc010wcy.1	-	22	3042	c.2050G>A	c.(2050-2052)GAC>AAC	p.D684N	MYO19_uc002hmw.2_Missense_Mutation_p.D484N|MYO19_uc010cuu.2_RNA	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	684	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35956338	35956338	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35956338G>A	uc002hoa.2	-	3	255	c.172C>T	c.(172-174)CCT>TCT	p.P58S	SYNRG_uc010wde.1_Missense_Mutation_p.P58S|SYNRG_uc010wdf.1_Missense_Mutation_p.P58S|SYNRG_uc002hoc.2_Missense_Mutation_p.P57S|SYNRG_uc002hoe.2_Missense_Mutation_p.P58S|SYNRG_uc002hod.2_Missense_Mutation_p.P58S|SYNRG_uc010wdg.1_Missense_Mutation_p.P58S|SYNRG_uc002hob.2_Missense_Mutation_p.P58S|SYNRG_uc002hog.1_Missense_Mutation_p.P91S|SYNRG_uc010wdh.1_Missense_Mutation_p.P58S	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	58					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
STAC2	342667	broad.mit.edu	37	17	37374387	37374387	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37374387G>T	uc002hrs.2	-	2	349	c.130C>A	c.(130-132)CTC>ATC	p.L44I	STAC2_uc010cvt.2_5'UTR	NM_198993	NP_945344	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	44					intracellular signal transduction		metal ion binding			pancreas(1)	1																		---	---	---	---
RARA	5914	broad.mit.edu	37	17	38510579	38510579	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38510579C>T	uc002huk.1	+	7	1288	c.833C>T	c.(832-834)ACG>ATG	p.T278M	RARA_uc002hul.3_Missense_Mutation_p.T278M|RARA_uc010wfe.1_Missense_Mutation_p.T181M|RARA_uc002hun.1_Missense_Mutation_p.T273M	NM_000964	NP_000955	P10276	RARA_HUMAN	retinoic acid receptor, alpha isoform 1	278	Ligand-binding.				apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)			T	PML|ZNF145|TIF1|NUMA1|NPM1	APL								---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38635953	38635953	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38635953C>T	uc010cxb.2	-	10	2047	c.1883G>A	c.(1882-1884)GGC>GAC	p.G628D	TNS4_uc002huu.3_Intron	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	628	Phosphatase tensin-type.				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)															---	---	---	---
KRT25	147183	broad.mit.edu	37	17	38907525	38907525	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38907525G>A	uc002hve.2	-	4	784	c.723C>T	c.(721-723)AAC>AAT	p.N241N		NM_181534	NP_853512	Q7Z3Z0	K1C25_HUMAN	keratin 25	241	Rod.|Linker 12.					cytoplasm|intermediate filament	structural molecule activity			ovary(2)	2		Breast(137;0.00526)																---	---	---	---
KRT17	3872	broad.mit.edu	37	17	39777084	39777084	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39777084G>A	uc002hxh.2	-	6	1129	c.1008C>T	c.(1006-1008)TGC>TGT	p.C336C	JUP_uc010wfs.1_Intron	NM_000422	NP_000413	Q04695	K1C17_HUMAN	keratin 17	336	Peptide epitope S4; induces T-cell and keratinocyte proliferation and IFN-gamma production.|Coil 2.|Rod.			C->A: No significant effect on T-cell proliferation but reduces IFN-gamma production when part of the altered peptide epitope S2.	epidermis development	cytoplasm|intermediate filament	protein binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2		Breast(137;0.000307)												Steatocystoma_Multiplex				---	---	---	---
GAST	2520	broad.mit.edu	37	17	39872102	39872102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39872102G>A	uc002hxl.2	+	3	316	c.284G>A	c.(283-285)CGC>CAC	p.R95H	JUP_uc010wfs.1_Intron	NM_000805	NP_000796	P01350	GAST_HUMAN	gastrin preproprotein	95		Cleavage.				extracellular region	hormone activity				0		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)															---	---	---	---
KLHL11	55175	broad.mit.edu	37	17	40011152	40011152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40011152C>T	uc002hyf.1	-	2	973	c.967G>A	c.(967-969)GCT>ACT	p.A323T		NM_018143	NP_060613	Q9NVR0	KLH11_HUMAN	kelch-like 11 precursor	323						extracellular region					0		Breast(137;0.00156)																---	---	---	---
NBR1	4077	broad.mit.edu	37	17	41362085	41362085	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41362085C>T	uc010czd.2	+	21	3033	c.2893C>T	c.(2893-2895)CGC>TGC	p.R965C	NBR1_uc010diz.2_Missense_Mutation_p.R965C|NBR1_uc010whv.1_Missense_Mutation_p.R965C|NBR1_uc010whw.1_3'UTR|TMEM106A_uc002idn.1_5'Flank|TMEM106A_uc010why.1_5'Flank|TMEM106A_uc010cze.1_5'Flank|TMEM106A_uc010whz.1_5'Flank	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	965					macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)														---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41585277	41585277	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41585277T>A	uc002idu.1	+	15	2283	c.2210T>A	c.(2209-2211)ATC>AAC	p.I737N	DHX8_uc010wif.1_Missense_Mutation_p.I646N|DHX8_uc010wig.1_Missense_Mutation_p.I737N	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	737	Helicase ATP-binding.					catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)														---	---	---	---
GRN	2896	broad.mit.edu	37	17	42429756	42429756	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42429756C>A	uc002igp.1	+	12	1680	c.1461C>A	c.(1459-1461)ACC>ACA	p.T487T	GRN_uc002igr.1_Silent_p.T281T	NM_002087	NP_002078	P28799	GRN_HUMAN	granulin precursor	487					signal transduction	extracellular space	cytokine activity|growth factor activity			ovary(2)|central_nervous_system(2)|skin(1)	5		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
FZD2	2535	broad.mit.edu	37	17	42636232	42636232	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42636232G>T	uc002igx.1	+	1	1308	c.1176G>T	c.(1174-1176)CAG>CAT	p.Q392H		NM_001466	NP_001457	Q14332	FZD2_HUMAN	frizzled 2 precursor	392	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|positive regulation of cGMP metabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42828496	42828496	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42828496A>G	uc002ihf.2	+	14	1936	c.1723A>G	c.(1723-1725)ACC>GCC	p.T575A	DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	575					cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
PLEKHM1	9842	broad.mit.edu	37	17	43545960	43545960	+	Splice_Site	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43545960C>A	uc002ija.2	-	5	1094	c.924_splice	c.e5-1	p.E308_splice	PLEKHM1_uc010wjm.1_Splice_Site_p.E280_splice|PLEKHM1_uc002ijb.2_Intron|PLEKHM1_uc010wjn.1_Splice_Site_p.E257_splice	NM_014798	NP_055613			pleckstrin homology domain containing, family M						intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)																	---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44109047	44109047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44109047C>T	uc002ikb.2	-	14	3198	c.3113G>A	c.(3112-3114)CGG>CAG	p.R1038Q	KIAA1267_uc002ikc.2_Missense_Mutation_p.R1038Q|KIAA1267_uc002ikd.2_Missense_Mutation_p.R1038Q|KIAA1267_uc010dav.2_Missense_Mutation_p.R1037Q|KIAA1267_uc010wkb.1_Missense_Mutation_p.R369Q|KIAA1267_uc010wkc.1_Missense_Mutation_p.R306Q	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	1038						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
ITGB3	3690	broad.mit.edu	37	17	45387554	45387554	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45387554C>T	uc002ilj.2	+	15	2371	c.2351C>T	c.(2350-2352)ACG>ATG	p.T784M	ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor	784	Cytoplasmic (Potential).				activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)													---	---	---	---
C17orf57	124989	broad.mit.edu	37	17	45421651	45421651	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45421651A>G	uc002iln.2	+	7	838	c.427A>G	c.(427-429)ATT>GTT	p.I143V	ITGB3_uc010wkr.1_RNA|C17orf57_uc002ilm.2_Missense_Mutation_p.I143V|C17orf57_uc002ill.1_5'UTR|C17orf57_uc010daz.1_Missense_Mutation_p.I143V	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	143							calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TBKBP1	9755	broad.mit.edu	37	17	45773469	45773469	+	5'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45773469G>A	uc002ilu.2	+	1						NM_014726	NP_055541			TBK1 binding protein 1						innate immune response						0																		---	---	---	---
CBX1	10951	broad.mit.edu	37	17	46152450	46152450	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46152450G>A	uc002ind.3	-	4	812	c.331C>T	c.(331-333)CGA>TGA	p.R111*	CBX1_uc002ine.3_Nonsense_Mutation_p.R111*	NM_006807	NP_006798	P83916	CBX1_HUMAN	heterochromatin protein 1-beta	111						nuclear heterochromatin|nucleoplasm|spindle	chromatin binding|enzyme binding				0																		---	---	---	---
PPP1R9B	84687	broad.mit.edu	37	17	48216811	48216811	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48216811C>T	uc002iqh.3	-	8	2005	c.2002G>A	c.(2002-2004)GTG>ATG	p.V668M		NM_032595	NP_115984	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	666	Potential.|Interacts with TGN38 (By similarity).				cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0																		---	---	---	---
COL1A1	1277	broad.mit.edu	37	17	48264049	48264049	+	Missense_Mutation	SNP	C	T	T	rs148216434		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48264049C>T	uc002iqm.2	-	48	3892	c.3766G>A	c.(3766-3768)GCC>ACC	p.A1256T		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	1256	Fibrillar collagen NC1.				axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						---	---	---	---
KIF2B	84643	broad.mit.edu	37	17	51901756	51901756	+	Silent	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51901756A>C	uc002iua.2	+	1	1518	c.1362A>C	c.(1360-1362)GGA>GGC	p.G454G	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	454	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8																		---	---	---	---
AKAP1	8165	broad.mit.edu	37	17	55183383	55183383	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55183383C>T	uc002iux.2	+	2	789	c.558C>T	c.(556-558)CCC>CCT	p.P186P	AKAP1_uc010wnl.1_Silent_p.P186P|AKAP1_uc002iuy.2_RNA|AKAP1_uc010dcm.2_Silent_p.P186P	NM_003488	NP_003479	Q92667	AKAP1_HUMAN	A-kinase anchor protein 1 precursor	186					blood coagulation	cytosol|integral to membrane|mitochondrial outer membrane	protein binding|RNA binding			ovary(1)	1	Breast(9;5.46e-08)																	---	---	---	---
SUPT4H1	6827	broad.mit.edu	37	17	56428826	56428826	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56428826G>A	uc002iwe.1	-	2	180	c.113C>T	c.(112-114)GCA>GTA	p.A38V	uc010dct.1_Intron|uc010dcu.1_Intron|uc002ivz.2_Intron|uc010dcv.1_Intron|uc002iwa.2_Intron|uc002iwb.2_Intron|uc002iwc.2_Intron|SUPT4H1_uc002iwd.1_RNA	NM_003168	NP_003159	P63272	SPT4H_HUMAN	suppressor of Ty 4 homolog 1	38	Interaction with SUPT5H.				chromatin remodeling|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56700329	56700329	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56700329G>A	uc010dcz.1	-	4	414	c.296C>T	c.(295-297)TCG>TTG	p.S99L	TEX14_uc002iwr.1_Missense_Mutation_p.S99L|TEX14_uc002iws.1_Missense_Mutation_p.S99L|TEX14_uc010dda.1_5'UTR	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	99	ANK 3.					cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57148316	57148316	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57148316A>G	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207			tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													Mulibrey_Nanism				---	---	---	---
USP32	84669	broad.mit.edu	37	17	58313587	58313587	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58313587C>T	uc002iyo.1	-	12	1437	c.1151G>A	c.(1150-1152)CGA>CAA	p.R384Q	USP32_uc002iyn.1_Missense_Mutation_p.R54Q	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	384	DUSP.				protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)															---	---	---	---
MRC2	9902	broad.mit.edu	37	17	60743471	60743471	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60743471G>T	uc002jad.2	+	3	939	c.537G>T	c.(535-537)CAG>CAT	p.Q179H	MRC2_uc002jac.2_Missense_Mutation_p.Q179H	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	179	Extracellular (Potential).				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61432392	61432392	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61432392C>T	uc002jal.3	+	12	2024	c.2001C>T	c.(1999-2001)GGC>GGT	p.G667G	TANC2_uc010wpe.1_Silent_p.G577G|TANC2_uc002jam.1_Silent_p.G34G	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	667							binding			ovary(2)	2																		---	---	---	---
KCNH6	81033	broad.mit.edu	37	17	61611655	61611655	+	Missense_Mutation	SNP	C	T	T	rs141581333		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61611655C>T	uc002jay.2	+	5	1164	c.1084C>T	c.(1084-1086)CGC>TGC	p.R362C	KCNH6_uc002jax.1_Missense_Mutation_p.R362C|KCNH6_uc010wpl.1_Missense_Mutation_p.R239C|KCNH6_uc010wpm.1_Missense_Mutation_p.R362C|KCNH6_uc002jaz.1_Missense_Mutation_p.R362C	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,	362	Extracellular (Potential).				regulation of transcription, DNA-dependent|signal transduction					skin(1)	1					Ibutilide(DB00308)													---	---	---	---
CSH1	1442	broad.mit.edu	37	17	61972785	61972785	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61972785C>T	uc002jcs.1	-						CSH2_uc002jck.2_Intron|CSH1_uc002jcp.1_Silent_p.S129S|CSH1_uc002jcq.1_Intron|CSH1_uc002jcr.1_3'UTR|CSH1_uc002jct.1_Intron|CSH1_uc002jcu.1_Silent_p.S168S|CSH1_uc002jcv.1_Intron|CSH1_uc002jcw.2_Intron|CSH1_uc002jcy.2_3'UTR	NM_001317	NP_001308			chorionic somatomammotropin hormone 1 isoform 1						female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding			skin(1)	1														Russell-Silver_syndrome				---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63534429	63534429	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63534429G>A	uc002jfi.2	-	5	1381	c.1092C>T	c.(1090-1092)CCC>CCT	p.P364P	AXIN2_uc010den.1_Silent_p.P364P|AXIN2_uc002jfh.2_Silent_p.P364P	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2	364	Interaction with GSK3B (By similarity).				cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
NOL11	25926	broad.mit.edu	37	17	65734379	65734379	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65734379C>T	uc002jgd.1	+	14	1674	c.1671C>T	c.(1669-1671)TGC>TGT	p.C557C	NOL11_uc010wql.1_Silent_p.C375C|NOL11_uc010deu.1_Silent_p.C152C|SNORA38B_uc010dev.2_5'Flank	NM_015462	NP_056277	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	557						nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67247919	67247919	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67247919G>A	uc002jif.2	-	34	5722	c.4504C>T	c.(4504-4506)CGA>TGA	p.R1502*	ABCA5_uc002jib.2_Nonsense_Mutation_p.R468*|ABCA5_uc002jic.2_Nonsense_Mutation_p.R725*|ABCA5_uc002jid.2_Nonsense_Mutation_p.R419*|ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Nonsense_Mutation_p.R1502*	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	1502	ABC transporter 2.				cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
CDC42EP4	23580	broad.mit.edu	37	17	71282342	71282342	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71282342G>A	uc002jjn.2	-	2	445	c.298C>T	c.(298-300)CGT>TGT	p.R100C	CDC42EP4_uc002jjo.2_Missense_Mutation_p.R100C|CDC42EP4_uc002jjp.1_Intron	NM_012121	NP_036253	Q9H3Q1	BORG4_HUMAN	Cdc42 effector protein 4	100					positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|cytoplasm|endomembrane system|membrane|microtubule cytoskeleton	GTP-Rho binding				0			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)															---	---	---	---
BTBD17	388419	broad.mit.edu	37	17	72356219	72356219	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72356219C>T	uc002jkn.2	-	2	251	c.251G>A	c.(250-252)CGC>CAC	p.R84H		NM_001080466	NP_001073935	A6NE02	BTBDH_HUMAN	BTB (POZ) domain containing 17 precursor	84	BTB.					extracellular region					0																		---	---	---	---
TMEM104	54868	broad.mit.edu	37	17	72832524	72832524	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72832524C>T	uc002jls.3	+	10	1351	c.1189C>T	c.(1189-1191)CGC>TGC	p.R397C	TMEM104_uc010wrf.1_Intron|TMEM104_uc010wrg.1_Intron|TMEM104_uc010dfx.2_Missense_Mutation_p.R397C	NM_017728	NP_060198	Q8NE00	TM104_HUMAN	transmembrane protein 104	397	Cytoplasmic (Potential).					integral to membrane					0	all_lung(278;0.23)																	---	---	---	---
KIAA0195	9772	broad.mit.edu	37	17	73491456	73491456	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73491456C>A	uc002jnz.3	+	21	3095	c.2820C>A	c.(2818-2820)CCC>CCA	p.P940P	KIAA0195_uc010wsa.1_Silent_p.P950P|KIAA0195_uc010wsb.1_Silent_p.P580P|KIAA0195_uc002job.3_5'Flank	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	940					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73726548	73726548	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73726548T>C	uc002jpg.2	+	8	1152	c.965T>C	c.(964-966)ATC>ACC	p.I322T	ITGB4_uc002jph.2_Missense_Mutation_p.I322T|ITGB4_uc010dgo.2_Missense_Mutation_p.I322T|ITGB4_uc002jpi.3_Missense_Mutation_p.I322T|ITGB4_uc010dgp.1_Missense_Mutation_p.I322T|ITGB4_uc002jpj.2_Missense_Mutation_p.I322T|ITGB4_uc010wsh.1_5'Flank	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	322	VWFA.|Extracellular (Potential).				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
UNC13D	201294	broad.mit.edu	37	17	73836152	73836152	+	Missense_Mutation	SNP	C	T	T	rs141499220		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73836152C>T	uc002jpp.2	-	11	1278	c.898G>A	c.(898-900)GTG>ATG	p.V300M	UNC13D_uc010wsk.1_Missense_Mutation_p.V300M|UNC13D_uc002jpq.1_Translation_Start_Site|UNC13D_uc010dgq.1_Missense_Mutation_p.V97M	NM_199242	NP_954712	Q70J99	UN13D_HUMAN	unc-13 homolog D	300	Interaction with RAB27A.				positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
AANAT	15	broad.mit.edu	37	17	74465003	74465003	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74465003C>T	uc002jro.2	+						AANAT_uc010wte.1_Intron	NM_001088	NP_001079			arylalkylamine N-acetyltransferase						circadian rhythm|melatonin biosynthetic process	cytosol	aralkylamine N-acetyltransferase activity				0																		---	---	---	---
RHBDF2	79651	broad.mit.edu	37	17	74471195	74471195	+	Missense_Mutation	SNP	C	T	T	rs140426459		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74471195C>T	uc002jrq.1	-	10	1524	c.1231G>A	c.(1231-1233)GTC>ATC	p.V411I	RHBDF2_uc002jrp.1_Missense_Mutation_p.V382I|RHBDF2_uc002jrr.1_Missense_Mutation_p.V263I|RHBDF2_uc010wtf.1_Missense_Mutation_p.V382I	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	411	Helical; (Potential).				negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0																		---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76045833	76045833	+	Silent	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76045833A>T	uc002jud.2	+	4	1290	c.690A>T	c.(688-690)GGA>GGT	p.G230G	TNRC6C_uc002juf.2_Silent_p.G230G|TNRC6C_uc002jue.2_Silent_p.G230G	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2	230	Sufficient for interaction with argonaute family proteins.|Gly-rich.				gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76475624	76475624	+	IGR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76475624G>A								DNAH17 (6768 upstream) : CYTH1 (194507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	76481768	76481768	+	IGR	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76481768C>T								DNAH17 (12912 upstream) : CYTH1 (188363 downstream)																																			---	---	---	---
ENGASE	64772	broad.mit.edu	37	17	77076456	77076456	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77076456C>A	uc002jwv.2	+						ENGASE_uc002jwu.1_Intron|ENGASE_uc010wtz.1_Intron|ENGASE_uc002jww.2_Intron	NM_001042573	NP_001036038			endo-beta-N-acetylglucosaminidase							cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1																		---	---	---	---
ENPP7	339221	broad.mit.edu	37	17	77709059	77709059	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77709059G>A	uc002jxa.2	+	3	637	c.617G>A	c.(616-618)GGC>GAC	p.G206D		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	206					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)															---	---	---	---
SLC26A11	284129	broad.mit.edu	37	17	78219973	78219973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78219973C>T	uc002jyb.1	+	12	1387	c.1118C>T	c.(1117-1119)TCG>TTG	p.S373L	SLC26A11_uc002jyc.1_Missense_Mutation_p.S373L|SLC26A11_uc002jyd.1_Missense_Mutation_p.S373L|SLC26A11_uc010dhv.1_Missense_Mutation_p.S373L	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	373	Cytoplasmic (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
SLC26A11	284129	broad.mit.edu	37	17	78223059	78223059	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78223059C>T	uc002jyb.1	+	16	1898	c.1629C>T	c.(1627-1629)GGC>GGT	p.G543G	SLC26A11_uc002jyc.1_Silent_p.G543G|SLC26A11_uc002jyd.1_Silent_p.G543G|SLC26A11_uc010dhv.1_Silent_p.G543G	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	543	Extracellular (Potential).|STAS.					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
ACTG1	71	broad.mit.edu	37	17	79478631	79478631	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79478631T>C	uc002kaj.1	-	3	410	c.385A>G	c.(385-387)ACC>GCC	p.T129A	ACTG1_uc002kah.1_Missense_Mutation_p.T7A|ACTG1_uc002kai.1_Missense_Mutation_p.T86A|ACTG1_uc002kak.1_Missense_Mutation_p.T129A|ACTG1_uc010wun.1_Missense_Mutation_p.T129A|ACTG1_uc002kal.1_Missense_Mutation_p.T129A|ACTG1_uc002kag.2_RNA	NM_001614	NP_001605	P63261	ACTG_HUMAN	actin, gamma 1 propeptide	129					adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)															---	---	---	---
P4HB	5034	broad.mit.edu	37	17	79803084	79803084	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79803084C>T	uc002kbn.1	-	10	1579	c.1382G>A	c.(1381-1383)CGC>CAC	p.R461H	P4HB_uc002kbl.1_Missense_Mutation_p.R138H|P4HB_uc002kbm.1_Missense_Mutation_p.R138H	NM_000918	NP_000909	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta subunit precursor	461	Thioredoxin 2.	Lowers pKa of C-terminal Cys of second active site (By similarity).			cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline	cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane	electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)															---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80137043	80137043	+	Missense_Mutation	SNP	C	T	T	rs140732712	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80137043C>T	uc002kdz.1	-	10	1589	c.1234G>A	c.(1234-1236)GCA>ACA	p.A412T	CCDC57_uc002kdx.1_Missense_Mutation_p.A412T|CCDC57_uc010dik.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	412	Potential.									ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80559377	80559377	+	3'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80559377G>A	uc002kfn.2	+	9					FOXK2_uc010diu.2_3'UTR|FOXK2_uc002kfo.2_RNA|FOXK2_uc002kfp.2_RNA	NM_004514	NP_004505			forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80851443	80851443	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80851443T>C	uc002kfz.2	+	17	1714	c.1584T>C	c.(1582-1584)ATT>ATC	p.I528I	TBCD_uc002kfx.1_Silent_p.I511I|TBCD_uc002kfy.1_Silent_p.I528I|TBCD_uc002kgb.1_5'Flank	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D	528					'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
ARHGAP28	79822	broad.mit.edu	37	18	6868145	6868145	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6868145G>A	uc010wzi.1	+						ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron					SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)																---	---	---	---
LRRC30	339291	broad.mit.edu	37	18	7231535	7231535	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7231535G>A	uc010wzk.1	+	1	399	c.399G>A	c.(397-399)CCG>CCA	p.P133P		NM_001105581	NP_001099051	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	133	LRR 3.									ovary(1)|liver(1)	2																		---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8069951	8069951	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8069951G>A	uc002knn.3	+	8	1903	c.1400G>A	c.(1399-1401)CGG>CAG	p.R467Q	PTPRM_uc010dkv.2_Missense_Mutation_p.R467Q|PTPRM_uc010wzl.1_Missense_Mutation_p.R254Q	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	467	Fibronectin type-III 2.|Extracellular (Potential).				homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9517296	9517296	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9517296T>C	uc002kob.2	+	3	921	c.698T>C	c.(697-699)GTA>GCA	p.V233A	RALBP1_uc002koc.2_Missense_Mutation_p.V233A	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1	233	Rho-GAP.				chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9522233	9522233	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9522233C>G	uc002kob.2	+	4	1002	c.779C>G	c.(778-780)CCT>CGT	p.P260R	RALBP1_uc002koc.2_Missense_Mutation_p.P260R	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1	260	Rho-GAP.				chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
APCDD1	147495	broad.mit.edu	37	18	10487683	10487683	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10487683T>C	uc002kom.3	+	5	1547	c.1193T>C	c.(1192-1194)GTG>GCG	p.V398A		NM_153000	NP_694545	Q8J025	APCD1_HUMAN	adenomatosis polyposis coli down-regulated 1	398	Extracellular (Potential).				hair follicle development|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to plasma membrane	Wnt-protein binding				0				READ - Rectum adenocarcinoma(15;0.08)														---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21140294	21140294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21140294G>A	uc002kum.3	-	6	1056	c.782C>T	c.(781-783)ACG>ATG	p.T261M	NPC1_uc010xaz.1_Missense_Mutation_p.T45M|NPC1_uc010xba.1_Missense_Mutation_p.T106M	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	261					autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21660872	21660872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21660872G>A	uc002kuw.2	+	5	1236	c.784G>A	c.(784-786)GAA>AAA	p.E262K	TTC39C_uc002kuu.2_Missense_Mutation_p.E201K	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1	262				E -> V (in Ref. 1; BAC03578).			binding			ovary(1)	1																		---	---	---	---
OSBPL1A	114876	broad.mit.edu	37	18	21819282	21819282	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21819282G>A	uc002kve.2	-	16	1520	c.1346C>T	c.(1345-1347)ACG>ATG	p.T449M	OSBPL1A_uc002kvd.2_Translation_Start_Site|OSBPL1A_uc010xbc.1_Missense_Mutation_p.T67M|OSBPL1A_uc002kvf.3_Missense_Mutation_p.T229M	NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B	449	Potential.				cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)																	---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22804990	22804990	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22804990G>A	uc002kvk.2	-	4	3139	c.2892C>T	c.(2890-2892)TGC>TGT	p.C964C	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Silent_p.C964C|ZNF521_uc002kvl.2_Silent_p.C744C	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	964	C2H2-type 23.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22902066	22902066	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22902066T>C	uc002kvk.2	-	3	373	c.126A>G	c.(124-126)GAA>GAG	p.E42E	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Silent_p.E42E|ZNF521_uc002kvl.2_5'UTR	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	42					cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29793504	29793504	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29793504G>T	uc002kxj.3	+	11	1608	c.1561G>T	c.(1561-1563)GAC>TAC	p.D521Y		NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor	521	Extracellular (Potential).|MATH.				digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31326246	31326246	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31326246A>G	uc010dmg.1	+	12	6489	c.6434A>G	c.(6433-6435)CAG>CGG	p.Q2145R	ASXL3_uc002kxq.2_Missense_Mutation_p.Q1852R	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	2145					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
GALNT1	2589	broad.mit.edu	37	18	33234679	33234679	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33234679T>C	uc010dmu.2	+	2	106	c.53T>C	c.(52-54)GTA>GCA	p.V18A	GALNT1_uc002kyz.3_5'UTR|GALNT1_uc002kza.2_Missense_Mutation_p.V18A|GALNT1_uc002kzb.2_Missense_Mutation_p.V18A	NM_020474	NP_065207	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	18	Helical; Signal-anchor for type II membrane protein; (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34340700	34340700	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34340700G>A	uc002kzt.1	+	22	4076	c.3979G>A	c.(3979-3981)GCC>ACC	p.A1327T	FHOD3_uc002kzs.1_Missense_Mutation_p.A1344T|FHOD3_uc010dmz.1_Missense_Mutation_p.A1059T|FHOD3_uc010dnb.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1327					actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47527645	47527645	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47527645C>T	uc002leb.2	-	5	880	c.592G>A	c.(592-594)GCA>ACA	p.A198T	MYO5B_uc002lec.1_Missense_Mutation_p.A197T	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	198	Myosin head-like.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
C18orf54	162681	broad.mit.edu	37	18	51888144	51888144	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51888144T>C	uc002lfn.3	+	3	531	c.415T>C	c.(415-417)TAT>CAT	p.Y139H	C18orf54_uc002lfo.3_Missense_Mutation_p.Y139H	NM_173529	NP_775800	Q8IYD9	CR054_HUMAN	hypothetical protein LOC162681 precursor	139						extracellular region				ovary(1)|skin(1)	2				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)														---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54285276	54285276	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54285276G>A	uc002lgg.2	-	4	700	c.451C>T	c.(451-453)CGA>TGA	p.R151*	TXNL1_uc010xdz.1_RNA|TXNL1_uc002lgh.2_RNA|TXNL1_uc002lgi.2_Nonsense_Mutation_p.R151*|TXNL1_uc002lgj.1_Nonsense_Mutation_p.R151*	NM_004786	NP_004777	O43396	TXNL1_HUMAN	thioredoxin-like 1	151	PITH.				cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54591218	54591218	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54591218C>T	uc002lgk.1	+	22	3803	c.3592C>T	c.(3592-3594)CGA>TGA	p.R1198*	WDR7_uc002lgl.1_Nonsense_Mutation_p.R1165*	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	1198										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
FECH	2235	broad.mit.edu	37	18	55240503	55240503	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55240503C>A	uc002lgq.3	-	3	406	c.289G>T	c.(289-291)GAC>TAC	p.D97Y	FECH_uc002lgp.3_Missense_Mutation_p.D103Y|FECH_uc002lgr.3_5'UTR	NM_000140	NP_000131	P22830	HEMH_HUMAN	ferrochelatase isoform b precursor	97					generation of precursor metabolites and energy|heme biosynthetic process|protoporphyrinogen IX metabolic process|response to light stimulus	mitochondrial inner membrane|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferrochelatase activity|ferrous iron binding|protein binding			central_nervous_system(1)	1		Colorectal(73;0.227)																---	---	---	---
ALPK2	115701	broad.mit.edu	37	18	56182221	56182221	+	Intron	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56182221T>G	uc002lhj.3	-							NM_052947	NP_443179			heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																		---	---	---	---
ALPK2	115701	broad.mit.edu	37	18	56246770	56246770	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56246770C>A	uc002lhj.3	-	4	1452	c.1238G>T	c.(1237-1239)AGG>ATG	p.R413M		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	413							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZNF532	55205	broad.mit.edu	37	18	56587560	56587560	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56587560A>T	uc002lho.2	+	4	2588	c.2041A>T	c.(2041-2043)ATT>TTT	p.I681F	ZNF532_uc002lhp.2_Missense_Mutation_p.I679F|ZNF532_uc010xeg.1_Missense_Mutation_p.I679F|ZNF532_uc002lhr.2_Missense_Mutation_p.I679F|ZNF532_uc002lhs.2_Missense_Mutation_p.I679F	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	681					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
PIGN	23556	broad.mit.edu	37	18	59780533	59780533	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59780533T>A	uc002lii.3	-	17	1716	c.1268A>T	c.(1267-1269)GAG>GTG	p.E423V	PIGN_uc002lij.3_Missense_Mutation_p.E423V	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	423	Lumenal (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)																---	---	---	---
VPS4B	9525	broad.mit.edu	37	18	61067303	61067303	+	Silent	SNP	C	T	T	rs146071226		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61067303C>T	uc002lix.2	-	7	1028	c.768G>A	c.(766-768)ACG>ACA	p.T256T	VPS4B_uc010dpx.2_Silent_p.T256T|VPS4B_uc010dpy.2_Silent_p.T138T|VPS4B_uc010dpz.1_Silent_p.T138T	NM_004869	NP_004860	O75351	VPS4B_HUMAN	vacuolar protein sorting factor 4B	256					cell cycle|cell division|cellular membrane organization|endosome to lysosome transport via multivesicular body sorting pathway|intracellular cholesterol transport|protein transport|response to lipid	cytosol|early endosome|late endosome membrane|lysosome|nucleus|vacuolar membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding			ovary(1)	1																		---	---	---	---
SOCS6	9306	broad.mit.edu	37	18	67992809	67992809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67992809C>T	uc002lkr.1	+	2	1221	c.905C>T	c.(904-906)GCG>GTG	p.A302V	SOCS6_uc010dqq.2_Missense_Mutation_p.A302V	NM_004232	NP_004223	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	302					defense response|JAK-STAT cascade|negative regulation of signal transduction|regulation of growth	cytoplasm				large_intestine(1)|lung(1)	2		Esophageal squamous(42;0.129)|Colorectal(73;0.152)																---	---	---	---
FBXO15	201456	broad.mit.edu	37	18	71791731	71791731	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71791731C>T	uc002lle.2	-	7	1096	c.760G>A	c.(760-762)GCT>ACT	p.A254T	FBXO15_uc002llf.2_Missense_Mutation_p.A330T	NM_152676	NP_689889	Q8NCQ5	FBX15_HUMAN	F-box protein 15 isoform 1	254										ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)														---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	72999512	72999512	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72999512A>G	uc002lly.2	+	2	2578	c.2015A>G	c.(2014-2016)GAG>GGG	p.E672G		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	717						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77134003	77134003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77134003C>T	uc002lmx.2	+	28	3190	c.3176C>T	c.(3175-3177)GCG>GTG	p.A1059V	ATP9B_uc002lmw.1_Missense_Mutation_p.A1059V|ATP9B_uc002lna.2_Missense_Mutation_p.A85V|ATP9B_uc002lnb.1_3'UTR|ATP9B_uc010drb.2_RNA	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	1059	Helical; (Potential).				ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
PPAP2C	8612	broad.mit.edu	37	19	288052	288052	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:288052C>T	uc002loi.2	-	2	271	c.172G>A	c.(172-174)GCT>ACT	p.A58T	PPAP2C_uc002loh.2_Missense_Mutation_p.A79T|PPAP2C_uc002loj.2_Missense_Mutation_p.A2T	NM_003712	NP_003703	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C isoform 1	58	Helical; (Potential).				sphingolipid metabolic process	integral to membrane|plasma membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
AZU1	566	broad.mit.edu	37	19	829655	829655	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:829655C>T	uc002lpz.1	+	3	325	c.309C>T	c.(307-309)AGC>AGT	p.S103S		NM_001700	NP_001691	P20160	CAP7_HUMAN	azurocidin 1 preproprotein	103	Peptidase S1.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cellular extravasation|defense response to Gram-negative bacterium|glial cell migration|induction of positive chemotaxis|inflammatory response|macrophage chemotaxis|microglial cell activation|monocyte activation|positive regulation of cell adhesion|positive regulation of fractalkine biosynthetic process|positive regulation of interleukin-1 beta biosynthetic process|positive regulation of MHC class II biosynthetic process|positive regulation of phagocytosis|positive regulation of tumor necrosis factor biosynthetic process|proteolysis|regulation of vascular permeability	azurophil granule|extracellular region	heparin binding|serine-type endopeptidase activity|toxin binding			pancreas(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ARID3A	1820	broad.mit.edu	37	19	971946	971946	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:971946G>A	uc002lql.2	+	9	1953	c.1663G>A	c.(1663-1665)GGC>AGC	p.G555S		NM_005224	NP_005215	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT- like)	555	Gly-rich.|Important for cytoplasmic localization (By similarity).					cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ABCA7	10347	broad.mit.edu	37	19	1043194	1043194	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1043194A>G	uc002lqw.3	+	8	965	c.734A>G	c.(733-735)GAC>GGC	p.D245G	ABCA7_uc010dsb.1_Missense_Mutation_p.D107G	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	245	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ABCA7	10347	broad.mit.edu	37	19	1061839	1061839	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1061839C>T	uc002lqw.3	+	41	5753	c.5522C>T	c.(5521-5523)ACG>ATG	p.T1841M	ABCA7_uc002lqy.2_Missense_Mutation_p.T294M|ABCA7_uc010dsc.2_RNA	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1841	ABC transporter 2.				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GPX4	2879	broad.mit.edu	37	19	1106408	1106408	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1106408G>A	uc010xgg.1	+	7	618	c.511G>A	c.(511-513)GAC>AAC	p.D171N	GPX4_uc010xgh.1_Missense_Mutation_p.R178Q|GPX4_uc010xgi.1_Missense_Mutation_p.D208N	NM_002085	NP_002076	P36969	GPX4_HUMAN	glutathione peroxidase 4 isoform A precursor	171					multicellular organismal development|phospholipid metabolic process		glutathione peroxidase activity|phospholipid-hydroperoxide glutathione peroxidase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Glutathione(DB00143)													---	---	---	---
MEX3D	399664	broad.mit.edu	37	19	1555360	1555360	+	3'UTR	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1555360G>A	uc010dsn.2	-	2						NM_203304	NP_976049			ring finger and KH domain containing 1						mRNA destabilization|posttranscriptional regulation of gene expression by mRNA localization|regulation of anti-apoptosis	nucleus|perinuclear region of cytoplasm	AU-rich element binding|zinc ion binding			lung(1)	1		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
UQCR11	10975	broad.mit.edu	37	19	1599523	1599523	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1599523G>A	uc002ltm.2	-	2	110	c.87C>T	c.(85-87)GCC>GCT	p.A29A		NM_006830	NP_006821	O14957	QCR10_HUMAN	ubiquinol-cytochrome c reductase, 6.4kDa	29	Helical; (Potential).				respiratory electron transport chain	integral to membrane|mitochondrial inner membrane|respiratory chain	electron carrier activity			ovary(1)|breast(1)	2																		---	---	---	---
ATP8B3	148229	broad.mit.edu	37	19	1800316	1800316	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1800316C>T	uc002ltw.2	-	13	1519	c.1285G>A	c.(1285-1287)GTC>ATC	p.V429I	ATP8B3_uc002ltv.2_Missense_Mutation_p.V382I|ATP8B3_uc002ltx.2_RNA|ATP8B3_uc002lty.1_Missense_Mutation_p.V177I|ATP8B3_uc002ltz.1_Missense_Mutation_p.V376I	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3	429	Extracellular (Potential).				ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF555	148254	broad.mit.edu	37	19	2853855	2853855	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2853855C>T	uc002lwo.2	+	4	1881	c.1792C>T	c.(1792-1794)CAT>TAT	p.H598Y	ZNF555_uc002lwn.3_Missense_Mutation_p.H597Y	NM_152791	NP_690004	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	598					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF77	58492	broad.mit.edu	37	19	2934642	2934642	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2934642C>A	uc002lws.3	-	4	614	c.483G>T	c.(481-483)CAG>CAT	p.Q161H		NM_021217	NP_067040	Q15935	ZNF77_HUMAN	zinc finger protein 77	161					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TBXA2R	6915	broad.mit.edu	37	19	3595792	3595792	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3595792A>T	uc002lyg.1	-	3	1140	c.926T>A	c.(925-927)ATC>AAC	p.I309N	TBXA2R_uc002lye.1_Nonsense_Mutation_p.Y179*	NM_001060	NP_001051	P21731	TA2R_HUMAN	thromboxane A2 receptor isoform alpha	309	Helical; Name=7; (Potential).				platelet activation	integral to plasma membrane	guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)													---	---	---	---
EEF2	1938	broad.mit.edu	37	19	3981333	3981333	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3981333G>A	uc002lze.2	-							NM_001961	NP_001952			eukaryotic translation elongation factor 2							cytosol|ribonucleoprotein complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SH3GL1	6455	broad.mit.edu	37	19	4361765	4361765	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4361765C>T	uc002maj.2	-	10	1045	c.939G>A	c.(937-939)GCG>GCA	p.A313A	SH3GL1_uc002mak.2_Silent_p.A249A|SH3GL1_uc010xig.1_Silent_p.A265A	NM_003025	NP_003016	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	313	SH3.				central nervous system development|endocytosis|signal transduction	early endosome membrane	lipid binding|protein binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)				T	MLL	AL								---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5207961	5207961	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5207961G>A	uc002mbv.2	-	37	5984	c.5750C>T	c.(5749-5751)ACC>ATC	p.T1917I	PTPRS_uc002mbu.1_Missense_Mutation_p.T1486I|PTPRS_uc010xin.1_Missense_Mutation_p.T1459I|PTPRS_uc002mbw.2_Missense_Mutation_p.T1879I|PTPRS_uc002mbx.2_Missense_Mutation_p.T1474I|PTPRS_uc002mby.2_Missense_Mutation_p.T1470I	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1917	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5273534	5273534	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5273534G>A	uc002mbv.2	-	4	532	c.298C>T	c.(298-300)CGG>TGG	p.R100W	PTPRS_uc002mbu.1_Missense_Mutation_p.R100W|PTPRS_uc010xin.1_Missense_Mutation_p.R100W|PTPRS_uc002mbw.2_Missense_Mutation_p.R100W|PTPRS_uc002mbx.2_Missense_Mutation_p.R100W|PTPRS_uc002mby.2_Missense_Mutation_p.R100W|PTPRS_uc002mbz.1_Missense_Mutation_p.R100W	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	100	Ig-like C2-type 1.|Extracellular (Potential).				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
LONP1	9361	broad.mit.edu	37	19	5699145	5699145	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5699145G>A	uc002mcx.2	-	10	1611	c.1578C>T	c.(1576-1578)GGC>GGT	p.G526G	LONP1_uc002mcy.2_Silent_p.G462G|LONP1_uc010duh.2_Silent_p.G267G|LONP1_uc010dui.2_Silent_p.G510G|LONP1_uc002mcz.2_Silent_p.G330G	NM_004793	NP_004784	P36776	LONM_HUMAN	mitochondrial lon peptidase 1 precursor	526	ATP (By similarity).				cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding				0																		---	---	---	---
FUT6	2528	broad.mit.edu	37	19	5831922	5831922	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5831922G>A	uc002mdf.1	-	4	1183	c.657C>T	c.(655-657)GAC>GAT	p.D219D	FUT6_uc002mdg.1_Silent_p.D219D|FUT6_uc002mdh.1_Silent_p.D219D|FUT6_uc010dul.1_Silent_p.D219D	NM_001040701	NP_001035791	P51993	FUT6_HUMAN	fucosyltransferase 6	219	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity|alpha(1,3)-fucosyltransferase activity				0																		---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6418523	6418523	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6418523G>A	uc002mer.3	-	9	960	c.850C>T	c.(850-852)CGC>TGC	p.R284C		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	284	Gly-rich.|KH 2.				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																		---	---	---	---
PEX11G	92960	broad.mit.edu	37	19	7550735	7550735	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7550735G>T	uc002mgk.1	-	2	247	c.238C>A	c.(238-240)CTG>ATG	p.L80M	PEX11G_uc002mgl.1_Missense_Mutation_p.L10M	NM_080662	NP_542393	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	80	Cytoplasmic (Potential).					integral to membrane|peroxisomal membrane					0																		---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7671278	7671278	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7671278C>T	uc002mgv.3	+	3	625	c.524C>T	c.(523-525)ACG>ATG	p.T175M	KIAA1543_uc002mgu.3_Missense_Mutation_p.T175M	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	175	CH.				epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
XAB2	56949	broad.mit.edu	37	19	7686169	7686169	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7686169G>A	uc002mgx.2	-	13	1658	c.1632C>T	c.(1630-1632)GGC>GGT	p.G544G		NM_020196	NP_064581	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	544	HAT 11.				transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4													Direct_reversal_of_damage|NER					---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8587343	8587343	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8587343G>A	uc002mkg.2	-	27	3252	c.3138C>T	c.(3136-3138)TGC>TGT	p.C1046C		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	1046	SH3.					unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9073746	9073746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9073746G>A	uc002mkp.2	-	3	13904	c.13700C>T	c.(13699-13701)CCA>CTA	p.P4567L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4569	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
ZNF426	79088	broad.mit.edu	37	19	9645941	9645941	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9645941C>A	uc002mlq.2	-	4	304	c.40G>T	c.(40-42)GGG>TGG	p.G14W	ZNF426_uc010dws.2_Intron	NM_024106	NP_077011	Q9BUY5	ZN426_HUMAN	zinc finger protein 426	14					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10265344	10265344	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10265344C>T	uc002mng.2	-	20	1882	c.1702G>A	c.(1702-1704)GGG>AGG	p.G568R	DNMT1_uc010xlc.1_Missense_Mutation_p.G584R|DNMT1_uc002mnh.2_Missense_Mutation_p.G463R|DNMT1_uc010xld.1_Missense_Mutation_p.G568R	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	568	Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
ICAM3	3385	broad.mit.edu	37	19	10446450	10446450	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10446450G>A	uc002mob.2	-	3	601	c.546C>T	c.(544-546)GAC>GAT	p.D182D	RAVER1_uc002moa.2_5'Flank|ICAM3_uc010dxd.1_Silent_p.D105D|ICAM3_uc010xlf.1_Silent_p.D105D	NM_002162	NP_002153	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3 precursor	182	Extracellular (Potential).|Ig-like C2-type 2.				cell-cell adhesion|regulation of immune response	integral to plasma membrane	integrin binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)															---	---	---	---
KRI1	65095	broad.mit.edu	37	19	10670030	10670030	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10670030C>T	uc002moy.1	-						KRI1_uc002mow.1_Intron|KRI1_uc002mox.1_Intron	NM_023008	NP_075384			KRI1 homolog											ovary(1)	1			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)															---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11942786	11942786	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11942786T>C	uc002msp.1	+	4	951	c.795T>C	c.(793-795)TTT>TTC	p.F265F		NM_152357	NP_689570	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	265	C2H2-type 5; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF20	7568	broad.mit.edu	37	19	12243769	12243769	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12243769C>T	uc002mtf.1	-	4	1375	c.1232G>A	c.(1231-1233)CGT>CAT	p.R411H	ZNF20_uc002mte.1_Missense_Mutation_p.R376H|ZNF20_uc002mtg.1_Missense_Mutation_p.R411H	NM_021143	NP_066966	P17024	ZNF20_HUMAN	zinc finger protein 20	411	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF625	90589	broad.mit.edu	37	19	12256820	12256820	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12256820A>G	uc002mth.2	-	4	563	c.213T>C	c.(211-213)TGT>TGC	p.C71C	ZNF20_uc002mtg.1_Intron|ZNF625_uc010dyn.1_RNA|ZNF625_uc010dyo.1_Silent_p.C105C	NM_145233	NP_660276	Q96I27	ZN625_HUMAN	zinc finger protein 625	71	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
NACC1	112939	broad.mit.edu	37	19	13249172	13249172	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13249172C>A	uc002mwm.2	+	6	1704	c.1536C>A	c.(1534-1536)ACC>ACA	p.T512T		NM_052876	NP_443108	Q96RE7	NACC1_HUMAN	transcriptional repressor NAC1	512					negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization|transcription, DNA-dependent	cytoplasm|nuclear body					0																		---	---	---	---
ZSWIM4	65249	broad.mit.edu	37	19	13941704	13941704	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13941704G>T	uc002mxh.1	+	13	2999	c.2810G>T	c.(2809-2811)CGG>CTG	p.R937L	ZSWIM4_uc010xng.1_Missense_Mutation_p.R860L	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	937							zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)															---	---	---	---
TECR	9524	broad.mit.edu	37	19	14674656	14674656	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14674656G>A	uc002mza.2	+	5	335	c.208G>A	c.(208-210)GTG>ATG	p.V70M	TECR_uc002mzb.2_Missense_Mutation_p.V85M|TECR_uc010xns.1_Translation_Start_Site|TECR_uc002mzc.2_Translation_Start_Site|TECR_uc002mzd.2_Missense_Mutation_p.V70M|TECR_uc002mze.2_5'Flank|TECR_uc002mzf.1_5'Flank	NM_138501	NP_612510	Q9NZ01	TECR_HUMAN	glycoprotein, synaptic 2	70					fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17038858	17038858	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17038858C>T	uc002nfb.2	-	25	3504	c.3472G>A	c.(3472-3474)GCC>ACC	p.A1158T		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1111						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
ANKLE1	126549	broad.mit.edu	37	19	17396576	17396576	+	Silent	SNP	C	T	T	rs143586031	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17396576C>T	uc002nga.2	+	8	1899	c.1623C>T	c.(1621-1623)CAC>CAT	p.H541H	ANKLE1_uc010xpm.1_RNA|ANKLE1_uc010eao.1_Silent_p.H537H|ANKLE1_uc010xpn.1_Intron|ANKLE1_uc002nfy.2_Silent_p.H504H|ANKLE1_uc002nfz.2_Silent_p.H247H	NM_152363	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat domain 41	541						nuclear envelope					0																		---	---	---	---
ANO8	57719	broad.mit.edu	37	19	17444362	17444362	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17444362G>A	uc002ngf.2	-	3	378	c.219C>T	c.(217-219)GAC>GAT	p.D73D	ANO8_uc010eap.2_RNA|GTPBP3_uc010xpo.1_5'Flank	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8	73	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(3)	3																		---	---	---	---
SLC27A1	376497	broad.mit.edu	37	19	17599652	17599652	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17599652T>C	uc002ngu.1	+						SLC27A1_uc002ngt.1_Intron|SLC27A1_uc010xpp.1_Intron	NM_198580	NP_940982			solute carrier family 27, member 1						cardiolipin biosynthetic process|fatty acid metabolic process|long-chain fatty acid transport|negative regulation of phospholipid biosynthetic process|phosphatidic acid biosynthetic process|phosphatidylcholine biosynthetic process|phosphatidylethanolamine biosynthetic process|phosphatidylinositol biosynthetic process|phosphatidylserine biosynthetic process|transmembrane transport	endomembrane system|integral to membrane	fatty acid transporter activity|nucleotide binding				0																		---	---	---	---
PDE4C	5143	broad.mit.edu	37	19	18329227	18329227	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18329227C>T	uc010xqc.1	-	10	1627	c.1147G>A	c.(1147-1149)GCC>ACC	p.A383T	PDE4C_uc002nik.3_Missense_Mutation_p.A383T|PDE4C_uc002nil.3_Missense_Mutation_p.A383T|PDE4C_uc002nif.3_Missense_Mutation_p.A152T|PDE4C_uc002nig.3_Intron|PDE4C_uc002nih.3_Missense_Mutation_p.A153T|PDE4C_uc010ebk.2_Missense_Mutation_p.A277T|PDE4C_uc002nii.3_Missense_Mutation_p.A351T|PDE4C_uc010ebl.2_Missense_Mutation_p.A97T|PDE4C_uc010xqd.1_Missense_Mutation_p.A152T	NM_001098819	NP_001092289	Q08493	PDE4C_HUMAN	phosphodiesterase 4C isoform PDE4C-2	383					signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|skin(2)|central_nervous_system(1)	5					Dyphylline(DB00651)													---	---	---	---
CRLF1	9244	broad.mit.edu	37	19	18707592	18707592	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18707592G>A	uc010ebt.1	-	6	1058	c.864C>T	c.(862-864)GAC>GAT	p.D288D		NM_004750	NP_004741	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1 precursor	288	Fibronectin type-III 2.				negative regulation of neuron apoptosis|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	cytokine binding|protein heterodimerization activity|receptor activity			central_nervous_system(1)	1																		---	---	---	---
UPF1	5976	broad.mit.edu	37	19	18956816	18956816	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18956816G>A	uc002nkg.2	+	2	534	c.259G>A	c.(259-261)GGG>AGG	p.G87R	UPF1_uc002nkf.2_Missense_Mutation_p.G87R	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1	87	Sufficient for interaction with RENT2.				cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19752682	19752682	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19752682C>T	uc002nnd.2	-						GMIP_uc010xrb.1_Intron|GMIP_uc010xrc.1_Intron	NM_016573	NP_057657			GEM interacting protein						negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
ATP13A1	57130	broad.mit.edu	37	19	19762565	19762565	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19762565G>A	uc002nnh.3	-	17	2296	c.2268C>T	c.(2266-2268)CAC>CAT	p.H756H	ATP13A1_uc002nne.2_Translation_Start_Site|ATP13A1_uc002nnf.3_Silent_p.H124H|ATP13A1_uc002nng.2_Silent_p.H638H	NM_020410	NP_065143	Q9HD20	AT131_HUMAN	ATPase type 13A1	756	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(3)|large_intestine(2)|central_nervous_system(1)	6																		---	---	---	---
ZNF101	94039	broad.mit.edu	37	19	19790858	19790858	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19790858C>T	uc002nni.1	+	4	1170	c.1060C>T	c.(1060-1062)CGA>TGA	p.R354*	ZNF101_uc010ecg.1_Nonsense_Mutation_p.R234*|ZNF101_uc002nnj.1_Nonsense_Mutation_p.R234*	NM_033204	NP_149981	Q8IZC7	ZN101_HUMAN	zinc finger protein 101	354	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF208	7757	broad.mit.edu	37	19	22154850	22154850	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22154850T>C	uc002nqp.2	-	6	2751	c.2602A>G	c.(2602-2604)ACT>GCT	p.T868A	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)																---	---	---	---
PLEKHF1	79156	broad.mit.edu	37	19	30164905	30164905	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30164905C>T	uc002nsh.3	+	2	261	c.159C>T	c.(157-159)CGC>CGT	p.R53R	PLEKHF1_uc002nsi.3_Silent_p.R138R	NM_024310	NP_077286	Q96S99	PKHF1_HUMAN	apoptosis-inducing protein D	53	PH.				apoptosis	lysosome|nucleus|perinuclear region of cytoplasm	metal ion binding				0	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)															---	---	---	---
ZNF507	22847	broad.mit.edu	37	19	32845353	32845353	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32845353G>A	uc002nte.2	+	3	1889	c.1617G>A	c.(1615-1617)GCG>GCA	p.A539A	ZNF507_uc002ntc.2_Silent_p.A539A|ZNF507_uc010xrn.1_Silent_p.A539A|ZNF507_uc002ntd.2_Silent_p.A539A	NM_001136156	NP_001129628	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	539					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)																	---	---	---	---
C19orf40	91442	broad.mit.edu	37	19	33464211	33464211	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33464211C>T	uc002nud.3	+						CCDC123_uc002nty.2_5'Flank|CCDC123_uc010edg.2_5'Flank|CCDC123_uc002ntz.1_5'Flank|CCDC123_uc002nua.2_5'Flank|CCDC123_uc002nuc.1_5'Flank	NM_152266	NP_689479			Fanconi anemia-associated protein, 24 kDa						DNA repair	Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding				0	Esophageal squamous(110;0.137)												Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks					---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33878397	33878397	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33878397G>A	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron|PEPD_uc002nuq.3_Intron	NM_000285	NP_000276			prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)																	---	---	---	---
LSM14A	26065	broad.mit.edu	37	19	34706019	34706019	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34706019T>C	uc002nvb.3	+						LSM14A_uc002nva.3_Intron|LSM14A_uc010xru.1_Intron|LSM14A_uc002nvc.3_Intron	NM_001114093	NP_001107565			LSM14 homolog A isoform a						cytoplasmic mRNA processing body assembly|multicellular organismal development|regulation of translation	cytoplasmic mRNA processing body|intracellular membrane-bounded organelle|stress granule				skin(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
ZNF599	148103	broad.mit.edu	37	19	35250976	35250976	+	Nonsense_Mutation	SNP	G	A	A	rs137997147		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35250976G>A	uc010edn.1	-	4	1118	c.730C>T	c.(730-732)CGA>TGA	p.R244*	ZNF599_uc010edm.1_Nonsense_Mutation_p.R207*	NM_001007248	NP_001007249	Q96NL3	ZN599_HUMAN	zinc finger protein 599	244	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)															---	---	---	---
FAM187B	148109	broad.mit.edu	37	19	35718977	35718977	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35718977C>T	uc002nyk.1	-	1	652	c.607G>A	c.(607-609)GTC>ATC	p.V203I		NM_152481	NP_689694	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	203	Extracellular (Potential).					integral to membrane				ovary(2)	2																		---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36228979	36228979	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36228979C>T	uc010eei.2	+	37	7759	c.7759C>T	c.(7759-7761)CGA>TGA	p.R2587*		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	2587	SET.	S-adenosyl-L-methionine (By similarity).			chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
NPHS1	4868	broad.mit.edu	37	19	36336669	36336669	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36336669G>A	uc002oby.2	-	13	1659	c.1659C>T	c.(1657-1659)AAC>AAT	p.N553N		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	553	Ig-like C2-type 6.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)|skin(1)	5	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
NFKBID	84807	broad.mit.edu	37	19	36381296	36381296	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36381296G>A	uc002oci.1	-	10	1277	c.703C>T	c.(703-705)CGG>TGG	p.R235W	NFKBID_uc002och.1_Missense_Mutation_p.R72W|NFKBID_uc002ocj.1_Missense_Mutation_p.R250W	NM_139239	NP_640332	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene	235	ANK 5.				inflammatory response	nucleus					0																		---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36595577	36595577	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36595577G>A	uc002odc.2	+	31	4387	c.4296G>A	c.(4294-4296)GTG>GTA	p.V1432V	WDR62_uc002odd.2_Silent_p.V1437V	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	1432					cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF829	374899	broad.mit.edu	37	19	37383218	37383218	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37383218T>C	uc002ofa.1	-	6	837	c.475A>G	c.(475-477)AAG>GAG	p.K159E	ZNF345_uc002oez.2_Intron	NM_001037232	NP_001032309	Q3KNS6	ZN829_HUMAN	zinc finger protein 829	159	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38572964	38572964	+	Silent	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38572964C>G	uc002ohk.2	+	3	1268	c.759C>G	c.(757-759)GGC>GGG	p.G253G		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	253					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38655190	38655190	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38655190C>T	uc002ohk.2	+	15	4361	c.3852C>T	c.(3850-3852)GAC>GAT	p.D1284D		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1284					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38948798	38948798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38948798C>T	uc002oit.2	+	18	2163	c.2033C>T	c.(2032-2034)GCC>GTC	p.A678V	RYR1_uc002oiu.2_Missense_Mutation_p.A678V	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	678	Cytoplasmic.|B30.2/SPRY 1.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
LGALS7	3963	broad.mit.edu	37	19	39262623	39262623	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39262623G>A	uc002oje.3	-	3	168	c.143C>T	c.(142-144)GCG>GTG	p.A48V		NM_002307	NP_002298	P47929	LEG7_HUMAN	galectin-7	48	Galectin.				apoptosis|heterophilic cell-cell adhesion	cytoplasm|extracellular space|nucleus	sugar binding				0	all_cancers(60;1.96e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
SAMD4B	55095	broad.mit.edu	37	19	39868424	39868424	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39868424C>T	uc002olb.2	+	10	2439	c.1404C>T	c.(1402-1404)GAC>GAT	p.D468D	SAMD4B_uc002ola.2_Silent_p.D468D	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	468							protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)															---	---	---	---
DYRK1B	9149	broad.mit.edu	37	19	40318985	40318985	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40318985G>A	uc002omj.2	-	6	1039	c.759C>T	c.(757-759)AGC>AGT	p.S253S	DYRK1B_uc002omi.2_Silent_p.S253S|DYRK1B_uc002omk.2_Silent_p.S253S	NM_004714	NP_004705	Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	253	Protein kinase.				positive regulation of transcription, DNA-dependent	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|transcription coactivator activity			ovary(4)|stomach(1)|central_nervous_system(1)|skin(1)	7	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)															---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40423980	40423980	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40423980G>A	uc002omp.3	-	4	2231	c.2223C>T	c.(2221-2223)TGC>TGT	p.C741C		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	741	Cys-rich.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40424430	40424430	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40424430C>A	uc002omp.3	-	4	1781	c.1773G>T	c.(1771-1773)TGG>TGT	p.W591C		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	591	VWFD 1.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
AKT2	208	broad.mit.edu	37	19	40771118	40771118	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40771118C>T	uc002onf.2	-						AKT2_uc010egs.2_Intron|AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc010egu.1_Intron|AKT2_uc010xvk.1_Intron	NM_001626	NP_001617			AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)					A		ovarian|pancreatic 								---	---	---	---
SHKBP1	92799	broad.mit.edu	37	19	41083151	41083151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41083151G>A	uc002oob.2	+	2	150	c.101G>A	c.(100-102)CGC>CAC	p.R34H	SHKBP1_uc002ooc.2_Missense_Mutation_p.R34H|SHKBP1_uc002ood.2_Missense_Mutation_p.R34H|SHKBP1_uc010xvl.1_5'UTR|SHKBP1_uc002ooe.2_5'UTR|SHKBP1_uc002oof.2_5'Flank|SHKBP1_uc010xvm.1_5'Flank	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	34	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
AXL	558	broad.mit.edu	37	19	41726691	41726691	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41726691C>T	uc010ehj.2	+	2	426	c.236C>T	c.(235-237)GCG>GTG	p.A79V	CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Missense_Mutation_p.A79V|AXL_uc010ehk.2_Missense_Mutation_p.A79V	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1	79	Extracellular (Potential).|Interaction with GAS6.|Ig-like C2-type 1.					integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13																		---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41920013	41920013	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41920013C>T	uc002oqq.2	+	4	464	c.435C>T	c.(433-435)GCC>GCT	p.A145A	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Silent_p.A179A|BCKDHA_uc002oqp.1_Silent_p.A37A|BCKDHA_uc002oqr.2_Silent_p.A145A|BCKDHA_uc010xvz.1_Silent_p.A123A	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	145					branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
CEACAM21	90273	broad.mit.edu	37	19	42083609	42083609	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42083609C>G	uc002ore.3	+	2	218	c.122C>G	c.(121-123)GCG>GGG	p.A41G	CEACAM21_uc002orc.1_RNA|CEACAM21_uc002ord.1_RNA|CEACAM21_uc002orf.2_RNA|CEACAM21_uc002org.3_Missense_Mutation_p.A41G	NM_001098506	NP_001091976	Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion	41	Extracellular (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
ERF	2077	broad.mit.edu	37	19	42753056	42753056	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42753056C>T	uc002ote.3	-	4	1366	c.1208G>A	c.(1207-1209)GGT>GAT	p.G403D	ERF_uc002otd.3_Missense_Mutation_p.G134D	NM_006494	NP_006485	P50548	ERF_HUMAN	Ets2 repressor factor	403					cell proliferation|regulation of transcription from RNA polymerase II promoter	nucleus	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	4		Prostate(69;0.00682)																---	---	---	---
ERF	2077	broad.mit.edu	37	19	42753303	42753303	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42753303C>T	uc002ote.3	-	4	1119	c.961G>A	c.(961-963)GTC>ATC	p.V321I	ERF_uc002otd.3_Missense_Mutation_p.V52I	NM_006494	NP_006485	P50548	ERF_HUMAN	Ets2 repressor factor	321					cell proliferation|regulation of transcription from RNA polymerase II promoter	nucleus	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	4		Prostate(69;0.00682)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43372432	43372432	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43372432G>A	uc002ovb.2	-	5	1202	c.1064C>T	c.(1063-1065)TCT>TTT	p.S355F	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Intron|PSG1_uc002our.1_Missense_Mutation_p.S355F|PSG1_uc010eio.1_Missense_Mutation_p.S355F|PSG1_uc002oux.1_Missense_Mutation_p.S284F|PSG1_uc002ouy.1_Missense_Mutation_p.S262F|PSG1_uc002ouz.1_Missense_Mutation_p.S355F|PSG1_uc002ova.1_Missense_Mutation_p.S262F|PSG1_uc002ovc.2_Missense_Mutation_p.S262F|PSG1_uc002ovd.1_Missense_Mutation_p.S355F	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	355	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43372434	43372434	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43372434A>G	uc002ovb.2	-	5	1200	c.1062T>C	c.(1060-1062)TGT>TGC	p.C354C	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Intron|PSG1_uc002our.1_Silent_p.C354C|PSG1_uc010eio.1_Silent_p.C354C|PSG1_uc002oux.1_Silent_p.C283C|PSG1_uc002ouy.1_Silent_p.C261C|PSG1_uc002ouz.1_Silent_p.C354C|PSG1_uc002ova.1_Silent_p.C261C|PSG1_uc002ovc.2_Silent_p.C261C|PSG1_uc002ovd.1_Silent_p.C354C	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	354	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43372445	43372445	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43372445A>C	uc002ovb.2	-	5	1189	c.1051T>G	c.(1051-1053)TAC>GAC	p.Y351D	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Intron|PSG1_uc002our.1_Missense_Mutation_p.Y351D|PSG1_uc010eio.1_Missense_Mutation_p.Y351D|PSG1_uc002oux.1_Missense_Mutation_p.Y280D|PSG1_uc002ouy.1_Missense_Mutation_p.Y258D|PSG1_uc002ouz.1_Missense_Mutation_p.Y351D|PSG1_uc002ova.1_Missense_Mutation_p.Y258D|PSG1_uc002ovc.2_Missense_Mutation_p.Y258D|PSG1_uc002ovd.1_Missense_Mutation_p.Y351D	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	351	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43411271	43411271	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43411271T>A	uc002ovj.1	-	5	1095	c.1043A>T	c.(1042-1044)AAC>ATC	p.N348I	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Missense_Mutation_p.N355I|PSG6_uc002ovi.2_Missense_Mutation_p.N349I|PSG6_uc010xwk.1_Missense_Mutation_p.N188I|PSG11_uc002ovk.1_Missense_Mutation_p.N347I|PSG6_uc002ove.1_Missense_Mutation_p.N138I|PSG6_uc002ovf.1_Missense_Mutation_p.N255I|PSG6_uc002ovg.1_Missense_Mutation_p.N348I	NM_002782	NP_002773	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6 isoform	348	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43411272	43411272	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43411272T>C	uc002ovj.1	-	5	1094	c.1042A>G	c.(1042-1044)AAC>GAC	p.N348D	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Missense_Mutation_p.N355D|PSG6_uc002ovi.2_Missense_Mutation_p.N349D|PSG6_uc010xwk.1_Missense_Mutation_p.N188D|PSG11_uc002ovk.1_Missense_Mutation_p.N347D|PSG6_uc002ove.1_Missense_Mutation_p.N138D|PSG6_uc002ovf.1_Missense_Mutation_p.N255D|PSG6_uc002ovg.1_Missense_Mutation_p.N348D	NM_002782	NP_002773	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6 isoform	348	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
IRGQ	126298	broad.mit.edu	37	19	44097282	44097282	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44097282C>T	uc002oww.2	-	2	886	c.768G>A	c.(766-768)TCG>TCA	p.S256S	IRGQ_uc010eiv.2_Silent_p.S256S	NM_001007561	NP_001007562	Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	256							protein binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0199)																---	---	---	---
CADM4	199731	broad.mit.edu	37	19	44129351	44129351	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44129351C>T	uc002oxc.1	-	7	856	c.807G>A	c.(805-807)GCG>GCA	p.A269A		NM_145296	NP_660339	Q8NFZ8	CADM4_HUMAN	cell adhesion molecule 4 precursor	269	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion	integral to membrane					0		Prostate(69;0.0199)																---	---	---	---
ZNF45	7596	broad.mit.edu	37	19	44417798	44417798	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44417798G>A	uc002oxu.1	-	4	1889	c.1790C>T	c.(1789-1791)TCC>TTC	p.S597F	ZNF45_uc002oxw.1_Missense_Mutation_p.S597F|ZNF45_uc002oxv.1_Missense_Mutation_p.S597F	NM_003425	NP_003416	Q02386	ZNF45_HUMAN	zinc finger protein 45	597	C2H2-type 16.				multicellular organismal development	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF227	7770	broad.mit.edu	37	19	44739958	44739958	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44739958A>G	uc002oyu.2	+	6	1580	c.1375A>G	c.(1375-1377)ACA>GCA	p.T459A	ZNF227_uc010xwu.1_Missense_Mutation_p.T408A|ZNF227_uc002oyv.2_Missense_Mutation_p.T459A|ZNF227_uc010xwv.1_Missense_Mutation_p.T408A|ZNF227_uc010xww.1_Missense_Mutation_p.T380A|ZNF227_uc002oyw.2_Missense_Mutation_p.T431A|ZNF227_uc010ejh.2_Missense_Mutation_p.T452A|ZNF235_uc002oyx.1_Intron	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	459					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)																---	---	---	---
BCAM	4059	broad.mit.edu	37	19	45315541	45315541	+	Missense_Mutation	SNP	G	A	A	rs114801603	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45315541G>A	uc002ozu.2	+	3	370	c.326G>A	c.(325-327)CGC>CAC	p.R109H	BCAM_uc002ozt.1_Missense_Mutation_p.R109H	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	109	Extracellular (Potential).|Ig-like V-type 1.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)																---	---	---	---
APOC1	341	broad.mit.edu	37	19	45419548	45419548	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45419548C>A	uc002pac.1	+	4	412	c.160C>A	c.(160-162)CGC>AGC	p.R54S	APOC1_uc002pad.1_Missense_Mutation_p.R54S|APOC1_uc002pae.1_Missense_Mutation_p.R54S|APOC1_uc002paf.1_RNA	NM_001645	NP_001636	P02654	APOC1_HUMAN	apolipoprotein C-I precursor	54					cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of fatty acid biosynthetic process|negative regulation of lipoprotein lipase activity|negative regulation of phosphatidylcholine catabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of cholesterol esterification|very-low-density lipoprotein particle assembly|very-low-density lipoprotein particle clearance	chylomicron|endoplasmic reticulum|high-density lipoprotein particle|very-low-density lipoprotein particle	fatty acid binding|phosphatidylcholine binding|phosphatidylcholine-sterol O-acyltransferase activator activity|phospholipase inhibitor activity				0	Lung NSC(12;0.0018)|all_lung(12;0.00481)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)														---	---	---	---
SFRS16	11129	broad.mit.edu	37	19	45571725	45571725	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45571725G>A	uc002pak.2	+	16	1853	c.1755G>A	c.(1753-1755)GCG>GCA	p.A585A	SFRS16_uc002pal.2_RNA|SFRS16_uc010xxh.1_Silent_p.A523A|SFRS16_uc002pam.2_Intron	NM_007056	NP_008987	Q8N2M8	CLASR_HUMAN	splicing factor, arginine/serine-rich 16	585	Potential.|Arg-rich.				mRNA processing|RNA splicing	nucleus					0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
EXOC3L2	90332	broad.mit.edu	37	19	45731515	45731515	+	Missense_Mutation	SNP	G	A	A	rs75426681	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45731515G>A	uc002pay.1	-	3	141	c.100C>T	c.(100-102)CGG>TGG	p.R34W		NM_138568	NP_612635	Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	34										ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)														---	---	---	---
PPP5C	5536	broad.mit.edu	37	19	46891872	46891872	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46891872C>A	uc002pem.2	+	11	1299	c.1239C>A	c.(1237-1239)GCC>GCA	p.A413A	PPP5C_uc010xya.1_Silent_p.A280A|PPP5C_uc002pen.2_Silent_p.A391A	NM_006247	NP_006238	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	413	Catalytic.				mitosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein dephosphorylation|transcription, DNA-dependent	Golgi apparatus|nucleus	metal ion binding|protein binding|protein serine/threonine phosphatase activity|signal transducer activity			lung(1)|pancreas(1)	2		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)														---	---	---	---
SPHK2	56848	broad.mit.edu	37	19	49131543	49131543	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49131543A>G	uc002pjr.2	+						SPHK2_uc010xzt.1_Intron|SPHK2_uc002pjs.2_Intron|SPHK2_uc002pjt.2_Intron|SPHK2_uc002pju.2_Intron|SPHK2_uc002pjv.2_Intron|SPHK2_uc002pjw.2_Intron|SPHK2_uc010xzu.1_3'UTR	NM_020126	NP_064511			sphingosine kinase 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)														---	---	---	---
FUT1	2523	broad.mit.edu	37	19	49254183	49254183	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49254183G>T	uc002pkk.2	-	4	1331	c.356C>A	c.(355-357)GCC>GAC	p.A119D		NM_000148	NP_000139	P19526	FUT1_HUMAN	fucosyltransferase 1	119	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to plasma membrane|membrane fraction	galactoside 2-alpha-L-fucosyltransferase activity			ovary(1)	1		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)														---	---	---	---
SNRNP70	6625	broad.mit.edu	37	19	49601946	49601946	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49601946C>T	uc002pmk.2	+	6	817	c.378C>T	c.(376-378)TAC>TAT	p.Y126Y	SNRNP70_uc002pmh.1_RNA|SNRNP70_uc002pmi.1_Silent_p.Y126Y|SNRNP70_uc002pml.2_Translation_Start_Site|SNRNP70_uc002pmm.2_RNA	NM_003089	NP_003080	P08621	RU17_HUMAN	U1 small nuclear ribonucleoprotein 70 kDa	126	RRM.				nuclear mRNA splicing, via spliceosome|regulation of RNA splicing	nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0																OREG0025616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PPFIA3	8541	broad.mit.edu	37	19	49637409	49637409	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49637409C>T	uc002pmr.2	+	11	1696	c.1364C>T	c.(1363-1365)GCG>GTG	p.A455V	PPFIA3_uc010yai.1_RNA|PPFIA3_uc010emt.2_Missense_Mutation_p.A379V|PPFIA3_uc010yaj.1_RNA|PPFIA3_uc002pms.2_Missense_Mutation_p.A323V	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	455	Potential.					cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49685864	49685864	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49685864C>T	uc002pmw.2	+	11	1365	c.1293C>T	c.(1291-1293)GAC>GAT	p.D431D	TRPM4_uc010emu.2_Silent_p.D431D|TRPM4_uc010yak.1_Translation_Start_Site|TRPM4_uc002pmx.2_Silent_p.D257D|TRPM4_uc010emv.2_Silent_p.D316D|TRPM4_uc010yal.1_Silent_p.D77D|TRPM4_uc002pmy.2_Translation_Start_Site	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	431	Cytoplasmic (Potential).				dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)														---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49863143	49863143	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49863143C>T	uc002pnj.2	-	2	281	c.190G>A	c.(190-192)GGC>AGC	p.G64S	TEAD2_uc002png.2_Missense_Mutation_p.G64S|TEAD2_uc002pnh.2_Missense_Mutation_p.G64S|TEAD2_uc002pni.2_Missense_Mutation_p.G64S|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Missense_Mutation_p.G64S	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	64	TEA.				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)														---	---	---	---
RRAS	6237	broad.mit.edu	37	19	50139001	50139001	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50139001G>A	uc002pop.1	-	5	607	c.562C>T	c.(562-564)CGG>TGG	p.R188W		NM_006270	NP_006261	P10301	RRAS_HUMAN	related RAS viral (r-ras) oncogene homolog	188					axon guidance|Ras protein signal transduction|synaptic transmission	intracellular|plasma membrane	GDP binding|GTP binding|GTPase activity|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00114)|GBM - Glioblastoma multiforme(134;0.0206)														---	---	---	---
CPT1C	126129	broad.mit.edu	37	19	50216032	50216032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50216032C>T	uc002ppj.2	+	17	2264	c.2059C>T	c.(2059-2061)CCT>TCT	p.P687S	CPT1C_uc002ppi.2_Missense_Mutation_p.P604S|CPT1C_uc002ppk.2_Missense_Mutation_p.P676S|CPT1C_uc010eng.2_Missense_Mutation_p.P687S|CPT1C_uc010enh.2_Missense_Mutation_p.P687S|CPT1C_uc010eni.1_Intron	NM_152359	NP_689572	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C isoform 2	687	Cytoplasmic (Potential).				fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)														---	---	---	---
FUZ	80199	broad.mit.edu	37	19	50311684	50311684	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50311684C>T	uc002ppq.1	-	10	1125	c.1020G>A	c.(1018-1020)ACG>ACA	p.T340T	FUZ_uc002ppr.1_Silent_p.T240T|FUZ_uc002pps.1_RNA|FUZ_uc002ppt.1_RNA|FUZ_uc002ppu.1_Silent_p.T304T|FUZ_uc002ppv.1_Silent_p.T290T	NM_025129	NP_079405	Q9BT04	FUZZY_HUMAN	fuzzy homolog	340	Leu-rich.				cilium assembly|embryonic body morphogenesis|embryonic skeletal system morphogenesis|establishment of planar polarity|hair follicle development|neural tube closure|protein transport|regulation of smoothened signaling pathway	cytoplasm|cytoskeleton					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50750385	50750385	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50750385C>T	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005			myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
JOSD2	126119	broad.mit.edu	37	19	51013606	51013606	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51013606G>A	uc002psn.1	-	2	114	c.83C>T	c.(82-84)GCC>GTC	p.A28V	JOSD2_uc002pso.1_Missense_Mutation_p.A28V|JOSD2_uc002psp.1_Missense_Mutation_p.A28V|JOSD2_uc002psq.1_Missense_Mutation_p.A28V	NM_138334	NP_612207	Q8TAC2	JOS2_HUMAN	Josephin domain containing 2	28	Josephin.				protein deubiquitination		ubiquitin-specific protease activity				0		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0364)														---	---	---	---
ZNF137	7696	broad.mit.edu	37	19	53100168	53100168	+	RNA	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53100168A>G	uc002pzt.2	+	1		c.232A>G				NR_023311				Homo sapiens zinc finger protein 137, mRNA (cDNA clone IMAGE:40016639).												0				GBM - Glioblastoma multiforme(134;0.0212)|OV - Ovarian serous cystadenocarcinoma(262;0.0221)														---	---	---	---
VN1R2	317701	broad.mit.edu	37	19	53762670	53762670	+	Silent	SNP	C	T	T	rs148663224		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53762670C>T	uc002qbi.2	+	1	1126	c.1042C>T	c.(1042-1044)CTA>TTA	p.L348L		NM_173856	NP_776255	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	348	Helical; Name=7; (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0				GBM - Glioblastoma multiforme(134;0.00301)														---	---	---	---
ZNF765	91661	broad.mit.edu	37	19	53911543	53911543	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53911543C>T	uc010ydx.1	+	6	1062	c.735C>T	c.(733-735)TGC>TGT	p.C245C	ZNF765_uc002qbm.2_Silent_p.C245C|ZNF765_uc002qbn.2_Intron	NM_001040185	NP_001035275	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	245	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)														---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54313469	54313469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54313469G>A	uc002qch.3	-	3	1664	c.1444C>T	c.(1444-1446)CGG>TGG	p.R482W	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.R482W|NLRP12_uc002qcj.3_Missense_Mutation_p.R482W|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.R482W	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	482	NACHT.				negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54313886	54313886	+	Missense_Mutation	SNP	G	A	A	rs112159191	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54313886G>A	uc002qch.3	-	3	1247	c.1027C>T	c.(1027-1029)CGG>TGG	p.R343W	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.R343W|NLRP12_uc002qcj.3_Missense_Mutation_p.R343W|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.R343W	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	343	NACHT.				negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
LILRA6	79168	broad.mit.edu	37	19	54744238	54744238	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54744238G>A	uc002qeu.1	-	6	1294	c.1170C>T	c.(1168-1170)CAC>CAT	p.H390H	LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Silent_p.H390H|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Silent_p.H390H|LILRA6_uc002qem.1_RNA|LILRB3_uc002qen.1_RNA|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Silent_p.H390H|LILRA6_uc010yeq.1_Silent_p.H390H|LILRA6_uc002qet.3_RNA|LILRA6_uc002qev.1_Silent_p.H251H	NM_024318	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor,	390	Extracellular (Potential).|Ig-like C2-type 2.					integral to membrane	receptor activity			skin(2)	2	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
LILRB5	10990	broad.mit.edu	37	19	54760501	54760501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54760501C>T	uc002qex.2	-	3	317	c.206G>A	c.(205-207)CGG>CAG	p.R69Q	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.R69Q|LILRB5_uc002qey.2_Missense_Mutation_p.R69Q|LILRB5_uc002qez.2_Missense_Mutation_p.R69Q|LILRB5_uc002qfa.1_Missense_Mutation_p.R59Q|LILRB5_uc010yes.1_RNA	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	69	Ig-like C2-type 1.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
LILRB4	11006	broad.mit.edu	37	19	55176288	55176288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55176288G>A	uc002qgp.2	+	5	1056	c.694G>A	c.(694-696)GTC>ATC	p.V232I	LILRB4_uc002qgq.2_Missense_Mutation_p.V232I|LILRB4_uc010ers.1_Missense_Mutation_p.V145I|LILRB4_uc002qgr.2_Missense_Mutation_p.V273I|LILRB4_uc010ert.2_Missense_Mutation_p.V273I|LILRB4_uc010eru.2_Missense_Mutation_p.V261I	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,	232	Extracellular (Potential).					integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)														---	---	---	---
TNNI3	7137	broad.mit.edu	37	19	55665463	55665463	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55665463G>A	uc002qjg.3	-	7	484	c.484C>T	c.(484-486)CGG>TGG	p.R162W	TNNI3_uc010yft.1_Missense_Mutation_p.R154W	NM_000363	NP_000354	P19429	TNNI3_HUMAN	troponin I, cardiac	162			R -> Q (in CMH7).|R -> P (in CMH7).		cardiac muscle contraction|cellular calcium ion homeostasis|muscle filament sliding|negative regulation of ATPase activity|regulation of systemic arterial blood pressure by ischemic conditions|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|calcium channel inhibitor activity|calcium-dependent protein binding|protein domain specific binding|protein kinase binding|troponin C binding|troponin T binding			lung(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)														---	---	---	---
ZNF628	89887	broad.mit.edu	37	19	55993007	55993007	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55993007G>A	uc002qld.2	+	3	1000	c.435G>A	c.(433-435)CCG>CCA	p.P145P		NM_033113	NP_149104	Q5EBL2	ZN628_HUMAN	zinc finger protein 628	145	C2H2-type 5.					nucleus	DNA binding|zinc ion binding				0	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)														---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56736361	56736361	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56736361C>A	uc002qmq.2	-	2	221	c.55G>T	c.(55-57)GGG>TGG	p.G19W	ZSCAN5A_uc010ygi.1_Intron|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.G19W|ZSCAN5A_uc002qms.1_Missense_Mutation_p.G19W	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	19					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ZNF71	58491	broad.mit.edu	37	19	57133388	57133388	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57133388G>A	uc002qnm.3	+	3	971	c.733G>A	c.(733-735)GGG>AGG	p.G245R		NM_021216	NP_067039	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	245	C2H2-type 5.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)														---	---	---	---
PEG3	5178	broad.mit.edu	37	19	57327918	57327918	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327918A>G	uc002qnu.2	-	7	2243	c.1892T>C	c.(1891-1893)GTG>GCG	p.V631A	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.V602A|PEG3_uc002qnv.2_Missense_Mutation_p.V631A|PEG3_uc002qnw.2_Missense_Mutation_p.V507A|PEG3_uc002qnx.2_Missense_Mutation_p.V505A|PEG3_uc010etr.2_Missense_Mutation_p.V631A	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	631	C2H2-type 4.				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)														---	---	---	---
ZNF264	9422	broad.mit.edu	37	19	57723830	57723830	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57723830C>T	uc002qob.2	+	4	1778	c.1365C>T	c.(1363-1365)TTC>TTT	p.F455F		NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264	455	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)														---	---	---	---
ZNF543	125919	broad.mit.edu	37	19	57839164	57839164	+	Missense_Mutation	SNP	G	A	A	rs34884181	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57839164G>A	uc002qoi.1	+	4	679	c.334G>A	c.(334-336)GCC>ACC	p.A112T		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	112					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
ZNF551	90233	broad.mit.edu	37	19	58196658	58196658	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58196658A>G	uc002qpw.3	+	2	285	c.62A>G	c.(61-63)TAT>TGT	p.Y21C	ZNF551_uc002qpv.3_Intron|ZNF776_uc002qpx.2_Intron	NM_138347	NP_612356	Q7Z340	ZN551_HUMAN	zinc finger protein 551	37	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
ZNF551	90233	broad.mit.edu	37	19	58199043	58199043	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58199043G>A	uc002qpw.3	+	3	1575	c.1352G>A	c.(1351-1353)AGC>AAC	p.S451N	ZNF551_uc002qpv.3_Missense_Mutation_p.S394N|ZNF776_uc002qpx.2_Intron	NM_138347	NP_612356	Q7Z340	ZN551_HUMAN	zinc finger protein 551	467	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
ZNF324B	388569	broad.mit.edu	37	19	58966635	58966635	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58966635C>T	uc002qsv.1	+	4	431	c.324C>T	c.(322-324)AGC>AGT	p.S108S	ZNF324B_uc002qsu.1_Silent_p.S98S|ZNF324B_uc010euq.1_Silent_p.S108S	NM_207395	NP_997278	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	108					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)														---	---	---	---
ZNF324B	388569	broad.mit.edu	37	19	58967142	58967142	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58967142C>T	uc002qsv.1	+	4	938	c.831C>T	c.(829-831)CGC>CGT	p.R277R	ZNF324B_uc002qsu.1_Silent_p.R267R|ZNF324B_uc010euq.1_Silent_p.R277R	NM_207395	NP_997278	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	277	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)														---	---	---	---
TRIM28	10155	broad.mit.edu	37	19	59061100	59061100	+	Intron	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59061100C>A	uc002qtg.1	+						TRIM28_uc010eut.1_Intron|TRIM28_uc002qth.1_Intron	NM_005762	NP_005753			tripartite motif-containing 28 protein						epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)														---	---	---	---
C20orf96	140680	broad.mit.edu	37	20	259899	259899	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:259899G>A	uc002wde.1	-	5	518	c.379C>T	c.(379-381)CGG>TGG	p.R127W	C20orf96_uc002wdc.2_Missense_Mutation_p.R74W|C20orf96_uc002wdd.2_Missense_Mutation_p.R92W|C20orf96_uc010zpi.1_Missense_Mutation_p.R74W|C20orf96_uc010zpj.1_Missense_Mutation_p.R92W|C20orf96_uc010zpk.1_Missense_Mutation_p.R65W	NM_153269	NP_695001	Q9NUD7	CT096_HUMAN	hypothetical protein LOC140680	127	Potential.										0		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)															---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	400030	400030	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:400030C>A	uc002wdp.3	+	5	1193	c.500C>A	c.(499-501)CCT>CAT	p.P167H	RBCK1_uc010zpl.1_Missense_Mutation_p.P167H|RBCK1_uc010zpm.1_RNA|RBCK1_uc002wdq.3_Missense_Mutation_p.P125H|RBCK1_uc010fzy.2_RNA|RBCK1_uc002wdr.3_Missense_Mutation_p.L51I	NM_031229	NP_112506	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing	167	Interaction with IRF3.|Interaction with TAB2.				interspecies interaction between organisms|negative regulation of NF-kappaB transcription factor activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|proteasomal ubiquitin-dependent protein catabolic process|protein linear polyubiquitination|T cell receptor signaling pathway	LUBAC complex	protein binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)																---	---	---	---
SCRT2	85508	broad.mit.edu	37	20	644711	644711	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:644711C>A	uc002wec.2	-	2	1106	c.528G>T	c.(526-528)ACG>ACT	p.T176T	SRXN1_uc002web.2_Intron	NM_033129	NP_149120	Q9NQ03	SCRT2_HUMAN	scratch 2 protein	176	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
TGM3	7053	broad.mit.edu	37	20	2308850	2308850	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2308850C>T	uc002wfx.3	+	9	1269	c.1172C>T	c.(1171-1173)GCG>GTG	p.A391V		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	391					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)													---	---	---	---
TGM3	7053	broad.mit.edu	37	20	2320521	2320521	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2320521C>T	uc002wfx.3	+	12	1919	c.1822C>T	c.(1822-1824)CGG>TGG	p.R608W		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	608					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity	p.R608Q(1)		large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)													---	---	---	---
NOP56	10528	broad.mit.edu	37	20	2637781	2637781	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2637781C>T	uc002wgh.2	+	11	1389	c.1336C>T	c.(1336-1338)CGC>TGC	p.R446C	NOP56_uc010zpy.1_RNA|NOP56_uc002wgi.2_Missense_Mutation_p.R280C|NOP56_uc002wgm.1_Missense_Mutation_p.R193C	NM_006392	NP_006383	O00567	NOP56_HUMAN	nucleolar protein 5A	446	Lys-rich.				rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2988067	2988067	+	Splice_Site	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2988067G>A	uc010zqd.1	+	10	1256	c.939_splice	c.e10+1	p.N313_splice	PTPRA_uc002whj.2_Splice_Site_p.N302_splice|PTPRA_uc002whk.2_Splice_Site_p.N293_splice|PTPRA_uc002whl.2_Splice_Site_p.N293_splice|PTPRA_uc002whm.2_Splice_Site_p.N69_splice|PTPRA_uc002whn.2_Splice_Site_p.N293_splice|PTPRA_uc002who.2_Splice_Site	NM_002836	NP_002827			protein tyrosine phosphatase, receptor type, A						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
OXT	5020	broad.mit.edu	37	20	3053038	3053038	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3053038G>A	uc002wht.1	+	3	388	c.352G>A	c.(352-354)GCG>ACG	p.A118T		NM_000915	NP_000906	P01178	NEU1_HUMAN	oxytocin-neurophysin I preproprotein	118					signal transduction		neurohypophyseal hormone activity				0					Oxytocin(DB00107)													---	---	---	---
UBOX5	22888	broad.mit.edu	37	20	3096036	3096036	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3096036G>T	uc002whw.2	-	4	1502	c.1332C>A	c.(1330-1332)TCC>TCA	p.S444S	uc002whv.1_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Silent_p.S444S	NM_014948	NP_055763	O94941	RNF37_HUMAN	U-box domain containing 5 isoform a	444						nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2																OREG0025729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DDRGK1	65992	broad.mit.edu	37	20	3180685	3180685	+	Missense_Mutation	SNP	T	C	C	rs147976775		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3180685T>C	uc002wic.2	-	4	494	c.472A>G	c.(472-474)AAG>GAG	p.K158E	DDRGK1_uc010gaw.2_RNA|DDRGK1_uc010gax.1_Missense_Mutation_p.K158E	NM_023935	NP_076424	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1 precursor	158						endoplasmic reticulum	protein binding				0																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3581583	3581583	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3581583C>T	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
CDC25B	994	broad.mit.edu	37	20	3782997	3782997	+	Nonsense_Mutation	SNP	C	T	T	rs138180783		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3782997C>T	uc002wjn.2	+	11	1946	c.1168C>T	c.(1168-1170)CGA>TGA	p.R390*	CDC25B_uc010zqk.1_Nonsense_Mutation_p.R326*|CDC25B_uc010zql.1_Nonsense_Mutation_p.R312*|CDC25B_uc010zqm.1_Nonsense_Mutation_p.R299*|CDC25B_uc002wjl.2_Nonsense_Mutation_p.R278*|CDC25B_uc002wjm.2_Nonsense_Mutation_p.R278*|CDC25B_uc002wjo.2_Nonsense_Mutation_p.R376*|CDC25B_uc002wjp.2_Nonsense_Mutation_p.R349*|CDC25B_uc002wjq.2_Nonsense_Mutation_p.R190*|CDC25B_uc010gbc.2_5'Flank	NM_021873	NP_068659	P30305	MPIP2_HUMAN	cell division cycle 25B isoform 1	390					cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation	cytosol|microtubule organizing center|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|ovary(2)	5																		---	---	---	---
MAVS	57506	broad.mit.edu	37	20	3835311	3835311	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3835311C>T	uc002wjw.3	+	2	209	c.40C>T	c.(40-42)CGC>TGC	p.R14C	MAVS_uc002wjv.2_Missense_Mutation_p.R14C|MAVS_uc010zqn.1_Missense_Mutation_p.R14C|MAVS_uc002wjx.3_5'UTR|MAVS_uc002wjy.3_5'UTR	NM_020746	NP_065797	Q7Z434	MAVS_HUMAN	virus-induced signaling adapter	14	Cytoplasmic (Probable).|Required for interaction with NLRX1.|CARD.				activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0																		---	---	---	---
MAVS	57506	broad.mit.edu	37	20	3846783	3846783	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3846783C>T	uc002wjw.3	+	7	1781	c.1612C>T	c.(1612-1614)CGT>TGT	p.R538C	MAVS_uc002wjx.3_Missense_Mutation_p.R397C|MAVS_uc002wjy.3_Missense_Mutation_p.R236C	NM_020746	NP_065797	Q7Z434	MAVS_HUMAN	virus-induced signaling adapter	538	Mitochondrial intermembrane (Probable).				activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0																		---	---	---	---
SMOX	54498	broad.mit.edu	37	20	4163402	4163402	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4163402G>A	uc002wkm.1	+	5	1477	c.1276G>A	c.(1276-1278)GGC>AGC	p.G426S	SMOX_uc002wkk.1_Missense_Mutation_p.G373S|SMOX_uc002wkl.1_Missense_Mutation_p.G373S|SMOX_uc002wkn.1_Intron|SMOX_uc002wkp.2_Missense_Mutation_p.G426S|SMOX_uc010zqo.1_Missense_Mutation_p.G350S|SMOX_uc002wko.1_Missense_Mutation_p.G426S	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	426					polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)													---	---	---	---
SMOX	54498	broad.mit.edu	37	20	4167471	4167471	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4167471G>A	uc002wkm.1	+						SMOX_uc002wkk.1_Missense_Mutation_p.A485T|SMOX_uc002wkl.1_Intron|SMOX_uc002wkn.1_Intron|SMOX_uc002wkp.2_Missense_Mutation_p.A538T|SMOX_uc010zqo.1_Intron|SMOX_uc002wko.1_Intron	NM_175839	NP_787033			spermine oxidase isoform 1						polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)													---	---	---	---
TRMT6	51605	broad.mit.edu	37	20	5927126	5927126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5927126C>T	uc002wmh.1	-	2	304	c.182G>A	c.(181-183)AGT>AAT	p.S61N	TRMT6_uc010zra.1_5'UTR|TRMT6_uc010gbn.1_5'UTR|TRMT6_uc010gbo.1_RNA	NM_015939	NP_057023	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6	61					regulation of translational initiation|tRNA processing	nucleus	protein binding|translation initiation factor activity			pancreas(1)	1																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8678262	8678262	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8678262G>A	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8707988	8707988	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8707988G>A	uc002wnb.2	+	17	1714	c.1711G>A	c.(1711-1713)GTG>ATG	p.V571M	PLCB1_uc010zrb.1_Missense_Mutation_p.V470M|PLCB1_uc002wna.2_Missense_Mutation_p.V571M|PLCB1_uc002wnc.1_Missense_Mutation_p.V470M|PLCB1_uc002wnd.1_Missense_Mutation_p.V148M	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	571	PI-PLC Y-box.				activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8862281	8862281	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8862281C>T	uc002wnb.2	+	32	3439	c.3436C>T	c.(3436-3438)CTG>TTG	p.L1146L	PLCB1_uc002wna.2_3'UTR	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	1146					activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
ANKRD5	63926	broad.mit.edu	37	20	10030046	10030046	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10030046C>A	uc002wno.2	+	7	1222	c.829C>A	c.(829-831)CTG>ATG	p.L277M	uc002wnn.1_Intron|ANKRD5_uc002wnp.2_Missense_Mutation_p.L277M|ANKRD5_uc010gbz.2_Missense_Mutation_p.L88M	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	277	ANK 4.						calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
JAG1	182	broad.mit.edu	37	20	10628701	10628701	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10628701G>A	uc002wnw.2	-	13	2143	c.1627C>T	c.(1627-1629)CGT>TGT	p.R543C	JAG1_uc010gcd.1_Missense_Mutation_p.R101C	NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor	543	Extracellular (Potential).|EGF-like 9.				angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9														Alagille_Syndrome				---	---	---	---
FLRT3	23767	broad.mit.edu	37	20	14307553	14307553	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14307553A>G	uc002wov.1	-	3	1067	c.600T>C	c.(598-600)AGT>AGC	p.S200S	MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Silent_p.S200S	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	200	Extracellular (Potential).|LRR 7.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			kidney(1)	1		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)														---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16506738	16506738	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16506738A>G	uc002wpg.1	-	3	388	c.230T>C	c.(229-231)ATG>ACG	p.M77T	KIF16B_uc010gch.1_Missense_Mutation_p.M77T|KIF16B_uc010gci.1_Missense_Mutation_p.M77T|KIF16B_uc010gcj.1_Missense_Mutation_p.M77T	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	77	Kinesin-motor.				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8																		---	---	---	---
RRBP1	6238	broad.mit.edu	37	20	17600950	17600950	+	Silent	SNP	C	A	A	rs138279227		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17600950C>A	uc002wpv.1	-	19	2628	c.2274G>T	c.(2272-2274)TCG>TCT	p.S758S	RRBP1_uc010zrp.1_5'Flank|RRBP1_uc002wpt.1_Silent_p.S128S|RRBP1_uc002wpu.2_Silent_p.S532S|RRBP1_uc002wpw.1_Silent_p.S758S|RRBP1_uc010gcl.1_Silent_p.S532S|RRBP1_uc010gcm.1_3'UTR	NM_001042576	NP_001036041	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1191	Cytoplasmic (Potential).				protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1																		---	---	---	---
RBBP9	10741	broad.mit.edu	37	20	18476497	18476497	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18476497T>G	uc002wqy.2	-	2	203	c.127A>C	c.(127-129)AAC>CAC	p.N43H		NM_006606	NP_006597	O75884	RBBP9_HUMAN	retinoblastoma binding protein 9	43						cytoplasm|nucleus	hydrolase activity			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20180413	20180413	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20180413T>C	uc002wru.2	+	17	1875	c.1799T>C	c.(1798-1800)TTC>TCC	p.F600S	C20orf26_uc010zse.1_Missense_Mutation_p.F580S	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	600										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
NKX2-2	4821	broad.mit.edu	37	20	21492829	21492829	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21492829C>T	uc002wsi.2	-	2	911	c.554G>A	c.(553-555)CGC>CAC	p.R185H		NM_002509	NP_002500	O95096	NKX22_HUMAN	NK2 transcription factor related, locus 2	185	Homeobox.				brain development|positive regulation of sequence-specific DNA binding transcription factor activity	nucleus	chromatin binding|core promoter proximal region DNA binding|transcription coactivator activity			pancreas(1)|skin(1)	2																		---	---	---	---
SSTR4	6754	broad.mit.edu	37	20	23017036	23017036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23017036G>A	uc002wsr.2	+	1	980	c.916G>A	c.(916-918)GCC>ACC	p.A306T		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	306	Helical; Name=7; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity			ovary(1)	1	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
CST4	1472	broad.mit.edu	37	20	23667795	23667795	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23667795C>T	uc002wto.1	-	2	328	c.272G>A	c.(271-273)CGC>CAC	p.R91H		NM_001899	NP_001890	P01036	CYTS_HUMAN	cystatin S precursor	91						extracellular region	cysteine-type endopeptidase inhibitor activity			breast(1)	1	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)																	---	---	---	---
TMEM90B	79953	broad.mit.edu	37	20	24523887	24523887	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24523887C>T	uc002wtw.1	+	2	787	c.154C>T	c.(154-156)CGG>TGG	p.R52W		NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B	52	Cytoplasmic (Potential).				response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0																		---	---	---	---
PYGB	5834	broad.mit.edu	37	20	25261039	25261039	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25261039G>A	uc002wup.2	+	10	1339	c.1230G>A	c.(1228-1230)CGG>CGA	p.R410R		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	410					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
PYGB	5834	broad.mit.edu	37	20	25264897	25264897	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25264897G>A	uc002wup.2	+							NM_002862	NP_002853			brain glycogen phosphorylase						glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30365419	30365419	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30365419T>C	uc002wwp.1	+	9	1558	c.860T>C	c.(859-861)CTA>CCA	p.L287P	TPX2_uc010gdv.1_Missense_Mutation_p.L287P	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog	287					activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)															---	---	---	---
TTLL9	164395	broad.mit.edu	37	20	30510763	30510763	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30510763T>C	uc010gdx.1	+						TTLL9_uc002wwy.1_Intron|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_Intron|TTLL9_uc002wxb.1_Intron|TTLL9_uc010zto.1_Intron|TTLL9_uc002wxc.2_Intron|TTLL9_uc010ztp.1_Intron|TTLL9_uc010ztq.1_Intron	NM_001008409	NP_001008409			tubulin tyrosine ligase-like family, member 9						protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
PLAGL2	5326	broad.mit.edu	37	20	30785042	30785042	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30785042G>A	uc002wxn.2	-	3	921	c.704C>T	c.(703-705)ACG>ATG	p.T235M		NM_002657	NP_002648	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	235	C2H2-type 6.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
KIF3B	9371	broad.mit.edu	37	20	30897764	30897764	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30897764G>A	uc002wxq.2	+	2	351	c.184G>A	c.(184-186)GTC>ATC	p.V62I	KIF3B_uc010ztv.1_Missense_Mutation_p.V62I|KIF3B_uc010ztw.1_Missense_Mutation_p.V62I	NM_004798	NP_004789	O15066	KIF3B_HUMAN	kinesin family member 3B	62	Kinesin-motor.				anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31368201	31368201	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31368201C>T	uc002wyc.2	+	2	393	c.72C>T	c.(70-72)AAC>AAT	p.N24N	DNMT3B_uc010ztx.1_RNA|DNMT3B_uc010zty.1_RNA|DNMT3B_uc002wyd.2_Silent_p.N24N|DNMT3B_uc002wye.2_Silent_p.N24N|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_RNA|DNMT3B_uc010ztz.1_Silent_p.N24N|DNMT3B_uc010zua.1_Silent_p.N24N|DNMT3B_uc002wyf.2_Silent_p.N36N	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	24	Interaction with DNMT1 and DNMT3A.				negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
C20orf70	140683	broad.mit.edu	37	20	31763310	31763310	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31763310G>A	uc002wyo.1	+	5	579	c.508G>A	c.(508-510)GTC>ATC	p.V170I		NM_080574	NP_542141	Q96DR5	SPLC2_HUMAN	chromosome 20 open reading frame 70 precursor	170						extracellular region	lipid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C20orf114	92747	broad.mit.edu	37	20	31890778	31890778	+	Silent	SNP	C	T	T	rs141498694		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31890778C>T	uc002wyw.1	+	11	1199	c.1038C>T	c.(1036-1038)CCC>CCT	p.P346P	C20orf114_uc002wyx.1_RNA	NM_033197	NP_149974	Q8TDL5	LPLC1_HUMAN	LPLUNC1 protein precursor	346						extracellular space	lipid binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32228200	32228200	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32228200G>A	uc002wzg.1	+	11	1915	c.1378G>A	c.(1378-1380)GTC>ATC	p.V460I	CBFA2T2_uc010zug.1_Missense_Mutation_p.V234I|CBFA2T2_uc002wze.1_Missense_Mutation_p.V451I|CBFA2T2_uc002wzf.1_RNA|CBFA2T2_uc002wzh.1_Missense_Mutation_p.V431I|CBFA2T2_uc002wzi.1_RNA|CBFA2T2_uc002wzj.1_RNA|CBFA2T2_uc002wzk.1_Missense_Mutation_p.V8I	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit	460	Potential.					nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
RALY	22913	broad.mit.edu	37	20	32660079	32660079	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32660079C>A	uc002xab.2	+	3	497	c.199C>A	c.(199-201)CAT>AAT	p.H67N	RALY_uc010zui.1_Missense_Mutation_p.H67N|RALY_uc002xac.2_Missense_Mutation_p.H67N|RALY_uc002xad.2_RNA|RALY_uc002xae.1_Missense_Mutation_p.H67N	NM_016732	NP_057951	Q9UKM9	RALY_HUMAN	RNA binding protein (autoantigenic,	67	RRM.					catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
GGT7	2686	broad.mit.edu	37	20	33433244	33433244	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33433244C>T	uc002xay.2	-	15	1919	c.1876G>A	c.(1876-1878)GTG>ATG	p.V626M	GGT7_uc010gex.2_RNA	NM_178026	NP_821158	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	626	Extracellular (Potential).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(1)	1																		---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33600864	33600864	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33600864G>A	uc002xbk.2	-	11	1390	c.1356C>T	c.(1354-1356)ATC>ATT	p.I452I	TRPC4AP_uc010zuq.1_Silent_p.I43I|TRPC4AP_uc002xbl.2_Silent_p.I444I|TRPC4AP_uc010zur.1_Silent_p.I413I|TRPC4AP_uc002xbm.1_Silent_p.I452I	NM_015638	NP_056453	Q8TEL6	TP4AP_HUMAN	TRPC4-associated protein isoform a	452					protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	34022132	34022132	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34022132G>A	uc002xck.1	-	2	1400	c.1081C>T	c.(1081-1083)CGC>TGC	p.R361C	GDF5_uc010gfc.1_Missense_Mutation_p.R361C|uc002xcj.2_Silent_p.A181A|GDF5_uc010zvc.1_Missense_Mutation_p.R361C	NM_000557	NP_000548	P43026	GDF5_HUMAN	growth differentiation factor 5 preproprotein	361					cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
NFS1	9054	broad.mit.edu	37	20	34260752	34260752	+	Missense_Mutation	SNP	C	T	T	rs149205059		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34260752C>T	uc002xdw.1	-	12	1299	c.1235G>A	c.(1234-1236)CGC>CAC	p.R412H	CPNE1_uc002xdn.1_RNA|CPNE1_uc002xdo.1_RNA|CPNE1_uc002xdp.1_RNA|NFS1_uc002xdt.1_Missense_Mutation_p.R352H|NFS1_uc002xdu.1_Missense_Mutation_p.R352H|NFS1_uc002xdv.1_RNA|NFS1_uc010zvk.1_Missense_Mutation_p.R210H|NFS1_uc010zvl.1_Missense_Mutation_p.R361H	NM_021100	NP_066923	Q9Y697	NFS1_HUMAN	NFS1 nitrogen fixation 1 precursor	412				R -> A (in Ref. 1; AAD09187).	cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
RBM39	9584	broad.mit.edu	37	20	34312979	34312979	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34312979A>G	uc002xeb.2	-	7	859	c.515T>C	c.(514-516)TTT>TCT	p.F172S	RBM39_uc002xdz.2_Missense_Mutation_p.F148S|RBM39_uc002xea.2_Missense_Mutation_p.F15S|RBM39_uc010gfn.2_Missense_Mutation_p.F15S|RBM39_uc010zvm.1_Missense_Mutation_p.F150S|RBM39_uc002xeg.2_Missense_Mutation_p.F150S|RBM39_uc002xec.2_Missense_Mutation_p.F172S|RBM39_uc002xed.2_5'UTR|RBM39_uc002xee.2_Missense_Mutation_p.F15S|RBM39_uc002xef.2_Missense_Mutation_p.F15S|RBM39_uc010zvn.1_Missense_Mutation_p.F15S	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	172	RRM 1.				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)																	---	---	---	---
C20orf4	25980	broad.mit.edu	37	20	34828409	34828409	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34828409C>T	uc002xfc.1	+	2	712	c.619C>T	c.(619-621)CGC>TGC	p.R207C	C20orf4_uc002xfd.1_Missense_Mutation_p.R207C|C20orf4_uc002xfe.1_Missense_Mutation_p.R207C	NM_015511	NP_056326	Q9Y312	CT004_HUMAN	hypothetical protein LOC25980	207											0	Breast(12;0.0162)	Myeloproliferative disorder(115;0.0393)																---	---	---	---
SLA2	84174	broad.mit.edu	37	20	35262912	35262912	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35262912G>T	uc002xfv.2	-	3	534	c.172C>A	c.(172-174)CCA>ACA	p.P58T	SLA2_uc002xfu.2_Missense_Mutation_p.P58T	NM_032214	NP_115590	Q9H6Q3	SLAP2_HUMAN	Src-like-adaptor 2 isoform a	58	SH3.				antigen receptor-mediated signaling pathway|B cell mediated immunity|intracellular receptor mediated signaling pathway|negative regulation of B cell activation|negative regulation of calcium-mediated signaling|negative regulation of transcription from RNA polymerase II promoter|T cell activation	cytoplasmic membrane-bounded vesicle|endosome membrane|plasma membrane	protein N-terminus binding|SH3/SH2 adaptor activity				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36361300	36361300	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36361300G>A	uc010zvw.1	+	2	141	c.50G>A	c.(49-51)CGT>CAT	p.R17H	CTNNBL1_uc010zvv.1_5'UTR	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1	17					apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
BPI	671	broad.mit.edu	37	20	36963994	36963994	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36963994T>C	uc002xib.2	+							NM_001725	NP_001716			bactericidal/permeability-increasing protein						defense response to bacterium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of macrophage activation|negative regulation of tumor necrosis factor production	extracellular region|integral to plasma membrane	lipid binding|lipopolysaccharide binding			ovary(4)	4		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41408894	41408894	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41408894C>T	uc002xkg.2	-	4	716	c.532G>A	c.(532-534)GCC>ACC	p.A178T	PTPRT_uc010ggj.2_Missense_Mutation_p.A178T	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	178	Extracellular (Potential).|MAM.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
SFRS6	6431	broad.mit.edu	37	20	42089452	42089452	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42089452C>T	uc010zwg.1	+	6	954	c.784C>T	c.(784-786)CGA>TGA	p.R262*	SFRS6_uc002xki.2_Nonsense_Mutation_p.R133*|SFRS6_uc002xkk.2_Intron	NM_006275	NP_006266	Q13247	SRSF6_HUMAN	arginine/serine-rich splicing factor 6	262	Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
SEMG2	6407	broad.mit.edu	37	20	43850388	43850388	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43850388T>A	uc010ggz.2	+	2	172	c.115T>A	c.(115-117)TTT>ATT	p.F39I	SEMG2_uc002xnk.2_Missense_Mutation_p.F39I|SEMG2_uc002xnl.2_Missense_Mutation_p.F39I	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	39					sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44574862	44574862	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44574862C>T	uc002xqs.2	+	14	1766	c.1452C>T	c.(1450-1452)TAC>TAT	p.Y484Y	PCIF1_uc002xqt.2_Silent_p.Y64Y|PCIF1_uc002xqu.2_5'Flank	NM_022104	NP_071387	Q9H4Z3	PCIF1_HUMAN	phosphorylated CTD interacting factor 1	484						nucleus				skin(1)	1																		---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44576241	44576241	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44576241G>A	uc002xqs.2	+	17	2276	c.1962G>A	c.(1960-1962)GCG>GCA	p.A654A	PCIF1_uc002xqt.2_Missense_Mutation_p.A263T|PCIF1_uc002xqu.2_Silent_p.A123A	NM_022104	NP_071387	Q9H4Z3	PCIF1_HUMAN	phosphorylated CTD interacting factor 1	654						nucleus				skin(1)	1																		---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44845630	44845630	+	Missense_Mutation	SNP	C	T	T	rs141292740	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44845630C>T	uc002xrm.2	-	4	1074	c.673G>A	c.(673-675)GTA>ATA	p.V225I	CDH22_uc010ghk.1_Missense_Mutation_p.V225I|CDH22_uc002xrn.1_5'UTR	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	225	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SLC35C2	51006	broad.mit.edu	37	20	44983754	44983754	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44983754G>A	uc002xro.2	-	6	1076	c.535C>T	c.(535-537)CGC>TGC	p.R179C	SLC35C2_uc002xrp.2_Missense_Mutation_p.R158C|SLC35C2_uc002xrq.2_Missense_Mutation_p.R179C|SLC35C2_uc002xrr.2_Missense_Mutation_p.R179C|SLC35C2_uc010zxn.1_Missense_Mutation_p.R44C|SLC35C2_uc010zxo.1_Missense_Mutation_p.R65C|SLC35C2_uc010zxp.1_Missense_Mutation_p.R208C	NM_173179	NP_775271	Q9NQQ7	S35C2_HUMAN	solute carrier family 35, member C2 isoform a	179					transport	integral to membrane				ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46292287	46292287	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46292287G>A	uc002xto.2	-	16	2467	c.2137C>T	c.(2137-2139)CGC>TGC	p.R713C	SULF2_uc002xtr.2_Missense_Mutation_p.R713C|SULF2_uc002xtq.2_Missense_Mutation_p.R713C|SULF2_uc010zyd.1_5'UTR	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	713					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46295173	46295173	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46295173C>T	uc002xto.2	-	12	1966	c.1636G>A	c.(1636-1638)GGC>AGC	p.G546S	SULF2_uc002xtr.2_Missense_Mutation_p.G546S|SULF2_uc002xtq.2_Missense_Mutation_p.G546S|SULF2_uc010zyd.1_5'Flank	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	546					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46311923	46311923	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46311923G>A	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron	NM_018837	NP_061325			sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47262476	47262476	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47262476C>A	uc002xtw.1	-	26	3448	c.3425G>T	c.(3424-3426)GGG>GTG	p.G1142V	PREX1_uc002xtv.1_Missense_Mutation_p.G439V	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1142					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47846875	47846875	+	Silent	SNP	C	T	T	rs150518737	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47846875C>T	uc002xuh.2	+	9	1174	c.1113C>T	c.(1111-1113)GAC>GAT	p.D371D		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	371	DEAD box.|Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47852930	47852930	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47852930G>A	uc002xuh.2	+	14	1724	c.1663G>A	c.(1663-1665)GCA>ACA	p.A555T		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	555	Helicase C-terminal.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47865077	47865077	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47865077A>T	uc002xui.2	-	14	4731	c.4484T>A	c.(4483-4485)GTC>GAC	p.V1495D		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1495							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52192435	52192435	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52192435C>T	uc002xwq.3	-	3	3139	c.2868G>A	c.(2866-2868)CCG>CCA	p.P956P	ZNF217_uc010gij.1_Silent_p.P948P	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	956					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)															---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52198369	52198369	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52198369G>A	uc002xwq.3	-	1	1268	c.997C>T	c.(997-999)CTT>TTT	p.L333F	ZNF217_uc010gij.1_Missense_Mutation_p.L325F	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	333					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)															---	---	---	---
BCAS1	8537	broad.mit.edu	37	20	52570160	52570160	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52570160C>A	uc002xws.2	-	11	1829	c.1491G>T	c.(1489-1491)GAG>GAT	p.E497D	BCAS1_uc010zza.1_Missense_Mutation_p.E163D|BCAS1_uc010zzb.1_Missense_Mutation_p.E423D|BCAS1_uc010gim.2_Missense_Mutation_p.E353D|BCAS1_uc002xwt.2_Missense_Mutation_p.E483D|BCAS1_uc010gil.1_Missense_Mutation_p.E419D	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	497						cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)															---	---	---	---
BCAS1	8537	broad.mit.edu	37	20	52612542	52612542	+	Silent	SNP	C	T	T	rs34375573		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52612542C>T	uc002xws.2	-	5	1109	c.771G>A	c.(769-771)GCG>GCA	p.A257A	BCAS1_uc010zza.1_5'UTR|BCAS1_uc010zzb.1_Silent_p.A160A|BCAS1_uc010gim.2_Silent_p.A160A|BCAS1_uc002xwt.2_Silent_p.A257A|BCAS1_uc010gil.1_Silent_p.A257A	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	257						cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)															---	---	---	---
MC3R	4159	broad.mit.edu	37	20	54824605	54824605	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54824605T>C	uc002xxb.2	+	1	818	c.706T>C	c.(706-708)TCA>CCA	p.S236P		NM_019888	NP_063941	P41968	MC3R_HUMAN	melanocortin 3 receptor	273	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)|breast(2)	4			Colorectal(105;0.202)															---	---	---	---
CASS4	57091	broad.mit.edu	37	20	55033618	55033618	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55033618G>A	uc002xxp.2	+	7	2401	c.2176G>A	c.(2176-2178)GAG>AAG	p.E726K	CASS4_uc002xxr.2_Missense_Mutation_p.E726K|CASS4_uc010zze.1_Missense_Mutation_p.E672K|CASS4_uc010gio.2_Missense_Mutation_p.E289K	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	726					cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3																		---	---	---	---
TUBB1	81027	broad.mit.edu	37	20	57599243	57599243	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57599243C>T	uc002yak.2	+	4	1030	c.761C>T	c.(760-762)GCG>GTG	p.A254V		NM_030773	NP_110400	Q9H4B7	TBB1_HUMAN	beta tubulin 1, class VI	254					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity			ovary(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)		Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)													---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58420254	58420254	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58420254G>A	uc002yau.2	+	12	2065	c.1598G>A	c.(1597-1599)CGT>CAT	p.R533H	PHACTR3_uc002yat.2_Missense_Mutation_p.R530H|PHACTR3_uc010zzw.1_Missense_Mutation_p.R492H|PHACTR3_uc002yav.2_Missense_Mutation_p.R492H|PHACTR3_uc002yaw.2_Missense_Mutation_p.R492H|PHACTR3_uc002yax.2_Missense_Mutation_p.R422H|PHACTR3_uc002yay.2_Missense_Mutation_p.R102H	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	533						nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58467694	58467694	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58467694G>T	uc002yaz.2	-	22	1995	c.1856C>A	c.(1855-1857)ACA>AAA	p.T619K		NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	619					cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)															---	---	---	---
C20orf177	63939	broad.mit.edu	37	20	58519096	58519096	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58519096C>T	uc002yba.2	+	5	513	c.98C>T	c.(97-99)CCG>CTG	p.P33L	C20orf177_uc010zzx.1_Intron|C20orf177_uc002ybc.2_Missense_Mutation_p.P33L	NM_022106	NP_071389	Q9NTX9	CT177_HUMAN	hypothetical protein LOC63939	33										ovary(2)|breast(1)	3	all_lung(29;0.00693)		BRCA - Breast invasive adenocarcinoma(7;1.22e-08)															---	---	---	---
CDH26	60437	broad.mit.edu	37	20	58563978	58563978	+	Missense_Mutation	SNP	G	A	A	rs148034325		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58563978G>A	uc002ybe.2	+	9	1343	c.1043G>A	c.(1042-1044)CGC>CAC	p.R348H	CDH26_uc002ybf.1_5'UTR|CDH26_uc010zzy.1_RNA	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	348	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60498520	60498520	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60498520C>T	uc002ybn.1	+	10	1400	c.1386C>T	c.(1384-1386)TAC>TAT	p.Y462Y	CDH4_uc002ybp.1_Silent_p.Y388Y	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	462	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60572687	60572687	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60572687G>A	uc002ybs.2	-	14	3009	c.3009C>T	c.(3007-3009)GAC>GAT	p.D1003D		NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4	1003					interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
SS18L1	26039	broad.mit.edu	37	20	60749600	60749600	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60749600A>G	uc002ycb.2	+	10	1119	c.1064A>G	c.(1063-1065)TAC>TGC	p.Y355C	SS18L1_uc011aaa.1_Missense_Mutation_p.Y355C|SS18L1_uc002ybz.1_RNA|SS18L1_uc002yca.1_RNA|SS18L1_uc002ycc.1_RNA	NM_198935	NP_945173	O75177	CREST_HUMAN	SS18-like protein 1	355	Gln-rich.|SH2-binding (Potential).|Necessary for nuclear localization (By similarity).				chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)					T	SSX1	synovial sarcoma								---	---	---	---
HRH3	11255	broad.mit.edu	37	20	60791141	60791141	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60791141C>T	uc002ycf.2	-	3	1556	c.1259G>A	c.(1258-1260)CGC>CAC	p.R420H	HRH3_uc002ycg.2_Missense_Mutation_p.R340H|HRH3_uc002ych.2_Missense_Mutation_p.R276H|HRH3_uc002yci.2_Missense_Mutation_p.R420H	NM_007232	NP_009163	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	420	Cytoplasmic (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|neurotransmitter secretion	integral to plasma membrane	histamine receptor activity				0	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Histamine Phosphate(DB00667)													---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61513557	61513557	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61513557C>T	uc002ydr.1	-	16	4015	c.3751G>A	c.(3751-3753)GCG>ACG	p.A1251T	DIDO1_uc002yds.1_Missense_Mutation_p.A1251T	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1251					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
MIR124-3	406909	broad.mit.edu	37	20	61809912	61809912	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61809912G>A	hsa-mir-124-3|MI0000445	+			c.61G>A			uc002yeg.1_RNA																	0																		---	---	---	---
RTEL1	51750	broad.mit.edu	37	20	62292680	62292680	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62292680G>A	uc002yfu.1	+	3	475	c.132G>A	c.(130-132)ACG>ACA	p.T44T	RTEL1_uc011abc.1_RNA|RTEL1_uc002yft.1_Silent_p.T44T|RTEL1_uc011abd.1_Silent_p.T44T|RTEL1_uc002yfv.2_Silent_p.T44T|RTEL1_uc011abe.1_5'UTR|RTEL1_uc002yfw.2_RNA	NM_016434	NP_057518	Q9NZ71	RTEL1_HUMAN	regulator of telomere elongation helicase 1	44	Helicase ATP-binding.|ATP (Probable).				DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)															---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62422026	62422026	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62422026C>T	uc002ygv.1	-	2	286	c.85G>A	c.(85-87)GTC>ATC	p.V29I	ZBTB46_uc002ygu.2_RNA	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	29					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62664259	62664259	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62664259C>T	uc002yho.2	+	21	2907	c.2739C>T	c.(2737-2739)TGC>TGT	p.C913C	PRPF6_uc002yhp.2_Silent_p.C873C|NCRNA00176_uc002yhq.2_5'Flank|NCRNA00176_uc011abq.1_5'Flank	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	913					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)																	---	---	---	---
OPRL1	4987	broad.mit.edu	37	20	62729512	62729512	+	Splice_Site	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62729512T>C	uc002yic.2	+	4	991	c.589_splice	c.e4+2	p.E197_splice	OPRL1_uc002yid.2_Splice_Site_p.E197_splice|OPRL1_uc002yif.3_Splice_Site_p.E192_splice	NM_182647	NP_872588			opiate receptor-like 1						elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)																	---	---	---	---
OPRL1	4987	broad.mit.edu	37	20	62729776	62729776	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62729776G>A	uc002yic.2	+	5	1139	c.737G>A	c.(736-738)CGC>CAC	p.R246H	OPRL1_uc002yid.2_Missense_Mutation_p.R246H|OPRL1_uc002yif.3_Missense_Mutation_p.R241H	NM_182647	NP_872588	P41146	OPRX_HUMAN	opiate receptor-like 1	246	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)																	---	---	---	---
ADAMTS1	9510	broad.mit.edu	37	21	28212637	28212637	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28212637G>A	uc002ymf.2	-	5	2078	c.1623C>T	c.(1621-1623)ATC>ATT	p.I541I		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	541	Disintegrin.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)														---	---	---	---
KRTAP27-1	643812	broad.mit.edu	37	21	31709520	31709520	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31709520C>T	uc002ynx.1	-	1	493	c.467G>A	c.(466-468)CGT>CAT	p.R156H		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	156						intermediate filament				ovary(2)	2																		---	---	---	---
KRTAP19-7	337974	broad.mit.edu	37	21	31933436	31933436	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31933436C>A	uc011adb.1	-	1	173	c.173G>T	c.(172-174)TGG>TTG	p.W58L		NM_181614	NP_853645	Q3SYF9	KR197_HUMAN	keratin associated protein 19-7	58						intermediate filament					0																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32526584	32526584	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32526584G>A	uc002yow.1	-	18	3624	c.3152C>T	c.(3151-3153)ACG>ATG	p.T1051M	TIAM1_uc011adk.1_Missense_Mutation_p.T1051M|TIAM1_uc011adl.1_Missense_Mutation_p.T991M	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1051	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
TCP10L	140290	broad.mit.edu	37	21	33949177	33949177	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33949177A>G	uc002ypw.3	-	5	671	c.555T>C	c.(553-555)AAT>AAC	p.N185N		NM_144659	NP_653260	Q9NV44	CU077_HUMAN	T-complex 10A-2	Error:Variant_position_missing_in_Q9NV44_after_alignment											0																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37649359	37649359	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37649359G>A	uc002yvg.2	+	28	5752	c.5673G>A	c.(5671-5673)CCG>CCA	p.P1891P	DOPEY2_uc011aeb.1_Silent_p.P1840P	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	1891					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DSCR10	259234	broad.mit.edu	37	21	39580289	39580289	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39580289G>A	uc010gnt.1	+	3		c.411G>A				NR_027695				Homo sapiens DSCR10 mRNA, complete cds.												0																		---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41450852	41450852	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41450852G>A	uc002yyq.1	-	26	4925	c.4473C>T	c.(4471-4473)CGC>CGT	p.R1491R	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1491	Extracellular (Potential).|Fibronectin type-III 6.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41725437	41725437	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41725437T>C	uc002yyq.1	-	5	1341	c.889A>G	c.(889-891)AAC>GAC	p.N297D	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	297	Extracellular (Potential).|Ig-like C2-type 3.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
MX2	4600	broad.mit.edu	37	21	42748932	42748932	+	Silent	SNP	A	G	G	rs138362036	by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42748932A>G	uc002yzf.1	+	2	203	c.99A>G	c.(97-99)CCA>CCG	p.P33P	MX2_uc011aer.1_RNA	NM_002463	NP_002454	P20592	MX2_HUMAN	myxovirus resistance protein 2	33					response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)																---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43240038	43240038	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43240038G>A	uc002yzq.1	-	25	3369	c.3258C>T	c.(3256-3258)TGC>TGT	p.C1086C	PRDM15_uc002yzo.2_Silent_p.C757C|PRDM15_uc002yzp.2_Silent_p.C777C|PRDM15_uc002yzr.1_Silent_p.C777C	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	1086	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43241502	43241502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43241502G>A	uc002yzq.1	-	23	3190	c.3079C>T	c.(3079-3081)CGG>TGG	p.R1027W	PRDM15_uc002yzo.2_Missense_Mutation_p.R698W|PRDM15_uc002yzp.2_Missense_Mutation_p.R718W|PRDM15_uc002yzr.1_Missense_Mutation_p.R718W	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	1027	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF295	49854	broad.mit.edu	37	21	43413996	43413996	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43413996A>G	uc002zab.3	-	3	423	c.209T>C	c.(208-210)TTT>TCT	p.F70S	ZNF295_uc002yzz.3_Missense_Mutation_p.F70S|ZNF295_uc002yzy.3_Missense_Mutation_p.F70S|ZNF295_uc002zaa.3_Missense_Mutation_p.F70S|ZNF295_uc010gov.1_Missense_Mutation_p.F70S|ZNF295_uc002zac.2_Missense_Mutation_p.F70S	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	70	Mediates homodimerization.|BTB.				negative regulation of transcription, DNA-dependent|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|nucleus	methyl-CpG binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TFF2	7032	broad.mit.edu	37	21	43767608	43767608	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43767608C>T	uc002zaw.2	-	3	505	c.363G>A	c.(361-363)CCG>CCA	p.P121P		NM_005423	NP_005414	Q03403	TFF2_HUMAN	trefoil factor 2 precursor	121	P-type 2.				digestion	extracellular region				pancreas(1)	1																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44182287	44182287	+	Missense_Mutation	SNP	G	A	A	rs140836666	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44182287G>A	uc002zbm.2	+	14	1243	c.1180G>A	c.(1180-1182)GCC>ACC	p.A394T	PDE9A_uc002zbn.2_Missense_Mutation_p.A267T|PDE9A_uc002zbo.2_Missense_Mutation_p.A341T|PDE9A_uc002zbp.2_Missense_Mutation_p.A187T|PDE9A_uc002zbq.2_Missense_Mutation_p.A292T|PDE9A_uc002zbs.2_Missense_Mutation_p.A187T|PDE9A_uc002zbr.2_Missense_Mutation_p.A187T|PDE9A_uc002zbt.2_Missense_Mutation_p.A266T|PDE9A_uc002zbu.2_Missense_Mutation_p.A260T|PDE9A_uc002zbv.2_Missense_Mutation_p.A234T|PDE9A_uc002zbw.2_Missense_Mutation_p.A177T|PDE9A_uc002zbx.2_Missense_Mutation_p.A334T|PDE9A_uc002zby.2_Missense_Mutation_p.A177T|PDE9A_uc002zbz.2_Missense_Mutation_p.A286T|PDE9A_uc002zca.2_Missense_Mutation_p.A353T|PDE9A_uc002zcb.2_Missense_Mutation_p.A368T|PDE9A_uc002zcc.2_Missense_Mutation_p.A293T|PDE9A_uc002zcd.2_Missense_Mutation_p.A308T|PDE9A_uc002zce.2_Missense_Mutation_p.A327T|PDE9A_uc002zcf.2_Missense_Mutation_p.A187T|PDE9A_uc002zcg.2_Missense_Mutation_p.A187T|PDE9A_uc002zch.2_Missense_Mutation_p.A177T|PDE9A_uc010gpf.1_Missense_Mutation_p.A187T	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a	394	Catalytic (By similarity).				platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
HSF2BP	11077	broad.mit.edu	37	21	44949823	44949823	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44949823G>A	uc002zdi.2	-	9	1148	c.816C>T	c.(814-816)TGC>TGT	p.C272C	HSF2BP_uc011aey.1_Silent_p.C197C	NM_007031	NP_008962	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding	272					spermatogenesis|transcription from RNA polymerase II promoter	cytosol	binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.18)														---	---	---	---
PWP2	5822	broad.mit.edu	37	21	45535194	45535194	+	Missense_Mutation	SNP	G	A	A	rs35001460	byFrequency;by1000genomes	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45535194G>A	uc002zeb.2	+	6	610	c.520G>A	c.(520-522)GAG>AAG	p.E174K		NM_005049	NP_005040	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog	174	WD 4.					cytoplasm|nucleolus	signal transducer activity			pancreas(1)	1				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)														---	---	---	---
SUMO3	6612	broad.mit.edu	37	21	46233966	46233966	+	Silent	SNP	G	A	A	rs144060064	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46233966G>A	uc002zfz.1	-	2	236	c.75C>T	c.(73-75)GAC>GAT	p.D25D	SUMO3_uc011afi.1_Silent_p.D25D|SUMO3_uc002zga.1_Silent_p.D25D	NM_006936	NP_008867	P55854	SUMO3_HUMAN	small ubiquitin-like modifier protein 3	25	Ubiquitin-like.				protein sumoylation	cytoplasm|kinetochore	protein binding				0				Colorectal(79;0.058)														---	---	---	---
POFUT2	23275	broad.mit.edu	37	21	46705585	46705585	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46705585G>A	uc002zhc.2	-						POFUT2_uc002zhb.2_Intron|POFUT2_uc002zhd.2_Intron|POFUT2_uc011afp.1_Intron|POFUT2_uc011afq.1_Silent_p.A130A|LOC642852_uc002zhf.2_5'Flank	NM_133635	NP_598368			protein O-fucosyltransferase 2 isoform C						fucose metabolic process	endoplasmic reticulum	peptide-O-fucosyltransferase activity				0				Colorectal(79;0.243)														---	---	---	---
COL6A2	1292	broad.mit.edu	37	21	47549313	47549313	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47549313C>T	uc002zia.1	+						COL6A2_uc002zhy.1_3'UTR|COL6A2_uc002zhz.1_Missense_Mutation_p.R889W|COL6A2_uc002zib.1_Intron|COL6A2_uc002zic.1_Intron|COL6A2_uc010gqe.1_5'Flank	NM_001849	NP_001840			alpha 2 type VI collagen isoform 2C2 precursor						axon guidance|cell-cell adhesion|extracellular matrix organization|protein heterotrimerization	collagen|extracellular space|protein complex	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(7)|ovary(1)	8	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47746281	47746281	+	Intron	SNP	T	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47746281T>G	uc002zji.3	+						PCNT_uc002zjj.2_Intron|C21orf58_uc011afx.1_5'Flank|C21orf58_uc002zjf.2_5'Flank|C21orf58_uc010gqj.1_5'Flank|C21orf58_uc002zjg.1_5'Flank	NM_006031	NP_006022			pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47863758	47863758	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47863758A>G	uc002zji.3	+	45	9843	c.9736A>G	c.(9736-9738)ACC>GCC	p.T3246A	PCNT_uc002zjj.2_Missense_Mutation_p.T3049A	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	3246	Interaction with NEK2.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
IL17RA	23765	broad.mit.edu	37	22	17585617	17585617	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17585617T>A	uc002zly.2	+	9	981	c.848T>A	c.(847-849)ATC>AAC	p.I283N	IL17RA_uc010gqt.2_Missense_Mutation_p.I283N	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor	283	Extracellular (Potential).				fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17956689	17956689	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17956689C>T	uc010gqw.1	+	1	186	c.60C>T	c.(58-60)TGC>TGT	p.C20C	CECR2_uc010gqv.1_5'UTR|CECR2_uc002zml.2_5'UTR	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	62					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
BID	637	broad.mit.edu	37	22	18222897	18222897	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18222897G>A	uc002znd.1	-						BID_uc002znc.1_Intron|BID_uc002zne.1_Intron|BID_uc010gra.1_RNA|BID_uc002znf.1_Intron|BID_uc010grb.1_Intron|BID_uc010grc.1_Intron	NM_001196	NP_001187			BH3 interacting domain death agonist isoform 2						activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria	cytosol|membrane fraction|mitochondrial outer membrane	death receptor binding				0		all_epithelial(15;0.198)		Lung(27;0.0419)														---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18314790	18314790	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18314790G>A	uc002zng.3	-	21	3238	c.2885C>T	c.(2884-2886)CCG>CTG	p.P962L	MICAL3_uc011agl.1_Missense_Mutation_p.P962L	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin	962	Glu-rich.					cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19203739	19203739	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19203739G>A	uc002zpb.2	-	19	3022	c.2947C>T	c.(2947-2949)CGG>TGG	p.R983W	CLTCL1_uc011agv.1_Missense_Mutation_p.R983W|CLTCL1_uc011agw.1_Missense_Mutation_p.R983W|CLTCL1_uc002zpe.2_5'Flank|CLTCL1_uc002zpd.1_5'Flank	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	983	Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19365423	19365423	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19365423T>C	uc002zpf.1	-	14	1802	c.1582A>G	c.(1582-1584)AGA>GGA	p.R528G	HIRA_uc011agx.1_Missense_Mutation_p.R394G|HIRA_uc010grn.1_Missense_Mutation_p.R528G|HIRA_uc010gro.1_Missense_Mutation_p.R484G|HIRA_uc010grp.2_RNA	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	528	Interaction with CCNA1.				chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
CDC45	8318	broad.mit.edu	37	22	19504123	19504123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19504123C>T	uc002zpr.2	+	16	1590	c.1514C>T	c.(1513-1515)ACC>ATC	p.T505I	CDC45_uc011aha.1_Missense_Mutation_p.T537I|CDC45_uc002zps.2_Missense_Mutation_p.T505I|CDC45_uc002zpt.2_Missense_Mutation_p.T459I	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like	505					DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1																		---	---	---	---
GNB1L	54584	broad.mit.edu	37	22	19799838	19799838	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19799838C>T	uc002zqe.1	-	4	781	c.387G>A	c.(385-387)ACG>ACA	p.T129T	GNB1L_uc002zqd.1_5'UTR|GNB1L_uc002zqf.1_Silent_p.T129T	NM_053004	NP_443730	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein	129					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular				breast(1)	1	Colorectal(54;0.0993)																	---	---	---	---
C22orf29	79680	broad.mit.edu	37	22	19839606	19839606	+	Missense_Mutation	SNP	G	A	A	rs143706825	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19839606G>A	uc002zqg.2	-	2	778	c.179C>T	c.(178-180)ACG>ATG	p.T60M	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Missense_Mutation_p.T60M|C22orf29_uc002zqi.2_Missense_Mutation_p.T60M|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	60											0	Colorectal(54;0.0993)																	---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20040988	20040988	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20040988T>C	uc010grw.1	+	6	631	c.294T>C	c.(292-294)ACT>ACC	p.T98T	C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Silent_p.T98T|C22orf25_uc002zrd.1_Silent_p.T64T|C22orf25_uc002zre.2_Silent_p.T98T|C22orf25_uc010grx.2_Intron|C22orf25_uc011ahe.1_Intron|C22orf25_uc011ahf.1_Intron|C22orf25_uc011ahg.1_Silent_p.T139T|C22orf25_uc002zrg.2_Silent_p.T139T|C22orf25_uc011ahh.1_Silent_p.T98T|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron|C22orf25_uc010gry.1_Intron|C22orf25_uc002zrh.1_Intron	NM_152906	NP_690870	Q6ICL3	CV025_HUMAN	hypothetical protein LOC128989	98											0	Colorectal(54;0.0533)																	---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21081658	21081658	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21081658C>T	uc002zsz.3	-	41	4858	c.4627G>A	c.(4627-4629)GCC>ACC	p.A1543T	PI4KA_uc002zsy.3_Missense_Mutation_p.A353T	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	1543					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)															---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21159362	21159362	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21159362G>A	uc002zsz.3	-	11	1317	c.1086C>T	c.(1084-1086)GAC>GAT	p.D362D	PI4KA_uc010gsq.1_Silent_p.D420D	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	362					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)															---	---	---	---
VPREB1	7441	broad.mit.edu	37	22	22599391	22599391	+	Missense_Mutation	SNP	C	T	T	rs142180774		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22599391C>T	uc002zvx.1	+	2	106	c.80C>T	c.(79-81)CCG>CTG	p.P27L	LOC96610_uc011aim.1_Intron	NM_007128	NP_009059	P12018	VPREB_HUMAN	immunoglobulin iota chain precursor	27	Framework-1.|Ig-like V-type.				immune response	extracellular region	antigen binding|protein binding				0	all_hematologic(9;0.0312)|Acute lymphoblastic leukemia(84;0.155)	all_cancers(3;3.14e-14)|Acute lymphoblastic leukemia(3;2.97e-57)|all_hematologic(3;5.9e-52)		READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22764330	22764330	+	RNA	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22764330G>A	uc011aim.1	+	58		c.6117G>A								Parts of antibodies, mostly variable regions.												0																OREG0026360	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
BCR	613	broad.mit.edu	37	22	23603709	23603709	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23603709C>T	uc002zww.2	+	4	2330	c.1734C>T	c.(1732-1734)GGC>GGT	p.G578G	BCR_uc002zwx.2_Silent_p.G578G|BCR_uc011aiy.1_Silent_p.G167G|BCR_uc010gtx.1_Silent_p.G81G|uc010gty.2_5'Flank	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1	578	DH.				regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24720352	24720352	+	Silent	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24720352T>C	uc002zzw.2	+	6	2410	c.2103T>C	c.(2101-2103)CGT>CGC	p.R701R	CYTSA_uc002zzv.3_Silent_p.R701R|CYTSA_uc011ajq.1_Silent_p.R701R	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A	701	Potential.				cell cycle|cell division						0																		---	---	---	---
GGT1	2678	broad.mit.edu	37	22	25011032	25011032	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25011032G>A	uc003aan.1	+	7	807	c.320G>A	c.(319-321)CGC>CAC	p.R107H	GGT1_uc003aas.1_Missense_Mutation_p.R107H|GGT1_uc003aat.1_Missense_Mutation_p.R107H|GGT1_uc003aau.1_Missense_Mutation_p.R107H|GGT1_uc003aav.1_Missense_Mutation_p.R107H|GGT1_uc003aaw.1_Missense_Mutation_p.R107H|GGT1_uc003aax.1_Missense_Mutation_p.R107H	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor	107	Extracellular (Potential).			R->Q,H: Abolishes enzyme activity.|R->K: Reduces enzyme activity by 99%.	glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)													---	---	---	---
TFIP11	24144	broad.mit.edu	37	22	26888277	26888277	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26888277C>T	uc003acr.2	-	14	2590	c.2216G>A	c.(2215-2217)CGG>CAG	p.R739Q	TFIP11_uc003acq.2_Missense_Mutation_p.R98Q|TFIP11_uc003acs.2_Missense_Mutation_p.R739Q|TFIP11_uc003act.2_Missense_Mutation_p.R739Q|uc003acu.1_RNA	NM_012143	NP_036275	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	739					biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29442840	29442840	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29442840C>A	uc003aeg.2	+	6	746	c.581C>A	c.(580-582)GCC>GAC	p.A194D	ZNRF3_uc003aeh.1_Missense_Mutation_p.A194D	NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	294	RING-type; atypical.|Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
RFPL1	5988	broad.mit.edu	37	22	29834817	29834817	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29834817T>C	uc003afn.2	+	1	246	c.37T>C	c.(37-39)TCA>CCA	p.S13P	RFPL1S_uc003afm.1_RNA	NM_021026	NP_066306	O75677	RFPL1_HUMAN	ret finger protein-like 1	13							zinc ion binding				0																		---	---	---	---
OSM	5008	broad.mit.edu	37	22	30660368	30660368	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30660368C>T	uc003ahb.2	-	3	315	c.263G>A	c.(262-264)AGG>AAG	p.R88K		NM_020530	NP_065391	P13725	ONCM_HUMAN	oncostatin M precursor	88					cell proliferation|immune response|negative regulation of cell proliferation|negative regulation of hormone secretion|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of MAPKKK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of growth	extracellular space|oncostatin-M receptor complex	cytokine activity|growth factor activity|oncostatin-M receptor binding			skin(1)	1			Epithelial(10;0.206)															---	---	---	---
GAL3ST1	9514	broad.mit.edu	37	22	30950997	30950997	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30950997G>A	uc003aig.1	-	4	1355	c.1215C>T	c.(1213-1215)GGC>GGT	p.G405G	GAL3ST1_uc003aih.1_Silent_p.G405G|GAL3ST1_uc003aii.1_Silent_p.G405G|GAL3ST1_uc010gvz.1_Silent_p.G405G	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	405	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0																		---	---	---	---
GAL3ST1	9514	broad.mit.edu	37	22	30952056	30952056	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30952056G>A	uc003aig.1	-	4	296	c.156C>T	c.(154-156)TGC>TGT	p.C52C	GAL3ST1_uc003aih.1_Silent_p.C52C|GAL3ST1_uc003aii.1_Silent_p.C52C|GAL3ST1_uc010gvz.1_Silent_p.C52C	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	52	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0																		---	---	---	---
TCN2	6948	broad.mit.edu	37	22	31011386	31011386	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31011386C>T	uc003aip.1	+	5	837	c.679C>T	c.(679-681)CGA>TGA	p.R227*	TCN2_uc003aiq.1_Nonsense_Mutation_p.R223*|TCN2_uc003air.1_Nonsense_Mutation_p.R200*	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor	227					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
LIMK2	3985	broad.mit.edu	37	22	31671260	31671260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31671260G>A	uc003akh.2	+	15	1883	c.1738G>A	c.(1738-1740)GCC>ACC	p.A580T	LIMK2_uc003akg.2_Missense_Mutation_p.A497T|LIMK2_uc003aki.2_Missense_Mutation_p.A334T|LIMK2_uc003akj.2_Missense_Mutation_p.A559T|LIMK2_uc003akk.2_Missense_Mutation_p.A559T|LIMK2_uc011aln.1_Missense_Mutation_p.A497T	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a	580	Protein kinase.					mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31927033	31927033	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31927033C>T	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468			spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
RFPL2	10739	broad.mit.edu	37	22	32586994	32586994	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32586994C>T	uc003amg.3	-	5	1838	c.902G>A	c.(901-903)CGC>CAC	p.R301H	RFPL2_uc003ame.3_Missense_Mutation_p.R240H|RFPL2_uc003amf.3_Missense_Mutation_p.R211H|RFPL2_uc003amh.3_Missense_Mutation_p.R211H	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2	301	B30.2/SPRY.						zinc ion binding			skin(1)	1																		---	---	---	---
FOXRED2	80020	broad.mit.edu	37	22	36902101	36902101	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36902101G>A	uc003apn.3	-	1	477	c.369C>T	c.(367-369)CGC>CGT	p.R123R	FOXRED2_uc003apo.3_Silent_p.R123R|FOXRED2_uc003app.3_Silent_p.R123R	NM_024955	NP_079231	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	123					ER-associated protein catabolic process	endoplasmic reticulum lumen	flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			lung(1)|kidney(1)	2																		---	---	---	---
EIF3D	8664	broad.mit.edu	37	22	36907674	36907674	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36907674C>A	uc003apq.2	-	14	1625	c.1509G>T	c.(1507-1509)GAG>GAT	p.E503D	EIF3D_uc011amr.1_Missense_Mutation_p.E330D|EIF3D_uc003apr.2_Missense_Mutation_p.E503D|EIF3D_uc011ams.1_Missense_Mutation_p.E406D|EIF3D_uc011amt.1_Missense_Mutation_p.E454D	NM_003753	NP_003744	O15371	EIF3D_HUMAN	eukaryotic translation initiation factor 3	503						cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			pancreas(1)	1																OREG0026522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CSF2RB	1439	broad.mit.edu	37	22	37334174	37334174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37334174G>A	uc003aqa.3	+	14	2541	c.2324G>A	c.(2323-2325)CGG>CAG	p.R775Q	CSF2RB_uc003aqc.3_Missense_Mutation_p.R781Q	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	775	Cytoplasmic (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)													---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37898705	37898705	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37898705G>T	uc003asx.1	-	11	1694	c.1691C>A	c.(1690-1692)CCT>CAT	p.P564H	CARD10_uc003ast.1_RNA|CARD10_uc003asw.1_Missense_Mutation_p.P278H|CARD10_uc003asy.1_Missense_Mutation_p.P564H	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	564					activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
GGA1	26088	broad.mit.edu	37	22	38019594	38019594	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38019594G>A	uc003atc.2	+	9	1151	c.786G>A	c.(784-786)ACG>ACA	p.T262T	GGA1_uc003atd.2_Silent_p.T262T|GGA1_uc003ate.2_Silent_p.T262T|GGA1_uc003atf.2_Silent_p.T189T	NM_013365	NP_037497	Q9UJY5	GGA1_HUMAN	golgi associated, gamma adaptin ear containing,	262	Interaction with ARF3.|GAT.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|Golgi apparatus part	protein binding			breast(2)|ovary(1)	3	Melanoma(58;0.0574)															OREG0026543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KCNJ4	3761	broad.mit.edu	37	22	38823465	38823465	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38823465T>C	uc003avs.1	-	2	770	c.673A>G	c.(673-675)AAG>GAG	p.K225E	KCNJ4_uc003avt.1_Missense_Mutation_p.K225E	NM_004981	NP_004972	P48050	IRK4_HUMAN	potassium inwardly-rectifying channel J4	225	Cytoplasmic (By similarity).				synaptic transmission	basolateral plasma membrane|voltage-gated potassium channel complex	inward rectifier potassium channel activity|PDZ domain binding				0	Melanoma(58;0.0286)																	---	---	---	---
CBY1	25776	broad.mit.edu	37	22	39064147	39064147	+	Intron	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39064147G>T	uc003awb.2	+						CBY1_uc011any.1_Intron|CBY1_uc003awc.2_Intron	NM_001002880	NP_001002880			PKD2 interactor, golgi and endoplasmic reticulum						cardiac muscle cell differentiation|fat cell differentiation|negative regulation of transcription, DNA-dependent|protein localization	nuclear speck|trans-Golgi network	beta-catenin binding|identical protein binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39907309	39907309	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39907309G>A	uc003axx.2	+	3	508	c.10G>A	c.(10-12)GCT>ACT	p.A4T	SMCR7L_uc003axw.2_Missense_Mutation_p.A4T|SMCR7L_uc010gxz.1_5'UTR|SMCR7L_uc003axy.2_5'UTR	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	4						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)																	---	---	---	---
FAM83F	113828	broad.mit.edu	37	22	40417387	40417387	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40417387G>A	uc003ayk.1	+	4	967	c.873G>A	c.(871-873)CTG>CTA	p.L291L		NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828	291										breast(1)	1																		---	---	---	---
ADSL	158	broad.mit.edu	37	22	40754971	40754971	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40754971C>T	uc003ayp.3	+	5	645	c.586C>T	c.(586-588)CGG>TGG	p.R196W	ADSL_uc003ays.3_Missense_Mutation_p.R196W|ADSL_uc003ayq.3_Missense_Mutation_p.R196W|ADSL_uc003ayr.3_5'UTR|ADSL_uc003ayt.3_Missense_Mutation_p.R181W|ADSL_uc010gyb.1_RNA	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a	196					AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1																		---	---	---	---
SGSM3	27352	broad.mit.edu	37	22	40803476	40803476	+	Silent	SNP	G	A	A	rs144704559		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40803476G>A	uc003ayu.1	+	13	1637	c.1428G>A	c.(1426-1428)GCG>GCA	p.A476A	SGSM3_uc011aos.1_Silent_p.A409A|SGSM3_uc011aot.1_Silent_p.A413A|SGSM3_uc010gyd.1_Silent_p.A547A	NM_015705	NP_056520	Q96HU1	SGSM3_HUMAN	small G protein signaling modulator 3	476					cell cycle arrest|Rap protein signal transduction	cytoplasm	Rab GTPase activator activity|Rab GTPase binding			ovary(2)	2																		---	---	---	---
EP300	2033	broad.mit.edu	37	22	41573146	41573146	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41573146C>T	uc003azl.3	+	31	5826	c.5431C>T	c.(5431-5433)CAG>TAG	p.Q1811*		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	1811	Binding region for E1A adenovirus.				apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
L3MBTL2	83746	broad.mit.edu	37	22	41615414	41615414	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41615414G>A	uc003azo.2	+						L3MBTL2_uc010gyi.1_Intron|L3MBTL2_uc003azn.2_Intron|uc003azp.1_5'Flank	NM_031488	NP_113676			l(3)mbt-like 2						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
PHF5A	84844	broad.mit.edu	37	22	41863525	41863525	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41863525C>T	uc003bab.2	-	3	221	c.170G>A	c.(169-171)CGC>CAC	p.R57H	ACO2_uc003bac.2_5'Flank|ACO2_uc003bad.2_5'Flank	NM_032758	NP_116147	Q7RTV0	PHF5A_HUMAN	PHD-finger 5A	57					nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent	nuclear speck|U12-type spliceosomal complex|U2 snRNP	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
PHF5A	84844	broad.mit.edu	37	22	41863622	41863622	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41863622T>C	uc003bab.2	-						ACO2_uc003bac.2_5'Flank|ACO2_uc003bad.2_5'Flank	NM_032758	NP_116147			PHD-finger 5A						nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent	nuclear speck|U12-type spliceosomal complex|U2 snRNP	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SREBF2	6721	broad.mit.edu	37	22	42289187	42289187	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42289187C>T	uc003bbi.2	+	12	2444	c.2275C>T	c.(2275-2277)CGC>TGC	p.R759C	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.2_RNA	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription	759	Cytoplasmic (Potential).				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
PNPLA3	80339	broad.mit.edu	37	22	44342042	44342042	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44342042T>C	uc003bei.1	+	9	1399	c.1226T>C	c.(1225-1227)ATG>ACG	p.M409T	PNPLA3_uc010gzm.1_Intron	NM_025225	NP_079501	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	409	Lumenal (Potential).				triglyceride biosynthetic process|triglyceride catabolic process	integral to membrane	diolein transacylation activity|mono-olein transacylation activity|phospholipase A2 activity|triglyceride lipase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)														OREG0026623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NUP50	10762	broad.mit.edu	37	22	45574201	45574201	+	Silent	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45574201C>A	uc003bfr.2	+	5	885	c.423C>A	c.(421-423)TCC>TCA	p.S141S	NUP50_uc003bfs.2_Silent_p.S113S|NUP50_uc011aqn.1_5'UTR|NUP50_uc003bft.2_Silent_p.S113S|NUP50_uc011aqo.1_5'UTR	NM_007172	NP_009103	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa isoform b	141	5 X 2 AA repeats of F-G.				carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
PKDREJ	10343	broad.mit.edu	37	22	46655629	46655629	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46655629G>A	uc003bhh.2	-	1	3591	c.3591C>T	c.(3589-3591)TAC>TAT	p.Y1197Y		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1197	Helical; (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46760103	46760103	+	Missense_Mutation	SNP	G	A	A	rs149360981		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46760103G>A	uc003bhw.1	-	34	8825	c.8825C>T	c.(8824-8826)ACG>ATG	p.T2942M		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	2942	Cytoplasmic (Potential).				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
ZBED4	9889	broad.mit.edu	37	22	50279575	50279575	+	Silent	SNP	G	A	A	rs149198396	byFrequency	TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50279575G>A	uc003bix.2	+	2	2735	c.2265G>A	c.(2263-2265)TCG>TCA	p.S755S		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	755						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TYMP	1890	broad.mit.edu	37	22	50967665	50967665	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50967665T>C	uc003bmb.3	-	2	437	c.317A>G	c.(316-318)GAG>GGG	p.E106G	TYMP_uc003bmc.3_Missense_Mutation_p.E106G|TYMP_uc003bmd.3_Missense_Mutation_p.E106G|TYMP_uc010hbd.2_Missense_Mutation_p.E106G|TYMP_uc003bme.3_Missense_Mutation_p.E106G|TYMP_uc003bmf.3_Missense_Mutation_p.E106G|TYMP_uc011arz.1_Missense_Mutation_p.E106G	NM_001113756	NP_001107228	P19971	TYPH_HUMAN	endothelial cell growth factor 1	106					angiogenesis|cell differentiation|chemotaxis|DNA replication|mitochondrial genome maintenance|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol	growth factor activity|platelet-derived growth factor receptor binding|pyrimidine-nucleoside phosphorylase activity|thymidine phosphorylase activity			ovary(1)	1		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Docetaxel(DB01248)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Sulfasalazine(DB00795)|Tamoxifen(DB00675)													---	---	---	---
SFRS17A	8227	broad.mit.edu	37	X	1712692	1712692	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1712692C>T	uc004cqa.2	+	2	533	c.337C>T	c.(337-339)CGC>TGC	p.R113C	SFRS17A_uc010ncx.1_Missense_Mutation_p.R113C|SFRS17A_uc004cqb.2_RNA|ASMT_uc004cqd.2_5'Flank	NM_005088	NP_005079	Q02040	AK17A_HUMAN	DNA segment on chromosome X and Y (unique) 155	113					B cell activation|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|signal transduction	nuclear speck|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13786334	13786334	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13786334G>A	uc004cvp.3	+	21	3278	c.2919G>A	c.(2917-2919)TCG>TCA	p.S973S	OFD1_uc004cvr.3_Silent_p.S503S|OFD1_uc011mil.1_Silent_p.S540S|OFD1_uc004cvq.3_Silent_p.S796S|OFD1_uc010nen.2_Silent_p.S971S|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_Silent_p.S932S|OFD1_uc004cvv.3_Silent_p.S931S	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	973	Mediates the interaction with SDCCAG8.				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																		---	---	---	---
PIGA	5277	broad.mit.edu	37	X	15343140	15343140	+	Splice_Site	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15343140A>G	uc004cwr.2	-	4	1081	c.981_splice	c.e4+1	p.Q327_splice	PIGA_uc010neu.2_Intron|PIGA_uc004cwq.2_Splice_Site_p.Q12_splice|PIGA_uc010nev.2_Splice_Site_p.Q158_splice|PIGA_uc004cws.2_Splice_Site_p.Q12_splice|PIGA_uc011miq.1_Splice_Site_p.Q93_splice	NM_002641	NP_002632			phosphatidylinositol						C-terminal protein lipidation|positive regulation of metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity|protein binding				0	Hepatocellular(33;0.183)																	---	---	---	---
CTPS2	56474	broad.mit.edu	37	X	16657037	16657037	+	Intron	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16657037A>G	uc004cxk.2	-						CTPS2_uc004cxl.2_Intron|CTPS2_uc004cxm.2_Intron	NM_001144002	NP_001137474			cytidine triphosphate synthase II						glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
SCML2	10389	broad.mit.edu	37	X	18278323	18278323	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18278323G>T	uc004cyl.2	-	9	1194	c.1037C>A	c.(1036-1038)GCT>GAT	p.A346D	SCML2_uc004cyk.3_RNA|SCML2_uc010nfd.1_Missense_Mutation_p.A346D|SCML2_uc011miz.1_Missense_Mutation_p.A280D|SCML2_uc010nfc.2_Missense_Mutation_p.A82D	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	346					anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
PHKA2	5256	broad.mit.edu	37	X	18936875	18936875	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18936875G>A	uc004cyv.3	-	19	2491	c.2061C>T	c.(2059-2061)CGC>CGT	p.R687R	PHKA2_uc004cyu.3_5'UTR	NM_000292	NP_000283	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	687					glucose metabolic process|glycogen catabolic process	cytosol|phosphorylase kinase complex|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(1)|central_nervous_system(1)	2	Hepatocellular(33;0.183)																	---	---	---	---
TAB3	257397	broad.mit.edu	37	X	30852246	30852246	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30852246C>T	uc004dcj.2	-	10	2575	c.1912G>A	c.(1912-1914)GAG>AAG	p.E638K	TAB3_uc004dck.2_Missense_Mutation_p.E638K|TAB3_uc010ngl.2_Missense_Mutation_p.E610K	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	638					activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46502752	46502752	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46502752G>A	uc004dgu.1	-	12	1540	c.1532C>T	c.(1531-1533)ACG>ATG	p.T511M		NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	511					regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46508110	46508110	+	Intron	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46508110C>T	uc004dgu.1	-							NM_032591	NP_115980			solute carrier family 9, member 7						regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
FOXP3	50943	broad.mit.edu	37	X	49107934	49107934	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49107934C>T	uc004dnf.3	-	12	1345	c.1157G>A	c.(1156-1158)CGC>CAC	p.R386H	FOXP3_uc011mnb.1_Missense_Mutation_p.R409H|FOXP3_uc011mnc.1_Missense_Mutation_p.R359H|FOXP3_uc004dne.3_Missense_Mutation_p.R351H|FOXP3_uc010niq.1_Missense_Mutation_p.R411H	NM_014009	NP_054728	Q9BZS1	FOXP3_HUMAN	forkhead box P3 isoform a	386	Fork-head.				B cell homeostasis|cerebellum development|chromatin remodeling|embryo development|myeloid cell homeostasis|negative regulation of activated T cell proliferation|negative regulation of chronic inflammatory response|negative regulation of CREB transcription factor activity|negative regulation of cytokine secretion|negative regulation of histone acetylation|negative regulation of histone deacetylation|negative regulation of interferon-gamma biosynthetic process|negative regulation of interferon-gamma production|negative regulation of interleukin-10 production|negative regulation of interleukin-2 biosynthetic process|negative regulation of interleukin-2 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of interleukin-6 production|negative regulation of isotype switching to IgE isotypes|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell cytokine production|negative regulation of tumor necrosis factor production|pattern specification process|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation|positive regulation of histone acetylation|positive regulation of immature T cell proliferation in thymus|positive regulation of peripheral T cell tolerance induction|positive regulation of T cell anergy|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transforming growth factor-beta1 production|post-embryonic development|regulation of isotype switching to IgG isotypes|response to virus|T cell homeostasis|T cell receptor signaling pathway|tolerance induction to self antigen	cytoplasm|cytoplasm|nucleus|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|histone acetyltransferase binding|histone deacetylase binding|NF-kappaB binding|NFAT protein binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription corepressor activity|zinc ion binding				0	Ovarian(276;0.236)																	---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54584930	54584930	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54584930G>A	uc004dth.1	+	15	1647	c.1508G>A	c.(1507-1509)CGC>CAC	p.R503H	GNL3L_uc004dti.2_RNA	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3	503					ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
TRO	7216	broad.mit.edu	37	X	54956964	54956964	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54956964C>T	uc004dtq.2	+	12	3914	c.3807C>T	c.(3805-3807)TTC>TTT	p.F1269F	TRO_uc004dts.2_Intron|TRO_uc004dtr.2_Intron|TRO_uc004dtt.2_Intron|TRO_uc004dtu.2_Intron|TRO_uc004dtv.2_Intron|TRO_uc011mok.1_Silent_p.F800F|TRO_uc004dtw.2_Silent_p.F872F|TRO_uc004dtx.2_Silent_p.F652F	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	1269	46; approximate.|62 X 10 AA approximate tandem repeats.				embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1																		---	---	---	---
ZC3H12B	340554	broad.mit.edu	37	X	64709206	64709206	+	Silent	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64709206C>T	uc010nko.2	+	1	501	c.492C>T	c.(490-492)AGC>AGT	p.S164S		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	164							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3																		---	---	---	---
MED12	9968	broad.mit.edu	37	X	70347909	70347909	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70347909C>T	uc004dyy.2	+	22	3347	c.3148C>T	c.(3148-3150)CGC>TGC	p.R1050C	MED12_uc011mpq.1_Missense_Mutation_p.R1050C|MED12_uc004dyz.2_Missense_Mutation_p.R1050C|MED12_uc004dza.2_Missense_Mutation_p.R897C|MED12_uc010nla.2_5'Flank	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1050					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)																	---	---	---	---
XIST	7503	broad.mit.edu	37	X	73070733	73070733	+	RNA	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73070733G>T	uc004ebm.1	-	1		c.1856C>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
MAGEE1	57692	broad.mit.edu	37	X	75651143	75651143	+	Silent	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75651143G>A	uc004ecm.1	+	1	3027	c.2820G>A	c.(2818-2820)GAG>GAA	p.E940E		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	940	Interaction with DTNA (By similarity).					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6																		---	---	---	---
ATRX	546	broad.mit.edu	37	X	76912118	76912118	+	Silent	SNP	A	G	G			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76912118A>G	uc004ecp.3	-	13	4378	c.4146T>C	c.(4144-4146)TCT>TCC	p.S1382S	ATRX_uc004ecq.3_Silent_p.S1344S|ATRX_uc004eco.3_Silent_p.S1167S|ATRX_uc004ecr.2_Silent_p.S1314S	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1382					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						---	---	---	---
POU3F4	5456	broad.mit.edu	37	X	82764114	82764114	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82764114C>T	uc004eeg.2	+	1	846	c.782C>T	c.(781-783)TCG>TTG	p.S261L		NM_000307	NP_000298	P49335	PO3F4_HUMAN	POU domain, class 3, transcription factor 4	261					sensory perception of sound	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
TSPAN6	7105	broad.mit.edu	37	X	99888927	99888927	+	Splice_Site	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99888927C>T	uc004ega.1	-	4	553	c.450_splice	c.e4+1	p.T150_splice	TSPAN6_uc010nna.1_Splice_Site_p.T56_splice	NM_003270	NP_003261			transmembrane 4 superfamily member 6						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity			ovary(1)	1																		---	---	---	---
BEX4	56271	broad.mit.edu	37	X	102471433	102471433	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102471433C>A	uc004ejv.3	+	3	587	c.352C>A	c.(352-354)CTC>ATC	p.L118I	BEX4_uc004ejw.3_Missense_Mutation_p.L118I	NM_001080425	NP_001073894	Q9NWD9	BEX4_HUMAN	BEX family member 4	118						cytoplasm|nucleus				skin(1)	1																		---	---	---	---
MORF4L2	9643	broad.mit.edu	37	X	102931615	102931615	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102931615G>A	uc004ekw.2	-	4	1573	c.341C>T	c.(340-342)GCG>GTG	p.A114V	MORF4L2_uc004ela.2_Missense_Mutation_p.A114V|MORF4L2_uc004ekx.2_Missense_Mutation_p.A114V|MORF4L2_uc004elb.2_Missense_Mutation_p.A114V|MORF4L2_uc004eky.2_Missense_Mutation_p.A114V|MORF4L2_uc010nos.2_Missense_Mutation_p.A114V|MORF4L2_uc004ekz.2_Missense_Mutation_p.A114V|MORF4L2_uc011mry.1_Missense_Mutation_p.A114V|MORF4L2_uc011mrz.1_Missense_Mutation_p.A114V|MORF4L2_uc004elc.2_Missense_Mutation_p.A114V|MORF4L2_uc004elf.2_Missense_Mutation_p.A114V|MORF4L2_uc004ele.2_Missense_Mutation_p.A114V|MORF4L2_uc011msa.1_Missense_Mutation_p.A114V|MORF4L2_uc011msb.1_Missense_Mutation_p.A114V|MORF4L2_uc011msc.1_Missense_Mutation_p.A114V|MORF4L2_uc011msd.1_Missense_Mutation_p.A114V|MORF4L2_uc004eld.2_Missense_Mutation_p.A114V	NM_012286	NP_036418	Q15014	MO4L2_HUMAN	mortality factor 4 like 2	114					chromatin modification|DNA repair|regulation of cell growth|transcription, DNA-dependent	nucleolus	protein binding				0																		---	---	---	---
NRK	203447	broad.mit.edu	37	X	105142714	105142714	+	Intron	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105142714G>A	uc004emd.2	+						NRK_uc010npc.1_Intron	NM_198465	NP_940867			Nik related kinase								ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14															HNSCC(51;0.14)			---	---	---	---
TBC1D8B	54885	broad.mit.edu	37	X	106070428	106070428	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106070428C>T	uc004emo.2	+	7	1229	c.1064C>T	c.(1063-1065)TCC>TTC	p.S355F	MORC4_uc004emp.3_Intron|TBC1D8B_uc004emm.2_Missense_Mutation_p.S355F|TBC1D8B_uc004emn.2_Missense_Mutation_p.S355F	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	355						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106808260	106808260	+	IGR	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106808260C>T								CXorf41 (320788 upstream) : PRPS1 (63394 downstream)																																			---	---	---	---
COL4A5	1287	broad.mit.edu	37	X	107930885	107930885	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107930885T>C	uc004enz.1	+	48	4691	c.4489T>C	c.(4489-4491)TAT>CAT	p.Y1497H	COL4A5_uc011mso.1_Missense_Mutation_p.Y1494H|COL4A5_uc011msp.1_Missense_Mutation_p.Y173H	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	1491	Collagen IV NC1.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119694119	119694119	+	Silent	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119694119G>T	uc004esw.2	-	3	866	c.429C>A	c.(427-429)TCC>TCA	p.S143S	CUL4B_uc004esv.2_Silent_p.S125S	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1	143	Ser-rich.				cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
FRMD7	90167	broad.mit.edu	37	X	131228096	131228096	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131228096G>A	uc004ewn.2	-	5	534	c.356C>T	c.(355-357)GCG>GTG	p.A119V	FRMD7_uc011muy.1_Missense_Mutation_p.A104V	NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	119	FERM.				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
RAP2C	57826	broad.mit.edu	37	X	131348187	131348187	+	3'UTR	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131348187T>C	uc004ewp.2	-	3					RAP2C_uc004ewo.2_3'UTR|RAP2C_uc010nrk.2_RNA|RAP2C_uc004ewq.3_3'UTR	NM_021183	NP_067006			RAP2C, member of RAS oncogene family precursor						negative regulation of cell migration|positive regulation of protein autophosphorylation|Rap protein signal transduction|regulation of protein tyrosine kinase activity	recycling endosome membrane	GTP binding|GTPase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135304578	135304578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135304578T>C	uc004ezt.2	-	15	2352	c.2261A>G	c.(2260-2262)GAC>GGC	p.D754G	MAP7D3_uc004ezs.2_Missense_Mutation_p.D718G|MAP7D3_uc011mwc.1_Missense_Mutation_p.D736G|MAP7D3_uc010nsa.1_Missense_Mutation_p.D712G	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	754						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147985795	147985795	+	Intron	SNP	T	C	C			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147985795T>C	uc004fcp.2	+						AFF2_uc004fco.2_3'UTR|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron|AFF2_uc011mxc.1_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PRRG3	79057	broad.mit.edu	37	X	150869427	150869427	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150869427G>T	uc004few.1	+	4	1008	c.618G>T	c.(616-618)GAG>GAT	p.E206D		NM_024082	NP_076987	Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3	206	Cytoplasmic (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PDZD4	57595	broad.mit.edu	37	X	153070051	153070051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153070051C>T	uc004fiz.1	-	8	1317	c.1067G>A	c.(1066-1068)CGC>CAC	p.R356H	PDZD4_uc004fiy.1_Missense_Mutation_p.R281H|PDZD4_uc004fix.2_Missense_Mutation_p.R260H|PDZD4_uc004fja.1_Missense_Mutation_p.R362H|PDZD4_uc011mze.1_Missense_Mutation_p.R247H	NM_032512	NP_115901	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	356						cell cortex				breast(1)	1	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
L1CAM	3897	broad.mit.edu	37	X	153130359	153130359	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153130359C>T	uc004fjb.2	-	22	3071	c.2963G>A	c.(2962-2964)CGG>CAG	p.R988Q	L1CAM_uc004fjc.2_Missense_Mutation_p.R988Q|L1CAM_uc010nuo.2_Missense_Mutation_p.R983Q	NM_000425	NP_000416	P32004	L1CAM_HUMAN	L1 cell adhesion molecule isoform 1 precursor	988	Extracellular (Potential).|Fibronectin type-III 4.				axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane				ovary(8)|central_nervous_system(1)	9	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MECP2	4204	broad.mit.edu	37	X	153295939	153295939	+	Missense_Mutation	SNP	G	A	A	rs61753978		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153295939G>A	uc004fjv.2	-	4	1566	c.1340C>T	c.(1339-1341)GCA>GTA	p.A447V	MECP2_uc004fjw.2_Missense_Mutation_p.A459V	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1	447					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PLXNA3	55558	broad.mit.edu	37	X	153689047	153689047	+	Missense_Mutation	SNP	C	T	T	rs138319096		TCGA-BR-4261-01A-01D-1126-08	TCGA-BR-4261-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153689047C>T	uc004flm.2	+	2	697	c.524C>T	c.(523-525)TCG>TTG	p.S175L		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3 precursor	175	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
