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
KCNAB2	8514	broad.mit.edu	37	1	6150425	6150425	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6150425delC	uc009vlv.1	+						KCNAB2_uc001alv.1_Intron|KCNAB2_uc001alw.1_Intron|KCNAB2_uc001alx.1_Intron|KCNAB2_uc001aly.1_Intron|KCNAB2_uc009vlw.1_Intron|KCNAB2_uc001alu.2_Intron	NM_003636	NP_003627			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPL22	6146	broad.mit.edu	37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6257785delT	uc001amd.2	-	2	90	c.44delA	c.(43-45)AAGfs	p.K15fs	RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs	NM_000983	NP_000974	P35268	RL22_HUMAN	ribosomal protein L22 proprotein	15					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|RNA binding|structural constituent of ribosome				0	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)				T	RUNX1	AML|CML								---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12414424	12414424	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12414424delA	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.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)														---	---	---	---
PRAMEF4	400735	broad.mit.edu	37	1	12942414	12942414	+	Intron	DEL	G	-	-	rs28438506	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12942414delG	uc001aun.2	-							NM_001009611	NP_001009611			PRAME family member 4											ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16237752	16237753	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16237752_16237753delTT	uc001axk.1	+	5	1403_1404	c.1199_1200delTT	c.(1198-1200)CTTfs	p.L400fs	SPEN_uc010obp.1_Frame_Shift_Del_p.L359fs	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	400	RRM 2.|By similarity.				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)														---	---	---	---
CLCNKA	1187	broad.mit.edu	37	1	16353414	16353414	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16353414delC	uc001axu.2	+						CLCNKA_uc001axt.2_Intron|CLCNKA_uc001axv.2_Intron|CLCNKA_uc010obw.1_Intron|CLCNKB_uc001axw.3_Intron|CLCNKA_uc010obx.1_5'Flank|CLCNKA_uc010oby.1_5'Flank	NM_004070	NP_004061			chloride channel Ka isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	18427885	18427886	+	IGR	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18427885_18427886insT								ACTL8 (274329 upstream) : IGSF21 (6354 downstream)																																			---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21014538	21014538	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21014538delT	uc001bdr.3	-						KIF17_uc001bdp.3_5'Flank|KIF17_uc001bdq.3_5'Flank|KIF17_uc009vpx.2_Intron|KIF17_uc001bds.3_Intron	NM_020816	NP_065867			kinesin family member 17 isoform a						microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)														---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22902610	22902610	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22902610delT	uc001bfx.1	+						EPHA8_uc001bfw.2_Intron	NM_020526	NP_065387			ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		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;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27101117	27101117	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27101117delC	uc001bmv.1	+	18	4772	c.4399delC	c.(4399-4401)CCCfs	p.P1467fs	ARID1A_uc001bmt.1_Frame_Shift_Del_p.P1466fs|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Frame_Shift_Del_p.P1084fs|ARID1A_uc001bmx.1_Frame_Shift_Del_p.P313fs|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1467					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								---	---	---	---
SDC3	9672	broad.mit.edu	37	1	31349751	31349752	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31349751_31349752insC	uc001bse.2	-	3	564_565	c.517_518insG	c.(517-519)GACfs	p.D173fs	SDC3_uc001bsd.2_Frame_Shift_Ins_p.D115fs	NM_014654	NP_055469	O75056	SDC3_HUMAN	syndecan 3	173	Extracellular (Potential).|Ser/Thr-rich (mucin-like).					integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EIF3I	8668	broad.mit.edu	37	1	32696849	32696849	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32696849delT	uc001bur.3	+	12					EIF3I_uc009vuc.2_3'UTR|EIF3I_uc001bus.2_3'UTR	NM_003757	NP_003748			eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	33777760	33777760	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33777760delG	uc001bxd.1	-	4	228	c.228delC	c.(226-228)CCCfs	p.P76fs		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;																														---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35816986	35816987	+	Intron	DEL	TC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35816986_35816987delTC	uc001byt.2	+						ZMYM4_uc009vuu.2_Intron|ZMYM4_uc001byu.2_Intron	NM_005095	NP_005086			zinc finger protein 262						multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
RHBDL2	54933	broad.mit.edu	37	1	39361599	39361599	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39361599delT	uc001ccu.1	-						RHBDL2_uc010oin.1_Intron|RHBDL2_uc010oio.1_Intron	NM_017821	NP_060291			rhomboid protease 2						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity				0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39914145	39914145	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39914145delA	uc010oiu.1	+						MACF1_uc010ois.1_Intron	NM_033044	NP_149033			microfilament and actin filament cross-linker						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)															---	---	---	---
ZNF642	339559	broad.mit.edu	37	1	40955180	40955180	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40955180delT	uc001cfo.2	+						ZNF642_uc009vwb.2_Intron|ZNF642_uc010ojk.1_Intron	NM_198494	NP_940896			zinc finger protein 642						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.81e-19)															---	---	---	---
EIF2B3	8891	broad.mit.edu	37	1	45443902	45443903	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45443902_45443903insA	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron|EIF2B3_uc001cmw.2_Intron	NM_020365	NP_065098			eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KIAA0494	9813	broad.mit.edu	37	1	47183474	47183474	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47183474delT	uc001cqk.3	-						KIAA0494_uc010omh.1_Intron|KIAA0494_uc001cql.1_Intron	NM_014774	NP_055589			hypothetical protein LOC9813								calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
SPATA6	54558	broad.mit.edu	37	1	48764291	48764291	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48764291delT	uc001crr.1	-	13					SPATA6_uc001crs.1_3'UTR|SPATA6_uc010omv.1_3'UTR	NM_019073	NP_061946			spermatogenesis associated 6 precursor						cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52937901	52937901	+	Intron	DEL	A	-	-	rs78098408		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53287007	53287007	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53287007delA	uc001cuj.2	+						ZYG11B_uc010onj.1_Intron|ZYG11B_uc009vzh.2_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
TMEM48	55706	broad.mit.edu	37	1	54291618	54291618	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54291618delA	uc001cvs.2	-						TMEM48_uc010onu.1_Intron|TMEM48_uc001cvt.2_Intron|TMEM48_uc009vzk.2_Intron|TMEM48_uc010onv.1_Intron	NM_018087	NP_060557			transmembrane protein 48						mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55609729	55609729	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55609729delT	uc001cyg.3	-							NM_015306	NP_056121			ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13																		---	---	---	---
C1orf168	199920	broad.mit.edu	37	1	57189194	57189194	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57189194delT	uc001cym.3	-						C1orf168_uc001cyl.2_Intron	NM_001004303	NP_001004303			hypothetical protein LOC199920											ovary(3)|skin(2)	5																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	63024585	63024585	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63024585delT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_5'Flank	NM_033407	NP_212132			dedicator of cytokinesis 7						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																		---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67142644	67142644	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67142644delT	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|uc010ope.1_Intron|SGIP1_uc009wat.2_Intron	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																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75862388	75862388	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75862388delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78281019	78281020	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78281019_78281020insA	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron|FAM73A_uc001dhy.1_Intron	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78319393	78319394	+	Intron	INS	-	AC	AC			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78319393_78319394insAC	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron|FAM73A_uc001dhy.1_Intron	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78325075	78325075	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78325075delT	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron|FAM73A_uc001dhy.1_3'UTR	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
GIPC2	54810	broad.mit.edu	37	1	78560481	78560481	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78560481delT	uc001dik.2	+							NM_017655	NP_060125			PDZ domain protein GIPC2							cytoplasm				ovary(1)	1																		---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85624415	85624415	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
CCBL2	56267	broad.mit.edu	37	1	89421044	89421044	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89421044delT	uc001dmp.2	-						CCBL2_uc001dmq.2_Intron|CCBL2_uc001dmr.2_Intron	NM_001008661	NP_001008661			kynurenine aminotransferase III isoform 1						biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding			ovary(1)	1		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
CCBL2	56267	broad.mit.edu	37	1	89427268	89427268	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89427268delA	uc001dmp.2	-						CCBL2_uc001dmq.2_Intron|CCBL2_uc001dmr.2_Intron	NM_001008661	NP_001008661			kynurenine aminotransferase III isoform 1						biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding			ovary(1)	1		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GBP3	2635	broad.mit.edu	37	1	89479706	89479706	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89479706delA	uc001dmt.2	-						GBP3_uc010oss.1_Intron|GBP3_uc001dmu.2_Intron|GBP3_uc001dmv.2_Intron	NM_018284	NP_060754			guanylate binding protein 3							integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)														---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94502549	94502549	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94502549delG	uc001dqh.2	-							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)														---	---	---	---
SASS6	163786	broad.mit.edu	37	1	100572825	100572825	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100572825delA	uc001dsu.2	-						SASS6_uc009wdz.2_Intron	NM_194292	NP_919268			spindle assembly abnormal protein 6						centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)														---	---	---	---
CDC14A	8556	broad.mit.edu	37	1	100950184	100950184	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100950184delA	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)														---	---	---	---
GNAI3	2773	broad.mit.edu	37	1	110129583	110129583	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110129583delT	uc001dxz.2	+							NM_006496	NP_006487			guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			ovary(1)	1		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115279333	115279333	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
TSPAN2	10100	broad.mit.edu	37	1	115593228	115593228	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115593228delA	uc001eft.2	-							NM_005725	NP_005716			tetraspan 2							integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145645968	145645968	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145645968delA	uc001emp.3	+						RNF115_uc001eoj.2_Intron|RNF115_uc001eok.2_Intron|RNF115_uc009wiy.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	146397278	146397278	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146397278delC	uc001emp.3	+						uc010ozk.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
ADAMTSL4	54507	broad.mit.edu	37	1	150531671	150531671	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150531671delG	uc001eux.2	+						ADAMTSL4_uc009wlw.2_Intron|ADAMTSL4_uc010pcg.1_Intron|ADAMTSL4_uc009wlx.2_Intron	NM_019032	NP_061905			thrombospondin repeat containing 1 isoform 1						apoptosis|positive regulation of apoptosis		metalloendopeptidase activity|protease binding			ovary(1)|skin(1)	2	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|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;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)															---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150935850	150935851	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150935850_150935851delAA	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)															---	---	---	---
CGN	57530	broad.mit.edu	37	1	151492611	151492611	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151492611delT	uc009wmw.2	+							NM_020770	NP_065821			cingulin							myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	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)															---	---	---	---
ILF2	3608	broad.mit.edu	37	1	153634950	153634952	+	In_Frame_Del	DEL	CTT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153634950_153634952delCTT	uc001fcr.2	-	14	1174_1176	c.1093_1095delAAG	c.(1093-1095)AAGdel	p.K365del	ILF2_uc010pdy.1_In_Frame_Del_p.K327del|ILF2_uc009wok.2_In_Frame_Del_p.K343del	NM_004515	NP_004506	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	365					immune response|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|ribonucleoprotein complex	ATP binding|DNA binding|double-stranded RNA binding|protein binding|transferase activity				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)															---	---	---	---
CCDC19	25790	broad.mit.edu	37	1	159863303	159863303	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159863303delA	uc001fui.2	-						CCDC19_uc009wtb.2_5'Flank|CCDC19_uc001fuj.2_Intron|CCDC19_uc001fuk.2_Intron|CCDC19_uc001ful.2_Intron|CCDC19_uc009wtc.1_Intron	NM_012337	NP_036469			nasopharyngeal epithelium specific protein 1							mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	161376915	161376915	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161376915delA								C1orf192 (39251 upstream) : FCGR2A (98290 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164789505	164789506	+	Intron	DEL	AG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164789505_164789506delAG	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
ILDR2	387597	broad.mit.edu	37	1	166944274	166944277	+	Intron	DEL	CACA	-	-	rs67253020		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166944274_166944277delCACA	uc001gdx.1	-							NM_199351	NP_955383			immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1																		---	---	---	---
F5	2153	broad.mit.edu	37	1	169528244	169528244	+	Intron	DEL	A	-	-	rs139315961		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169528244delA	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121			coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)													---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174210540	174210540	+	Intron	DEL	A	-	-	rs61628461	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174210540delA	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	175958359	175958359	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175958359delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902			ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
ABL2	27	broad.mit.edu	37	1	179095896	179095896	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179095896delA	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Intron|ABL2_uc001gmh.3_Intron|ABL2_uc010pne.1_Intron|ABL2_uc009wxf.1_Intron|ABL2_uc001gmk.2_Intron	NM_007314	NP_009298			arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)			T	ETV6	AML								---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185191344	185191344	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185191344delA	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988			hypothetical protein LOC54823												0																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186307132	186307132	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186307132delT	uc001grv.2	-							NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196438097	196438097	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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	196683187	196683187	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196683187delT	uc001gtj.3	+							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	196759037	196759037	+	Intron	DEL	G	-	-	rs374905	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196759037delG	uc001gtl.2	+						CFHR3_uc001gtk.2_3'UTR|CFHR3_uc010poy.1_Intron|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303			complement factor H-related 3 precursor							extracellular space					0																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197411573	197411573	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197411573delA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Intron|CRB1_uc001gub.1_3'UTR	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																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202440924	202440924	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202440924delT	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
KDM5B	10765	broad.mit.edu	37	1	202697993	202697993	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202697993delT	uc001gyf.2	-	27					KDM5B_uc009xag.2_3'UTR	NM_006618	NP_006609			jumonji, AT rich interactive domain 1B						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																		---	---	---	---
KCNK2	3776	broad.mit.edu	37	1	215256538	215256538	+	5'Flank	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215256538delC	uc001hkq.2	+						KCNK2_uc001hko.2_Intron|KCNK2_uc009xdm.2_Intron|KCNK2_uc001hkp.2_Intron|KCNK2_uc010pua.1_5'Flank|KCNK2_uc001hkr.3_5'Flank	NM_001017425	NP_001017425			potassium channel, subfamily K, member 2 isoform								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)													---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215753428	215753428	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220346115	220346115	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220346115delA	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	221307068	221307068	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221307068delA								HLX (248670 upstream) : LOC400804 (196202 downstream)																																			---	---	---	---
TLR5	7100	broad.mit.edu	37	1	223283695	223283695	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223283695delA	uc001hnv.1	-	4					TLR5_uc001hnw.1_3'UTR	NM_003268	NP_003259			toll-like receptor 5 precursor						cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)														---	---	---	---
SRP9	6726	broad.mit.edu	37	1	225970839	225970839	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225970839delT	uc001hpg.2	+						SRP9_uc001hpf.3_Intron|SRP9_uc001hph.2_Intron|SRP9_uc001hpi.3_Intron|SRP9_uc001hpj.1_Intron	NM_003133	NP_003124			signal recognition particle 9kDa isoform 2						negative regulation of translational elongation|SRP-dependent cotranslational protein targeting to membrane	cytosol|signal recognition particle receptor complex|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding				0																		---	---	---	---
C1orf55	163859	broad.mit.edu	37	1	226180814	226180816	+	Intron	DEL	TTC	-	-	rs66975923		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226180814_226180816delTTC	uc001hpu.3	-						C1orf55_uc001hpv.2_Intron	NM_152608	NP_689821			hypothetical protein LOC163859											lung(1)	1	Breast(184;0.197)																	---	---	---	---
ABCB10	23456	broad.mit.edu	37	1	229678130	229678130	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229678130delA	uc001htp.3	-							NM_012089	NP_036221			ATP-binding cassette, sub-family B, member 10							integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(2)	2	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
URB2	9816	broad.mit.edu	37	1	229770586	229770586	+	Intron	DEL	T	-	-	rs113038970		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229770586delT	uc001hts.1	+						URB2_uc009xfd.1_Intron	NM_014777	NP_055592			URB2 ribosome biogenesis 2 homolog							nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
COG2	22796	broad.mit.edu	37	1	230828972	230828972	+	Intron	DEL	T	-	-	rs111313789		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)																---	---	---	---
DISC1	27185	broad.mit.edu	37	1	231837573	231837573	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231837573delT	uc001huz.2	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc010pwm.1_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132			disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)																---	---	---	---
KCNK1	3775	broad.mit.edu	37	1	233807425	233807425	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233807425delA	uc010pxo.1	+	3					KCNK1_uc001hvw.2_RNA|KCNK1_uc001hvx.2_RNA	NM_002245	NP_002236			potassium channel, subfamily K, member 1							voltage-gated potassium channel complex	inward rectifier potassium channel activity			central_nervous_system(1)	1		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine(DB00908)													---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235331782	235331782	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235331782delA	uc001hwq.2	-	24					ARID4B_uc001hwr.2_3'UTR|ARID4B_uc001hwp.2_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)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235345419	235345419	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235345419delT	uc001hwq.2	-	20	3313	c.2815delA	c.(2815-2817)ACGfs	p.T939fs	ARID4B_uc001hwr.2_Frame_Shift_Del_p.T853fs|ARID4B_uc001hws.3_Frame_Shift_Del_p.T853fs|ARID4B_uc001hwp.2_RNA|ARID4B_uc001hwt.3_Frame_Shift_Del_p.T620fs	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	939					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)															---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243434124	243434124	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243434124delT	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
ITGB1BP1	9270	broad.mit.edu	37	2	9554563	9554563	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9554563delA	uc002qzj.2	-						ITGB1BP1_uc002qzk.2_Intron|ITGB1BP1_uc002qzl.2_Intron|ITGB1BP1_uc002qzm.2_Intron|ITGB1BP1_uc010yiy.1_Intron|ITGB1BP1_uc002qzn.1_Intron	NM_004763	NP_004754			integrin cytoplasmic domain-associated protein 1						cell migration|cell-matrix adhesion|intracellular protein kinase cascade	cytosol|lamellipodium|membrane|ruffle	protein binding|protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)														---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15537482	15537483	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15537482_15537483insT	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15644509	15644509	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15644509delA	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20138013	20138013	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20138013delT	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26363043	26363043	+	IGR	DEL	A	-	-	rs112696641		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26363043delA								RAB10 (2721 upstream) : HADHA (50462 downstream)																																			---	---	---	---
SLC4A1AP	22950	broad.mit.edu	37	2	27890449	27890449	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27890449delA	uc002rlk.3	+							NM_018158	NP_060628			solute carrier family 4 (anion exchanger),							cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
WDR43	23160	broad.mit.edu	37	2	29149283	29149283	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29149283delT	uc002rmo.2	+						SNORD53_uc002rmq.1_5'Flank	NM_015131	NP_055946			WD repeat domain 43							nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
MEMO1	51072	broad.mit.edu	37	2	32145996	32145996	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32145996delA	uc002rnx.2	-						MEMO1_uc010ymu.1_Intron|MEMO1_uc010ezq.2_Intron|MEMO1_uc002rny.2_Intron|MEMO1_uc002rnz.2_Intron|MEMO1_uc010ymv.1_Intron	NM_015955	NP_057039			mediator of cell motility 1 isoform 1						regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
YIPF4	84272	broad.mit.edu	37	2	32517177	32517177	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32517177delT	uc002rok.2	+							NM_032312	NP_115688			Yip1 domain family, member 4							endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SFRS7	6432	broad.mit.edu	37	2	38976952	38976952	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38976952delC	uc002rqz.2	-						SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron|GEMIN6_uc002rrb.2_5'Flank	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	42303348	42303348	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42303348delA								PKDCC (17682 upstream) : EML4 (93142 downstream)																																			---	---	---	---
MSH6	2956	broad.mit.edu	37	2	48032323	48032323	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48032323delT	uc002rwd.3	+						MSH6_uc010fbj.2_Intron|MSH6_uc010yoi.1_Intron|MSH6_uc010yoj.1_Intron	NM_000179	NP_000170			mutS homolog 6						determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	53713243	53713243	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53713243delA								None (None upstream) : ASB3 (183875 downstream)																																			---	---	---	---
ASB3	51130	broad.mit.edu	37	2	54040317	54040317	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54040317delT	uc002rxi.3	-						ERLEC1_uc002rxl.2_Intron|ERLEC1_uc002rxm.2_Intron|ERLEC1_uc002rxn.2_Intron	NM_001164165	NP_001157637			hypothetical protein LOC100302652						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
CCDC104	112942	broad.mit.edu	37	2	55749310	55749310	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55749310delT	uc002ryy.2	+						CCDC104_uc002ryx.2_Intron	NM_080667	NP_542398			coiled-coil domain containing 104											ovary(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58312004	58312004	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58312004delT	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|VRK2_uc010yph.1_5'Flank	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																		---	---	---	---
FANCL	55120	broad.mit.edu	37	2	58392721	58392721	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58392721delA	uc002rzw.3	-						FANCL_uc002rzx.3_Intron|FANCL_uc010fce.2_Intron|FANCL_uc010fcf.1_Intron	NM_018062	NP_060532			Fanconi anemia, complementation group L isoform						DNA repair	cytoplasm|nucleoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2													Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
USP34	9736	broad.mit.edu	37	2	61417274	61417274	+	Intron	DEL	T	-	-	rs78059296		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61417274delT	uc002sbe.2	-						USP34_uc002sbd.2_Intron	NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61575853	61575853	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61575853delA	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)															---	---	---	---
GFPT1	2673	broad.mit.edu	37	2	69583700	69583700	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69583700delA	uc002sfh.2	-						GFPT1_uc002sfi.1_Intron	NM_002056	NP_002047			glucosamine-fructose-6-phosphate						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			skin(1)	1																		---	---	---	---
NFU1	27247	broad.mit.edu	37	2	69642276	69642276	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69642276delA	uc002sfk.2	-						NFU1_uc002sfj.2_Intron|NFU1_uc002sfl.2_Intron|NFU1_uc002sfm.2_Intron|NFU1_uc010fdi.2_Intron|NFU1_uc002sfn.1_Intron	NM_001002755	NP_001002755			HIRA interacting protein 5 isoform 2						iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0																		---	---	---	---
MIR1285-2	100302268	broad.mit.edu	37	2	70480799	70480799	+	5'Flank	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70480799delT	hsa-mir-1285-2|MI0006347	-																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	81428038	81428038	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81428038delT								CTNNA2 (552134 upstream) : None (None downstream)																																			---	---	---	---
C2orf68	388969	broad.mit.edu	37	2	85835992	85835992	+	3'UTR	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85835992delC	uc002sqc.2	-	4					USP39_uc002sqb.2_Intron	NM_001013649	NP_001013671			hypothetical protein LOC388969											central_nervous_system(1)	1																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86701876	86701876	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86701876delT	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	90464855	90464855	+	IGR	DEL	C	-	-	rs71218065	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90464855delC								None (None upstream) : None (None downstream)																																			---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	99999545	99999545	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99999545delT	uc002tab.2	+							NM_015904	NP_056988			eukaryotic translation initiation factor 5B						regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
SEPT10	151011	broad.mit.edu	37	2	110310463	110310463	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110310463delA	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	NM_144710	NP_653311			septin 10 isoform 1						cell cycle|cell division	septin complex	GTP binding				0																		---	---	---	---
DDX18	8886	broad.mit.edu	37	2	118588346	118588346	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118588346delT	uc002tlh.1	+	14						NM_006773	NP_006764			DEAD (Asp-Glu-Ala-Asp) box polypeptide 18								ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	122466740	122466740	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122466740delT	uc002tnj.1	+											Homo sapiens cDNA FLJ40945 fis, clone UTERU2008747.																														---	---	---	---
FAM168B	130074	broad.mit.edu	37	2	131840238	131840238	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131840238delA	uc002tsd.2	-							NM_001009993	NP_001009993			hypothetical protein LOC130074												0																		---	---	---	---
PLEKHB2	55041	broad.mit.edu	37	2	131883312	131883312	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131883312delT	uc002tsg.3	+						PLEKHB2_uc002tsh.2_Intron|PLEKHB2_uc002tsj.3_Intron|PLEKHB2_uc002tsf.3_Intron|PLEKHB2_uc010zao.1_Intron|PLEKHB2_uc010zap.1_Intron|PLEKHB2_uc010zaq.1_Intron|PLEKHB2_uc002tsi.3_Intron	NM_001100623	NP_001094093			pleckstrin homology domain containing, family B							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)														---	---	---	---
DARS	1615	broad.mit.edu	37	2	136673772	136673772	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136673772delA	uc002tux.1	-						DARS_uc010fnj.1_Intron	NM_001349	NP_001340			aspartyl-tRNA synthetase						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)													---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138163173	138163173	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138163173delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139742577	139742578	+	IGR	INS	-	CCTC	CCTC	rs146767415	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139742577_139742578insCCTC								NXPH2 (204766 upstream) : None (None downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141598364	141598364	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141598364delT	uc002tvj.1	-							NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152330652	152330652	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152330652delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc002txp.2_Intron|uc010fnw.1_5'Flank	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152363488	152363488	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152363488delT	uc010fnx.2	-	135	18579	c.18388delA	c.(18388-18390)ATTfs	p.I6130fs	NEB_uc002txr.2_Frame_Shift_Del_p.I2553fs|RIF1_uc002txp.2_Intron|NEB_uc010zca.1_5'Flank|NEB_uc010zcb.1_5'UTR|NEB_uc002txt.3_Frame_Shift_Del_p.I635fs	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	6130	Nebulin 168.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
STAM2	10254	broad.mit.edu	37	2	153004497	153004497	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153004497delT	uc002tyc.3	-						STAM2_uc010foa.1_Intron|STAM2_uc002tyd.2_Intron	NM_005843	NP_005834			signal transducing adaptor molecule 2						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.22)														---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160284756	160284756	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160284756delT	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uar.1_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162903784	162903784	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162903784delA	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)													---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165551296	165551296	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166903618	166903618	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166903618delT	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	NM_006920	NP_008851			sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)													---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171092488	171092488	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171092488delT	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002uga.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																OREG0014376	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GORASP2	26003	broad.mit.edu	37	2	171808085	171808085	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171808085delA	uc002ugk.2	+						GORASP2_uc002ugj.2_Intron|GORASP2_uc010zdl.1_Intron|GORASP2_uc010zdm.1_Intron|GORASP2_uc002ugl.2_Intron|GORASP2_uc002ugm.2_5'Flank	NM_015530	NP_056345			golgi reassembly stacking protein 2							Golgi membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174103089	174103089	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174103089delT	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)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179185169	179185169	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179185169delA	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|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)															---	---	---	---
SESTD1	91404	broad.mit.edu	37	2	179989383	179989383	+	Intron	DEL	T	-	-	rs77134645		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179989383delT	uc002uni.3	-						SESTD1_uc002unh.3_5'Flank	NM_178123	NP_835224			SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
MYO1B	4430	broad.mit.edu	37	2	192258086	192258087	+	Intron	INS	-	T	T	rs78004419		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192258086_192258087insT	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron|MYO1B_uc002usu.2_Intron	NM_001130158	NP_001123630			myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)															---	---	---	---
HSPD1	3329	broad.mit.edu	37	2	198360213	198360214	+	Intron	DEL	AT	-	-	rs13432424		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198360213_198360214delAT	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)															---	---	---	---
AOX1	316	broad.mit.edu	37	2	201495240	201495240	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201495240delA	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	201931967	201931967	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201931967delA	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																		---	---	---	---
CASP10	843	broad.mit.edu	37	2	202060401	202060401	+	Intron	DEL	T	-	-	rs41363644		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202060401delT	uc002uxl.1	+						CASP10_uc002uxi.1_Intron|CASP10_uc010zhn.1_Intron|CASP10_uc002uxj.1_Intron|CASP10_uc002uxk.1_Intron|CASP10_uc010fta.1_Intron|CASP10_uc002uxm.1_Intron|CASP10_uc010ftb.1_Intron	NM_032974	NP_116756			caspase 10 isoform b preproprotein						apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6																		---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202698437	202698443	+	Intron	DEL	TTCTTTT	-	-	rs10597284		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202698437_202698443delTTCTTTT	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897			PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)													---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202711958	202711958	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202711958delT	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897			PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)													---	---	---	---
SUMO1	7341	broad.mit.edu	37	2	203079026	203079026	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203079026delA	uc002uyz.1	-						SUMO1_uc002uza.1_Intron	NM_001005781	NP_001005781			SMT3 suppressor of mif two 3 homolog 1 isoform a						DNA repair|interferon-gamma-mediated signaling pathway|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|palate development|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein complex assembly|protein sumoylation|regulation of interferon-gamma-mediated signaling pathway|regulation of protein localization	cytoplasm|nuclear membrane|nuclear pore|nuclear speck	ubiquitin protein ligase binding				0																		---	---	---	---
FASTKD2	22868	broad.mit.edu	37	2	207639168	207639168	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207639168delA	uc002vbu.2	+						FASTKD2_uc002vbv.2_Intron|FASTKD2_uc002vbx.2_Intron|FASTKD2_uc002vbw.1_Intron	NM_001136193	NP_001129665			FAST kinase domains 2						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|skin(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215812346	215812346	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215812346delA	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)														---	---	---	---
ATIC	471	broad.mit.edu	37	2	216191030	216191030	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216191030delA	uc002vex.3	+						ATIC_uc010zjo.1_Intron|ATIC_uc002vey.3_Intron	NM_004044	NP_004035			5-aminoimidazole-4-carboxamide ribonucleotide						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								---	---	---	---
STK11IP	114790	broad.mit.edu	37	2	220470827	220470828	+	Intron	INS	-	C	C	rs35440832		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220470827_220470828insC	uc002vml.2	+						STK11IP_uc010zlk.1_Intron|STK11IP_uc010zll.1_Intron|STK11IP_uc002vmm.1_Intron	NM_052902	NP_443134			LKB1 interacting protein						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)												OREG0003992	type=REGULATORY REGION|Gene=STK11IP|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233660685	233660685	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233660685delA	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	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)														---	---	---	---
ILKAP	80895	broad.mit.edu	37	2	239079047	239079047	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239079047delA	uc002vxv.2	-	12					ILKAP_uc010zns.1_3'UTR|ILKAP_uc002vxw.2_3'UTR	NM_030768	NP_110395			integrin-linked kinase-associated protein							cytoplasm|protein serine/threonine phosphatase complex	metal ion binding|protein binding			ovary(3)	3		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)														---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240111871	240111871	+	Intron	DEL	G	-	-	rs74761897		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240111871delG	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc002vyl.1_Intron|HDAC4_uc010fyy.2_5'Flank	NM_006037	NP_006028			histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase 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)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8673804	8673804	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8673804delA	uc003bqu.2	-						C3orf32_uc003bqz.2_Intron|C3orf32_uc003bqt.2_Intron|C3orf32_uc011atg.1_Intron|C3orf32_uc003bqv.2_Intron|C3orf32_uc003bqw.2_Intron|C3orf32_uc003bqx.2_Intron|C3orf32_uc003bqy.2_Intron	NM_015931	NP_057015			hypothetical protein LOC51066											skin(1)	1																		---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9739253	9739253	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9739253delT	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)																	---	---	---	---
IL17RC	84818	broad.mit.edu	37	3	9969633	9969633	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9969633delA	uc003bua.2	+						CIDEC_uc003bto.2_Intron|IL17RC_uc011ato.1_Intron|IL17RC_uc010hcs.2_Intron|IL17RC_uc003btz.2_Intron|IL17RC_uc011atp.1_Intron|IL17RC_uc003bud.2_Intron|IL17RC_uc003bub.2_Intron|IL17RC_uc010hct.2_Intron|IL17RC_uc010hcu.2_Intron|IL17RC_uc010hcv.2_Intron|IL17RC_uc011atq.1_Intron|IL17RC_uc003buc.2_Intron|IL17RC_uc003bue.2_5'Flank	NM_153461	NP_703191			interleukin 17 receptor C isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
TMEM111	55831	broad.mit.edu	37	3	10015949	10015949	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10015949delT	uc003bun.2	-						CIDEC_uc003bto.2_Intron|TMEM111_uc003buo.2_Intron	NM_018447	NP_060917			transmembrane protein 111							integral to membrane					0																		---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10119557	10119557	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10119557delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_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				---	---	---	---
C3orf10	55845	broad.mit.edu	37	3	10167449	10167449	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10167449delA	uc003bvb.2	+							NM_018462	NP_060932			chromosome 3 open reading frame 10							cytoplasm|cytoskeleton					0																		---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	13094263	13094263	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13094263delT	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	14415403	14415404	+	IGR	DEL	TC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14415403_14415404delTC								LSM3 (175567 upstream) : SLC6A6 (28702 downstream)																																			---	---	---	---
SLC4A7	9497	broad.mit.edu	37	3	27465427	27465427	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27465427delA	uc003cdv.2	-						SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Intron|SLC4A7_uc011aww.1_Intron|SLC4A7_uc011awx.1_Intron|SLC4A7_uc011awy.1_Intron|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Intron|SLC4A7_uc011axb.1_Intron|SLC4A7_uc010hfm.2_3'UTR|SLC4A7_uc010hfl.2_Intron|SLC4A7_uc003cdw.2_Intron	NM_003615	NP_003606			solute carrier family 4, sodium bicarbonate							apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32676649	32676649	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32676649delT								DYNC1LI1 (64299 upstream) : CNOT10 (50049 downstream)																																			---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33868211	33868211	+	Intron	DEL	T	-	-	rs35254856		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33868211delT	uc003cfx.2	+						PDCD6IP_uc011axv.1_3'UTR|PDCD6IP_uc003cfy.2_Intron|PDCD6IP_uc011axw.1_5'Flank	NM_013374	NP_037506			programmed cell death 6 interacting protein						apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport	cytosol|melanosome|microtubule organizing center	calcium-dependent protein binding			ovary(1)|skin(1)	2																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37370690	37370690	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37370690delT	uc003cgv.2	+						GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Intron	NM_002078	NP_002069			golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38951623	38951623	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38951623delA	uc011ays.1	-	8	1234	c.1035delT	c.(1033-1035)TTTfs	p.F345fs		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	345	I.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	39376897	39376897	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39376897delA								CCR8 (1726 upstream) : SLC25A38 (47918 downstream)																																			---	---	---	---
SCAP	22937	broad.mit.edu	37	3	47476328	47476328	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47476328delA	uc003crh.1	-						SCAP_uc011baz.1_Intron|SCAP_uc003crg.2_Intron	NM_012235	NP_036367			SREBF chaperone protein						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)														---	---	---	---
FBXW12	285231	broad.mit.edu	37	3	48420121	48420122	+	Intron	DEL	TG	-	-	rs9311422	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48420121_48420122delTG	uc003csr.2	+						FBXW12_uc010hjv.2_Intron|FBXW12_uc003css.2_Intron|FBXW12_uc010hjw.2_Intron	NM_207102	NP_996985			F-box and WD repeat domain containing 12 isoform												0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
P4HTM	54681	broad.mit.edu	37	3	49043643	49043643	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49043643delG	uc003cvg.2	+						P4HTM_uc003cvh.2_Intron|WDR6_uc011bbx.1_5'Flank|WDR6_uc003cvj.2_5'Flank|WDR6_uc011bby.1_5'Flank|WDR6_uc010hkn.2_5'Flank|WDR6_uc011bbz.1_5'Flank	NM_177939	NP_808808			hypoxia-inducible factor prolyl 4-hydroxylase							endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)													---	---	---	---
WDR6	11180	broad.mit.edu	37	3	49051382	49051382	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49051382delG	uc003cvj.2	+	2	2643	c.2505delG	c.(2503-2505)GCGfs	p.A835fs	WDR6_uc011bbx.1_3'UTR|WDR6_uc011bby.1_Frame_Shift_Del_p.A283fs|WDR6_uc010hkn.2_Frame_Shift_Del_p.A779fs|WDR6_uc011bbz.1_Frame_Shift_Del_p.A754fs	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	805					cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)												OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
USP19	10869	broad.mit.edu	37	3	49153503	49153503	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49153503delC	uc003cwd.1	-	9	1306	c.1145delG	c.(1144-1146)GGCfs	p.G382fs	USP19_uc003cwa.2_Frame_Shift_Del_p.G188fs|USP19_uc003cvz.3_Frame_Shift_Del_p.G483fs|USP19_uc011bcg.1_Frame_Shift_Del_p.G473fs|USP19_uc003cwb.2_Frame_Shift_Del_p.G468fs|USP19_uc003cwc.1_Frame_Shift_Del_p.G138fs|USP19_uc011bch.1_Frame_Shift_Del_p.G483fs|USP19_uc011bci.1_Frame_Shift_Del_p.G468fs	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	382	CS 2.|Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49568688	49568688	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49568688delA	uc003cxc.3	+	3	1162	c.744delA	c.(742-744)GCAfs	p.A248fs		NM_004393	NP_004384	Q14118	DAG1_HUMAN	dystroglycan 1 preproprotein	248	Required for laminin recognition.			A -> P (in Ref. 1; AAA81779).	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)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50103612	50103612	+	Intron	DEL	A	-	-	rs77592512	byFrequency;by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50103612delA	uc003cyc.2	+						RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	51788351	51788354	+	IGR	DEL	AAGG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51788351_51788354delAAGG								GRM2 (35728 upstream) : IQCF6 (24224 downstream)																																			---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52420142	52420142	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52420142delG	uc011bef.1	+						DNAH1_uc003ddv.2_Intron	NM_015512	NP_056327			dynein, axonemal, heavy chain 1						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)														---	---	---	---
BAP1	8314	broad.mit.edu	37	3	52440912	52440912	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52440912delC	uc003ddx.2	-	8	707	c.592delG	c.(592-594)GAGfs	p.E198fs	BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	198					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)				N|Mis|F|S|O		uveal melanoma|breast|NSCLC								---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52537755	52537755	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52537755delG	uc003dej.2	+						STAB1_uc003dei.1_Intron	NM_015136	NP_055951			stabilin 1 precursor						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)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	55052208	55052208	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57509313	57509313	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57509313delT	uc003dit.2	-	4	457	c.276delA	c.(274-276)AAAfs	p.K92fs	DNAH12_uc003diu.2_Frame_Shift_Del_p.K92fs	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1	92	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57850103	57850103	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57850103delA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.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)														---	---	---	---
UBA3	9039	broad.mit.edu	37	3	69104477	69104477	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69104477delA	uc003dno.2	-	18					TMF1_uc003dnn.2_5'Flank|TMF1_uc011bfx.1_5'Flank|UBA3_uc003dnq.2_3'UTR|UBA3_uc011bfy.1_3'UTR|UBA3_uc011bfz.1_3'UTR	NM_003968	NP_003959			ubiquitin-activating enzyme 3 isoform 1						protein neddylation|proteolysis	nucleus	acid-amino acid ligase activity|ATP binding|protein heterodimerization activity			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	75449778	75449779	+	IGR	INS	-	TCTC	TCTC	rs147246223	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75449778_75449779insTCTC								CNTN3 (879435 upstream) : FAM86D (20926 downstream)																																			---	---	---	---
PROS1	5627	broad.mit.edu	37	3	93592935	93592935	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93592935delT	uc003drb.3	-	15					PROS1_uc010hoo.2_3'UTR|PROS1_uc003dqz.3_3'UTR	NM_000313	NP_000304			protein S, alpha preproprotein						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)													---	---	---	---
CEP97	79598	broad.mit.edu	37	3	101445761	101445761	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101445761delA	uc003dvk.1	+						CEP97_uc010hpm.1_Intron|CEP97_uc011bhf.1_Intron|CEP97_uc003dvl.1_5'Flank	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-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115342811	115342811	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115342811delT	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)														---	---	---	---
C3orf15	89876	broad.mit.edu	37	3	119459550	119459550	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119459550delT	uc010hqy.1	+	13	1765	c.1688delT	c.(1687-1689)CTTfs	p.L563fs	C3orf15_uc003ede.3_Intron|C3orf15_uc010hqz.2_Intron|C3orf15_uc011bjd.1_Intron|C3orf15_uc011bje.1_Intron|C3orf15_uc010hra.1_Frame_Shift_Del_p.L324fs	NM_033364	NP_203528	Q7Z4T9	AAT1_HUMAN	AAT1-alpha	399	Potential.					mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124048962	124048962	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124048962delT	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																		---	---	---	---
KBTBD12	166348	broad.mit.edu	37	3	127646442	127646442	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127646442delA	uc010hsr.2	+						KBTBD12_uc003ejy.3_Intron|KBTBD12_uc010hsq.2_Intron|KBTBD12_uc003eka.3_Intron|KBTBD12_uc003ejz.2_Intron	NM_207335	NP_997218			kelch domain containing 6											ovary(1)	1																		---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130682615	130682615	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130682615delT	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron|ATP2C1_uc003enu.2_5'UTR	NM_014382	NP_055197			calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130711967	130711967	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130711967delT	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron|ATP2C1_uc003enu.2_Intron	NM_014382	NP_055197			calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132172401	132172401	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132172401delA	uc003eor.2	+						DNAJC13_uc010htq.1_Intron|DNAJC13_uc003eos.1_5'Flank	NM_015268	NP_056083			DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132193659	132193660	+	Intron	DEL	CC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132193659_132193660delCC	uc003eor.2	+							NM_015268	NP_056083			DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
NPHP3	27031	broad.mit.edu	37	3	132401046	132401047	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132401046_132401047insT	uc003epe.1	-						NPHP3_uc003eoz.1_Intron|NPHP3_uc003epd.1_Intron	NM_153240	NP_694972			nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137958222	137958222	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137958222delT	uc003esa.1	+						ARMC8_uc003erw.2_Intron|ARMC8_uc003erx.2_Intron|ARMC8_uc003ery.2_Intron|ARMC8_uc003erz.2_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142051517	142051517	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150845627	150845627	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150845627delA	uc003eyp.2	+	4	450	c.412delA	c.(412-414)AAAfs	p.K138fs	MED12L_uc011bnz.1_Frame_Shift_Del_p.K138fs|MED12L_uc003eym.1_Frame_Shift_Del_p.K138fs|MED12L_uc003eyn.2_Frame_Shift_Del_p.K138fs|MED12L_uc003eyo.2_Frame_Shift_Del_p.K138fs	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	138					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)															---	---	---	---
SGEF	26084	broad.mit.edu	37	3	153842162	153842164	+	Intron	DEL	TTT	-	-	rs66618151		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153842162_153842164delTTT	uc011bog.1	+						SGEF_uc011boh.1_Intron	NM_015595	NP_056410			Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
MME	4311	broad.mit.edu	37	3	154834153	154834153	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154834153delT	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155654423	155654423	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155654423delT	uc003faq.2	+						GMPS_uc011bom.1_Intron	NM_003875	NP_003866			guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)			T	MLL	AML								---	---	---	---
TBCCD1	55171	broad.mit.edu	37	3	186268857	186268857	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186268857delT	uc003fqg.2	-						TBCCD1_uc011bry.1_Intron|TBCCD1_uc003fqh.2_Intron	NM_018138	NP_060608			TBCC domain containing 1						cell morphogenesis|maintenance of centrosome location|maintenance of Golgi location|regulation of cell migration|regulation of cell shape	spindle pole centrosome	binding			large_intestine(1)|ovary(1)	2	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)														---	---	---	---
KNG1	3827	broad.mit.edu	37	3	186459145	186459145	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186459145delA	uc011bsa.1	+						KNG1_uc003fqr.2_Intron	NM_001102416	NP_001095886			kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)													---	---	---	---
RTP1	132112	broad.mit.edu	37	3	186918002	186918002	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186918002delT	uc003frg.2	+	2						NM_153708	NP_714919			receptor transporting protein 1						protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding			ovary(2)|breast(1)	3	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)														---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193039761	193039762	+	Intron	DEL	TG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193039761_193039762delTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194284079	194284079	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194284079delT								ATP13A3 (95111 upstream) : TMEM44 (24324 downstream)																																			---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195538502	195538503	+	Intron	DEL	TC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195538502_195538503delTC	uc011bto.1	-						MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzv.2_Intron	NM_018406	NP_060876			mucin 4 isoform a						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)														---	---	---	---
SDHAP1	255812	broad.mit.edu	37	3	195704127	195704127	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195704127delA	uc011btq.1	-						SDHAP1_uc003fvx.3_Intron|SDHAP1_uc011btp.1_Intron					SubName: Full=cDNA FLJ56858, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0																		---	---	---	---
TFRC	7037	broad.mit.edu	37	3	195792272	195792273	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195792272_195792273insA	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								---	---	---	---
GAK	2580	broad.mit.edu	37	4	845369	845370	+	Intron	DEL	AG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:845369_845370delAG	uc003gbm.3	-						GAK_uc003gbn.3_Intron|GAK_uc003gbk.3_Intron|GAK_uc010ibi.2_Intron|GAK_uc010ibj.2_Intron|GAK_uc003gbl.3_Intron	NM_005255	NP_005246			cyclin G associated kinase						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)														---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2698177	2698177	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2698177delA	uc010icl.2	+	16	2842	c.2491delA	c.(2491-2493)AAAfs	p.K831fs	FAM193A_uc010ick.2_Frame_Shift_Del_p.K1031fs|FAM193A_uc003gfd.2_Frame_Shift_Del_p.K831fs|FAM193A_uc011bvm.1_Frame_Shift_Del_p.K853fs|FAM193A_uc011bvn.1_Frame_Shift_Del_p.K831fs|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Frame_Shift_Del_p.K685fs	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	831										ovary(3)	3																		---	---	---	---
ZBTB49	166793	broad.mit.edu	37	4	4303627	4303627	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4303627delT	uc003ghu.2	+						ZBTB49_uc003ghv.2_Intron|ZBTB49_uc010icy.2_Intron|ZBTB49_uc010icz.2_5'Flank	NM_145291	NP_660334			zinc finger protein 509						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
WDR1	9948	broad.mit.edu	37	4	10086017	10086017	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10086017delC	uc003gmf.2	-						WDR1_uc003gmg.2_Intron|WDR1_uc010idm.2_5'Flank	NM_017491	NP_059830			WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)														---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13582681	13582681	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
CC2D2A	57545	broad.mit.edu	37	4	15511681	15511681	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15511681delG	uc010idv.2	+						CC2D2A_uc003gnx.2_Intron|CC2D2A_uc003gnu.2_Intron|CC2D2A_uc003gnv.2_Intron	NM_001080522	NP_001073991			coiled-coil and C2 domain containing 2A isoform						cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3																		---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42557859	42557860	+	Intron	INS	-	TAAA	TAAA	rs145505019	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42557859_42557860insTAAA	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_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)													---	---	---	---
TXK	7294	broad.mit.edu	37	4	48078395	48078396	+	Intron	INS	-	AT	AT			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48078395_48078396insAT	uc003gxx.3	-						TXK_uc010igj.2_Intron|TXK_uc011bzj.1_Intron	NM_003328	NP_003319			TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
PPAT	5471	broad.mit.edu	37	4	57267244	57267244	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57267244delT	uc003hbr.2	-							NM_002703	NP_002694			phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	57459693	57459694	+	IGR	DEL	TG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57459693_57459694delTG								ARL9 (69635 upstream) : HOPX (54460 downstream)																																			---	---	---	---
REST	5978	broad.mit.edu	37	4	57785837	57785837	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57785837delA	uc003hch.2	+						REST_uc003hci.2_Intron|REST_uc010ihf.2_Intron	NM_005612	NP_005603			RE1-silencing transcription factor						cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	69444612	69444612	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69444612delT								YTHDC1 (228788 upstream) : UGT2B15 (67704 downstream)																																			---	---	---	---
CSN2	1447	broad.mit.edu	37	4	70826811	70826811	+	5'Flank	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70826811delA	uc003hes.3	-						CSN2_uc003het.3_5'Flank	NM_001891	NP_001882			casein beta precursor						calcium ion transport	extracellular region	calcium ion binding|enzyme inhibitor activity|transporter activity				0																		---	---	---	---
AMBN	258	broad.mit.edu	37	4	71465157	71465157	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71465157delA	uc003hfl.2	+							NM_016519	NP_057603			ameloblastin precursor						bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)|skin(1)	4			Lung(101;0.235)															---	---	---	---
PARM1	25849	broad.mit.edu	37	4	75959192	75959192	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75959192delA	uc003hih.1	+							NM_015393	NP_056208			prostatic androgen-repressed message-1						positive regulation of telomerase activity	early endosome|endosome membrane|Golgi membrane|integral to membrane|late endosome|plasma membrane				ovary(1)	1																		---	---	---	---
CXCL9	4283	broad.mit.edu	37	4	76926198	76926198	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76926198delT	uc003hjh.1	-							NM_002416	NP_002407			small inducible cytokine B9 precursor						cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response	extracellular space	chemokine activity			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
NUP54	53371	broad.mit.edu	37	4	77045927	77045927	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77045927delG	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																		---	---	---	---
AGPAT9	84803	broad.mit.edu	37	4	84519056	84519057	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84519056_84519057insT	uc003how.2	+						AGPAT9_uc003hox.2_Intron|AGPAT9_uc003hoy.2_Intron	NM_032717	NP_116106			1-acylglycerol-3-phosphate O-acyltransferase 9						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)																---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87653519	87653520	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87653519_87653520insA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_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)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88097823	88097824	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88097823_88097824insA	uc011cdb.1	-						KLHL8_uc003hql.1_Intron|KLHL8_uc003hqm.1_Intron|KLHL8_uc003hqn.1_Intron|KLHL8_uc010ikj.1_Intron	NM_020803	NP_065854			kelch-like 8												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95174173	95174173	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95174173delT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_5'Flank	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104066537	104066538	+	Intron	INS	-	AC	AC	rs146614886	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104066537_104066538insAC	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804			centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
CFI	3426	broad.mit.edu	37	4	110667668	110667668	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110667668delA	uc003hzr.3	-						CFI_uc003hzq.2_Intron|CFI_uc011cft.1_Intron|CFI_uc003hzs.3_Intron	NM_000204	NP_000195			complement factor I preproprotein						complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)														---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113186056	113186056	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113186056delT	uc003iaj.3	+						AP1AR_uc010imm.1_Intron|AP1AR_uc003iak.3_Intron	NM_018569	NP_061039			adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0																		---	---	---	---
METTL14	57721	broad.mit.edu	37	4	119621927	119621927	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119621927delA	uc003icf.2	+						METTL14_uc003icg.2_Intron	NM_020961	NP_066012			methyltransferase like 14							nucleus	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity				0																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123111049	123111049	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123111049delT	uc003ieh.2	+						KIAA1109_uc003iei.1_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
SMAD1	4086	broad.mit.edu	37	4	146479246	146479247	+	3'UTR	DEL	AC	-	-	rs55948666		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146479246_146479247delAC	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)	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151356863	151356863	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151356863delA	uc010ipj.2	-						LRBA_uc010ipi.2_Intron|LRBA_uc003ils.3_Intron|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)																	---	---	---	---
RPS3A	6189	broad.mit.edu	37	4	152023353	152023353	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152023353delT	uc003ilz.2	+						RPS3A_uc011cie.1_Intron|SNORD73A_uc003ima.1_5'Flank	NM_001006	NP_000997			ribosomal protein S3a						cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
TRIM2	23321	broad.mit.edu	37	4	154098799	154098799	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154098799delA	uc003ing.2	+							NM_001130067	NP_001123539			tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)														---	---	---	---
CPE	1363	broad.mit.edu	37	4	166403589	166403589	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166403589delT	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)													---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166935414	166935415	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166935414_166935415insT	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596			tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
KIAA1712	80817	broad.mit.edu	37	4	175220290	175220290	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175220290delA	uc003itr.2	+	3	432	c.18delA	c.(16-18)TTAfs	p.L6fs	KIAA1712_uc010iro.2_Frame_Shift_Del_p.L6fs|KIAA1712_uc003its.2_RNA	NM_001040157	NP_001035247	Q9C0F1	CEP44_HUMAN	HBV PreS1-transactivated protein 3 isoform a	6						centrosome|midbody|spindle pole					0		Prostate(90;0.00276)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;4.06e-18)|Epithelial(43;1.18e-15)|OV - Ovarian serous cystadenocarcinoma(60;4.65e-09)|GBM - Glioblastoma multiforme(59;0.00098)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0949)														---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13727544	13727544	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13727544delT	uc003jfd.2	-						DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14477004	14477004	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14477004delT	uc003jff.2	+	41	6091	c.6085delT	c.(6085-6087)TTTfs	p.F2029fs	TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Frame_Shift_Del_p.F1678fs	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2029	DH 2.				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)																	---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32786466	32786466	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32786466delT	uc003jhv.2	+	8					NPR3_uc011cnz.1_3'UTR|NPR3_uc003jhu.2_3'UTR|C5orf23_uc003jhw.1_5'Flank	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37701133	37701133	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37701133delT	uc003jkv.2	+							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	40066666	40066666	+	IGR	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40066666delC								DAB2 (641331 upstream) : PTGER4 (613366 downstream)																																			---	---	---	---
NNT	23530	broad.mit.edu	37	5	43666736	43666736	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)													---	---	---	---
ISL1	3670	broad.mit.edu	37	5	50680238	50680238	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50680238delA	uc003jor.2	+						uc003joq.1_5'Flank	NM_002202	NP_002193			islet-1						generation of precursor metabolites and energy|multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3		Lung NSC(810;0.000845)|Breast(144;0.0411)																---	---	---	---
C5orf35	133383	broad.mit.edu	37	5	56209591	56209591	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56209591delT	uc003jqx.2	+						C5orf35_uc003jqy.2_Intron	NM_153706	NP_714917			hypothetical protein LOC133383											ovary(1)	1		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.173)		OV - Ovarian serous cystadenocarcinoma(10;2.58e-39)														---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61648395	61648395	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61648395delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
SMN2	6607	broad.mit.edu	37	5	69372317	69372317	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69372317delT	uc003jyd.2	+						GUSBP3_uc003jxm.2_Intron|uc003jxp.3_Intron|uc011crh.1_Intron|uc011crl.1_Intron|SMN2_uc011crm.1_Intron|SMN2_uc003jye.2_Intron|SMN2_uc003jyf.2_Intron|SMN2_uc003jyg.2_Intron|SMN2_uc003jyi.1_Intron	NM_017411	NP_059107			survival of motor neuron 2, centromeric isoform						cell death|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding|protein binding|RNA binding				0		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75969475	75969475	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75969475delA	uc003kek.2	+						IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron|IQGAP2_uc010izw.1_5'Flank	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	76842129	76842129	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76842129delA								WDR41 (53797 upstream) : OTP (82409 downstream)																																			---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79794833	79794835	+	Intron	DEL	AAA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79794833_79794835delAAA	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)														---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80515513	80515513	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80515513delT	uc003kha.1	+						RNU5E_uc011cto.1_Intron|RASGRF2_uc011ctn.1_Intron	NM_006909	NP_008840			Ras protein-specific guanine						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)														---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83258821	83258821	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83258821delT	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)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87536740	87536740	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87536740delA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctz.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90025688	90025690	+	Intron	DEL	TTT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90025688_90025690delTTT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.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)														---	---	---	---
ANKRD32	84250	broad.mit.edu	37	5	94014799	94014800	+	Intron	INS	-	AC	AC	rs1549179	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94014799_94014800insAC	uc003kkr.3	+						ANKRD32_uc003kks.2_Intron	NM_032290	NP_115666			ankyrin repeat domain 32											ovary(2)	2		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)														---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98199049	98199049	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98199049delA	uc003knf.2	-						CHD1_uc010jbn.2_Intron	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	98208017	98208017	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98208017delT	uc003knf.2	-						CHD1_uc010jbn.2_5'UTR	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)													---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112874753	112874753	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112874753delT	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)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115831788	115831788	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115831788delT	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)														---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118310505	118310505	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
HSD17B4	3295	broad.mit.edu	37	5	118867259	118867260	+	Intron	DEL	GG	-	-	rs112037211		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118867259_118867260delGG	uc003ksj.2	+						HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron|HSD17B4_uc010jco.1_Intron	NM_000414	NP_000405			hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	120952552	120952552	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120952552delA								PRR16 (929590 upstream) : FTMT (235098 downstream)																																			---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126783035	126783035	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126783035delT	uc003kuh.3	+						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-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127872255	127872255	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127872255delC	uc003kuu.2	-						FBN2_uc003kuv.2_Intron|FBN2_uc003kuw.3_Intron|FBN2_uc003kux.1_Intron	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)														---	---	---	---
LYRM7	90624	broad.mit.edu	37	5	130515638	130515638	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130515638delT	uc003kvg.1	+							NM_181705	NP_859056			Lyrm7 homolog												0		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131054985	131054985	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131054985delA	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron|FNIP1_uc003kvu.2_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)														---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132234183	132234183	+	Intron	DEL	T	-	-	rs67779737		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132234183delT	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)															---	---	---	---
LECT2	3950	broad.mit.edu	37	5	135283270	135283271	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135283270_135283271insA	uc003lbe.1	-						FBXL21_uc003lbc.2_Intron	NM_002302	NP_002293			leukocyte cell-derived chemotaxin 2 precursor						chemotaxis|skeletal system development	cytoplasm|extracellular space				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
RBM22	55696	broad.mit.edu	37	5	150072483	150072483	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150072483delG	uc003lst.2	-	10	1228	c.1106delC	c.(1105-1107)CCTfs	p.P369fs		NM_018047	NP_060517	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	369	Pro-rich.				protein import into nucleus, translocation	catalytic step 2 spliceosome|cytoplasm	calcium-dependent protein binding|nucleotide binding|RNA binding|zinc ion binding				0		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
DCTN4	51164	broad.mit.edu	37	5	150102363	150102364	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150102363_150102364delTT	uc003lsv.2	-						DCTN4_uc003lsu.2_Intron|DCTN4_uc010jhi.2_Intron	NM_016221	NP_057305			dynactin 4 (p62) isoform b							centrosome|nucleus	protein N-terminus binding			central_nervous_system(1)	1		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151174927	151174930	+	Intron	DEL	TTTG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151174927_151174930delTTTG	uc003lun.2	+						G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron|G3BP1_uc003luq.2_5'Flank	NM_005754	NP_005745			Ras-GTPase-activating protein SH3-domain-binding						Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158608809	158608809	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158608809delA	uc003lxp.2	-						RNF145_uc011ddy.1_Intron|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.1_Intron	NM_144726	NP_653327			ring finger protein 145							integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169506958	169506958	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169506958delC	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|DOCK2_uc003mah.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)															---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170395219	170395219	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170395219delT	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	5	174353447	174353447	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174353447delT								MSX2 (195546 upstream) : DRD1 (514229 downstream)																																			---	---	---	---
UNC5A	90249	broad.mit.edu	37	5	176289899	176289899	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176289899delC	uc003mey.2	+						UNC5A_uc003mex.1_Intron|UNC5A_uc010jkg.1_Intron	NM_133369	NP_588610			netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
SERPINB1	1992	broad.mit.edu	37	6	2840633	2840633	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2840633delT	uc003mub.2	-						SERPINB1_uc003muc.2_Intron	NM_030666	NP_109591			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytoplasm|extracellular space	serine-type endopeptidase inhibitor activity			breast(4)|ovary(1)	5	Ovarian(93;0.0412)			OV - Ovarian serous cystadenocarcinoma(45;0.0717)														---	---	---	---
RIOK1	83732	broad.mit.edu	37	6	7417589	7417589	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7417589delC	uc003mxn.2	+	17	1796	c.1622delC	c.(1621-1623)GCCfs	p.A541fs	RIOK1_uc003mxo.2_Frame_Shift_Del_p.A300fs	NM_031480	NP_113668	Q9BRS2	RIOK1_HUMAN	RIO kinase 1 isoform 1	541							ATP binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|skin(1)	4	Ovarian(93;0.0418)																	---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15511598	15511598	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15511598delC	uc003nbj.2	+	13	3162	c.2918delC	c.(2917-2919)ACCfs	p.T973fs	JARID2_uc011div.1_Frame_Shift_Del_p.T801fs	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	973	JmjC.				central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31322269	31322270	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31322269_31322270delGA	uc003nth.2	-	7	1133_1134	c.1079_1080delTC	c.(1078-1080)CTCfs	p.L360fs	HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_RNA|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Frame_Shift_Del_p.L239fs|HLA-B_uc003nti.1_RNA	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B	360	Cytoplasmic (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
DAXX	1616	broad.mit.edu	37	6	33287677	33287677	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33287677delA	uc003oec.2	-						ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Intron|DAXX_uc011dre.1_Intron|DAXX_uc003oed.2_Intron	NM_001350	NP_001341			death-domain associated protein isoform a						activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23								Mis|F|N		Pancreatic neuroendocrine tumors								---	---	---	---
TBC1D22B	55633	broad.mit.edu	37	6	37250063	37250063	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37250063delC	uc003onn.2	+	4	670	c.524delC	c.(523-525)GCCfs	p.A175fs	TBC1D22B_uc010jwt.2_RNA	NM_017772	NP_060242	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	175						intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)															---	---	---	---
PRICKLE4	29964	broad.mit.edu	37	6	41752759	41752759	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41752759delG	uc011duf.1	+	5	575	c.327delG	c.(325-327)CAGfs	p.Q109fs	PRICKLE4_uc003ord.2_RNA|TOMM6_uc003org.2_5'Flank|TOMM6_uc011dug.1_5'Flank	NM_013397	NP_037529	Q2TBC4	PRIC4_HUMAN	over-expressed breast tumor protein	69	PET.					nucleus	zinc ion binding				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42643695	42643695	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42643695delA	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron|UBR2_uc011dut.1_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43126779	43126779	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43126779delG	uc003oub.1	+						PTK7_uc003ouc.1_Intron|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_Intron|PTK7_uc003oug.1_Intron|PTK7_uc011dve.1_Intron|PTK7_uc010jyj.1_Intron|PTK7_uc003ouh.1_5'Flank	NM_002821	NP_002812			PTK7 protein tyrosine kinase 7 isoform a						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)															---	---	---	---
TTBK1	84630	broad.mit.edu	37	6	43227330	43227330	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43227330delC	uc003ouq.1	+	12	1589	c.1310delC	c.(1309-1311)GCCfs	p.A437fs		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	437						cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44371468	44371468	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44371468delT	uc003oxl.2	+							NM_001253	NP_001244			CDC5-like						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
DEFB114	245928	broad.mit.edu	37	6	49928267	49928267	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49928267delA	uc011dwp.1	-							NM_001037499	NP_001032588			beta-defensin 114 precursor						defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51923569	51923570	+	Intron	INS	-	TCTATCTA	TCTATCTA	rs144129939	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51923569_51923570insTCTATCTA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						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)																	---	---	---	---
EYS	346007	broad.mit.edu	37	6	66115021	66115021	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66115021delA	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																		---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70639396	70639396	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70639396delT	uc003pfc.1	+	6	587	c.470delT	c.(469-471)ATTfs	p.I157fs	COL19A1_uc010kam.1_Frame_Shift_Del_p.I53fs	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	157	TSP N-terminal.				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72961148	72961148	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72961148delT	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_5'Flank|RIMS1_uc003pgb.3_Intron|RIMS1_uc010kas.1_Intron	NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						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)																---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84302875	84302875	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84302875delA	uc011dze.1	-						SNAP91_uc011dzd.1_Intron|SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_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)														---	---	---	---
C6orf165	154313	broad.mit.edu	37	6	88125702	88125702	+	Intron	DEL	A	-	-	rs34892535		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88125702delA	uc003plv.2	+						C6orf165_uc003plw.2_Intron|C6orf165_uc010kbv.1_Intron|C6orf165_uc003plu.1_Intron	NM_001031743	NP_001026913			hypothetical protein LOC154313 isoform 1											central_nervous_system(1)	1		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;0.0419)														---	---	---	---
SLC35A1	10559	broad.mit.edu	37	6	88220956	88220956	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88220956delT	uc011dzj.1	+						SLC35A1_uc003plx.2_Intron|SLC35A1_uc010kbw.2_Intron|SLC35A1_uc003plz.2_Intron|SLC35A1_uc011dzi.1_Intron|SLC35A1_uc003ply.2_Intron|SLC35A1_uc010kbx.2_Intron|SLC35A1_uc010kby.2_Intron	NM_006416	NP_006407			solute carrier family 35 (CMP-sialic acid						carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		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;0.0429)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88318838	88318838	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88318838delA	uc003pmh.2	+	7	648	c.604delA	c.(604-606)AAAfs	p.K202fs	ORC3L_uc011dzl.1_Frame_Shift_Del_p.K202fs|ORC3L_uc011dzm.1_Frame_Shift_Del_p.K202fs|ORC3L_uc011dzn.1_RNA|ORC3L_uc003pmg.2_Frame_Shift_Del_p.K202fs|ORC3L_uc003pmi.2_Frame_Shift_Del_p.K202fs|ORC3L_uc011dzo.1_Frame_Shift_Del_p.K59fs|ORC3L_uc011dzp.1_Frame_Shift_Del_p.K59fs	NM_012381	NP_036513	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3 isoform 2	202					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
SPACA1	81833	broad.mit.edu	37	6	88769152	88769152	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88769152delT	uc003pmn.2	+							NM_030960	NP_112222			sperm acrosome associated 1 precursor							integral to membrane					0		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90433197	90433197	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90433197delA	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	90583372	90583372	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90583372delT	uc003pnr.2	+						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)														---	---	---	---
KIAA0776	23376	broad.mit.edu	37	6	96972044	96972044	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96972044delA	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)														---	---	---	---
KIAA0776	23376	broad.mit.edu	37	6	96986656	96986656	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96986656delC	uc003por.2	+	10	1176	c.1128delC	c.(1126-1128)TTCfs	p.F376fs	KIAA0776_uc010kck.2_RNA	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376	376					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)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108843371	108843371	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108843371delA	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	109649160	109649160	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109649160delT								C6orf182 (164047 upstream) : CD164 (38558 downstream)																																			---	---	---	---
CDK19	23097	broad.mit.edu	37	6	110988787	110988787	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110988787delA	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																		---	---	---	---
C6orf225	619208	broad.mit.edu	37	6	112421815	112421815	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112421815delA	uc003pvs.2	+							NM_001033564	NP_001028736			hypothetical protein LOC619208												0																		---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114378456	114378456	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114378456delA	uc003pwg.3	-	2	1038	c.1006delT	c.(1006-1008)TACfs	p.Y336fs	uc003pwf.2_Intron|HS3ST5_uc003pwh.3_Frame_Shift_Del_p.Y336fs	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)	336	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124979215	124979215	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124979215delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129573211	129573211	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129573211delT	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)														---	---	---	---
SAMD3	154075	broad.mit.edu	37	6	130535448	130535449	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130535448_130535449delAA	uc003qbv.2	-						SAMD3_uc003qbx.2_Intron|SAMD3_uc003qbw.2_Intron|SAMD3_uc010kfg.1_Intron|SAMD3_uc003qby.2_Intron|SAMD3_uc003qbz.1_Intron	NM_001017373	NP_001017373			sterile alpha motif domain containing 3 isoform											ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134747283	134747286	+	IGR	DEL	TCTT	-	-	rs67886112		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134747283_134747286delTCTT								SGK1 (108087 upstream) : ALDH8A1 (491243 downstream)																																			---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143090598	143090598	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
PHACTR2	9749	broad.mit.edu	37	6	144128096	144128096	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144128096delA	uc003qjq.3	+						PHACTR2_uc010khh.2_Intron|PHACTR2_uc010khi.2_Intron|PHACTR2_uc003qjr.3_Intron	NM_014721	NP_055536			phosphatase and actin regulator 2 isoform 3								actin binding|protein phosphatase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146243488	146243488	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146243488delA	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148			SNF2 histone linker PHD RING helicase isoform a						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)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146247197	146247199	+	Intron	DEL	ACA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146247197_146247199delACA	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148			SNF2 histone linker PHD RING helicase isoform a						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)														---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151413789	151413790	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151413789_151413790delTT	uc003qob.2	+						MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255			methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152644919	152644919	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152644919delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kiz.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	152783720	152783720	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)			---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158579538	158579538	+	Intron	DEL	A	-	-	rs111829898		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158579538delA	uc003qrc.2	-						SERAC1_uc003qrb.2_Intron	NM_032861	NP_116250			serine active site containing 1						GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160505862	160505862	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160505862delT	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)														---	---	---	---
LPAL2	80350	broad.mit.edu	37	6	160931972	160931972	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160931972delA	uc003qtj.2	-						LPAL2_uc011efy.1_Intron	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)														---	---	---	---
FGFR1OP	11116	broad.mit.edu	37	6	167446008	167446008	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167446008delT	uc003qvj.2	+						CCR6_uc003qvl.2_Intron|FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvk.2_Intron	NM_007045	NP_008976			FGFR1 oncogene partner isoform a						G2/M transition of mitotic cell cycle|microtubule anchoring|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation	centrosome|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity|protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(1)	1		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)				T	FGFR1	MPD|NHL								---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1513674	1513675	+	Intron	INS	-	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1513674_1513675insG	uc003skn.2	-						INTS1_uc003skm.1_Intron	NM_001080453	NP_001073922			integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)												OREG0017827	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
IQCE	23288	broad.mit.edu	37	7	2644634	2644634	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2644634delG	uc003smo.3	+						IQCE_uc003sml.1_Intron|IQCE_uc011jvy.1_Intron|IQCE_uc011jvz.1_Intron|IQCE_uc003smk.3_Intron|IQCE_uc003smn.3_Intron	NM_152558	NP_689771			IQ motif containing E isoform 1												0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4171854	4171854	+	Intron	DEL	T	-	-	rs113599151		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4171854delT	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)														---	---	---	---
RSPH10B2	728194	broad.mit.edu	37	7	5985001	5985001	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5985001delG	uc003sph.1	-						RSPH10B2_uc003spg.1_Intron|RSPH10B2_uc010ktd.1_Intron|RSPH10B2_uc011jwk.1_Intron	NM_173565	NP_775836			radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TRA2A	29896	broad.mit.edu	37	7	23552393	23552394	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23552393_23552394delAA	uc003swi.2	-						TRA2A_uc011jzb.1_Intron|TRA2A_uc011jzc.1_Intron|TRA2A_uc011jzd.1_Intron	NM_013293	NP_037425			transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	26316251	26316251	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26316251delA								CBX3 (63277 upstream) : SNX10 (15264 downstream)																																			---	---	---	---
CRHR2	1395	broad.mit.edu	37	7	30694783	30694783	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
ANLN	54443	broad.mit.edu	37	7	36458736	36458736	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36458736delT	uc003tff.2	+						ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Intron|ANLN_uc010kxe.2_Intron	NM_018685	NP_061155			anillin, actin binding protein						cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3																		---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38948695	38948695	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38948695delA	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron	NM_014396	NP_055211			vacuolar protein sorting 41 isoform 1						Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39491108	39491108	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39491108delT	uc003thb.1	+							NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
POLD2	5425	broad.mit.edu	37	7	44154375	44154375	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44154375delT	uc010kxz.2	-	12					POLD2_uc003tke.3_3'UTR|POLD2_uc010kya.2_3'UTR|POLD2_uc003tkf.3_3'UTR	NM_006230	NP_006221			DNA-directed DNA polymerase delta 2						base-excision repair|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	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity|protein binding			ovary(2)	2																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48559611	48559611	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48559611delT	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72040751	72040751	+	Intron	DEL	A	-	-	rs72347331		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
ELN	2006	broad.mit.edu	37	7	73456758	73456758	+	Intron	DEL	A	-	-	rs72489767		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73456758delA	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224			elastin isoform a precursor						blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
ABCB4	5244	broad.mit.edu	37	7	87032452	87032452	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87032452delT	uc003uiv.1	-	27	3729	c.3653delA	c.(3652-3654)AAGfs	p.K1218fs	ABCB4_uc003uiw.1_Frame_Shift_Del_p.K1211fs|ABCB4_uc003uix.1_Frame_Shift_Del_p.K1164fs	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	1218	ABC transporter 2.|Cytoplasmic (By similarity).				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)																	---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98546921	98546923	+	Intron	DEL	CTT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98546921_98546923delCTT	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PDAP1	11333	broad.mit.edu	37	7	98994127	98994127	+	3'UTR	DEL	C	-	-	rs113663373		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98994127delC	uc003uqe.2	-	6						NM_014891	NP_055706			PDGFA associated protein 1						cell proliferation|signal transduction						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)		Becaplermin(DB00102)													---	---	---	---
PILRB	29990	broad.mit.edu	37	7	99943553	99943554	+	5'UTR	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99943553_99943554delTT	uc003uuk.2	+	4					PILRB_uc003uul.2_5'UTR	NM_013440	NP_038468			paired immunoglobulin-like type 2 receptor beta						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	101967964	101967964	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101967964delA								SH2B2 (5787 upstream) : SPDYE6 (18229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	102020719	102020719	+	Intron	DEL	A	-	-	rs77963773		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102020719delA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																														---	---	---	---
DPY19L2P2	349152	broad.mit.edu	37	7	102902926	102902926	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102902926delA	uc003vbh.3	-						DPY19L2P2_uc003vbg.3_Intron|DPY19L2P2_uc010lit.2_Intron	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0																		---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107745286	107745286	+	Intron	DEL	T	-	-	rs138912987		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107745286delT	uc010ljo.1	-						LAMB4_uc003vey.2_Intron	NM_007356	NP_031382			laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111409819	111409819	+	Intron	DEL	A	-	-	rs113706132		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111409819delA	uc003vfx.2	-						DOCK4_uc011kml.1_Intron|DOCK4_uc011kmm.1_Intron|DOCK4_uc003vfw.2_Intron|DOCK4_uc003vfy.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)																---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117351404	117351404	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117351404delA	uc003vjf.2	-	23						NM_033427	NP_219499			cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	117523430	117523430	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117523430delA								CTTNBP2 (9869 upstream) : NAA38 (300656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119210558	119210558	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119210558delA								None (None upstream) : KCND2 (703164 downstream)																																			---	---	---	---
WASL	8976	broad.mit.edu	37	7	123333088	123333088	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123333088delT	uc003vkz.2	-							NM_003941	NP_003932			Wiskott-Aldrich syndrome gene-like protein						actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138943422	138943422	+	Intron	DEL	T	-	-	rs74531371		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138943422delT	uc011kqr.1	+						UBN2_uc003vuv.2_Intron	NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
GSTK1	373156	broad.mit.edu	37	7	142965961	142965961	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142965961delA	uc003wci.2	+	8					GSTK1_uc011ksy.1_3'UTR|GSTK1_uc003wcj.2_3'UTR|GSTK1_uc011ksz.1_3'UTR	NM_015917	NP_057001			glutathione S-transferase kappa 1 isoform a							outer membrane-bounded periplasmic space|peroxisome	glutathione transferase activity|identical protein binding|protein disulfide oxidoreductase activity				0	Melanoma(164;0.059)				Glutathione(DB00143)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	143815704	143815704	+	IGR	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143815704delG								OR2A2 (8074 upstream) : OR2A14 (10502 downstream)																																			---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151921038	151921038	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151921038delT	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	155907140	155907140	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155907140delA								SHH (302173 upstream) : C7orf4 (426045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5325343	5325344	+	IGR	DEL	TT	-	-	rs66941724		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5325343_5325344delTT								CSMD1 (473015 upstream) : MCPH1 (938777 downstream)																																			---	---	---	---
MSR1	4481	broad.mit.edu	37	8	16012445	16012446	+	Intron	DEL	AC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16012445_16012446delAC	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_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	26290665	26290665	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26290665delA								BNIP3L (20021 upstream) : PNMA2 (71531 downstream)																																			---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38163092	38163092	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38163092delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	8	41041780	41041781	+	IGR	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41041780_41041781insA								ZMAT4 (286437 upstream) : SFRP1 (77698 downstream)																																			---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42129579	42129579	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42129579delC	uc003xow.1	+						IKBKB_uc003xov.2_Intron|IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)											OREG0018746	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48586205	48586205	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48586205delT	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_5'UTR|KIAA0146_uc010lxv.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62412295	62412295	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62412295delT	uc003xuh.2	+	6					CLVS1_uc003xui.2_RNA|CLVS1_uc010lyp.2_3'UTR	NM_173519	NP_775790			retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5																		---	---	---	---
ASPH	444	broad.mit.edu	37	8	62438739	62438740	+	Intron	INS	-	T	T	rs78239105		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62438739_62438740insT	uc003xuj.2	-						ASPH_uc011leg.1_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
TRIM55	84675	broad.mit.edu	37	8	67039908	67039908	+	Intron	DEL	A	-	-	rs72514875		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67039908delA	uc003xvv.2	+						TRIM55_uc003xvu.2_Intron|TRIM55_uc003xvw.2_Intron|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973			tripartite motif-containing 55 isoform 1							cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)															---	---	---	---
C8orf45	157777	broad.mit.edu	37	8	67795863	67795863	+	Intron	DEL	A	-	-	rs79553261		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67795863delA	uc003xwz.3	+						C8orf45_uc003xwv.2_Intron|C8orf45_uc011lev.1_Intron|C8orf45_uc011lew.1_Intron|C8orf45_uc011lex.1_Intron|C8orf45_uc003xwy.3_Intron	NM_173518	NP_775789			minichromosome maintenance complex						DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
LRRC67	286187	broad.mit.edu	37	8	67925535	67925535	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67925535delT	uc003xxc.2	-							NM_001013626	NP_001013648			leucine rich repeat containing 67												0																		---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67961711	67961712	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67961711_67961712delAA	uc003xxe.2	-						COPS5_uc003xxd.2_Intron|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.1_Intron	NM_006837	NP_006828			COP9 signalosome subunit 5						cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68030957	68030957	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68030957delT	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)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68536561	68536561	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68536561delA	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71071923	71071923	+	Intron	DEL	A	-	-	rs76234321		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71071923delA	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
LY96	23643	broad.mit.edu	37	8	74939176	74939176	+	Intron	DEL	T	-	-	rs34219418		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)															---	---	---	---
GDAP1	54332	broad.mit.edu	37	8	75276702	75276703	+	3'UTR	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75276702_75276703insT	uc003yah.2	+	6					GDAP1_uc011lfj.1_3'UTR|GDAP1_uc003yai.2_3'UTR	NM_018972	NP_061845			ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)															---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76463542	76463542	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76463542delA	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)															---	---	---	---
STMN2	11075	broad.mit.edu	37	8	80577225	80577226	+	Intron	DEL	AA	-	-	rs78006622		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80577225_80577226delAA	uc011lfn.1	+						STMN2_uc003ybk.2_RNA	NM_007029	NP_008960			superiorcervical ganglia, neural specific 10						intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)															---	---	---	---
SLC7A13	157724	broad.mit.edu	37	8	87229783	87229784	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87229783_87229784insA	uc003ydq.1	-	3	1192_1193	c.1094_1095insT	c.(1093-1095)TTCfs	p.F365fs	SLC7A13_uc003ydr.1_Frame_Shift_Ins_p.F356fs	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	365	Helical; Name=10; (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88800612	88800612	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88800612delT								CNBD1 (405657 upstream) : DCAF4L2 (82361 downstream)																																			---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90936586	90936586	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	93156235	93156235	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93156235delT								RUNX1T1 (48529 upstream) : C8orf83 (739630 downstream)																																			---	---	---	---
ESRP1	54845	broad.mit.edu	37	8	95686611	95686611	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95686611delA	uc003ygq.3	+	12	1711	c.1528delA	c.(1528-1530)AAAfs	p.K510fs	ESRP1_uc003ygr.3_Frame_Shift_Del_p.K510fs|ESRP1_uc003ygs.3_Frame_Shift_Del_p.K510fs|ESRP1_uc003ygt.3_Frame_Shift_Del_p.K510fs|ESRP1_uc003ygu.3_Frame_Shift_Del_p.K510fs|ESRP1_uc003ygv.2_Frame_Shift_Del_p.K350fs|ESRP1_uc003ygw.2_Frame_Shift_Del_p.K350fs	NM_017697	NP_060167	Q6NXG1	ESRP1_HUMAN	RNA binding motif protein 35A isoform 1	510	RRM 3.				mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4																		---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95796165	95796166	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95796165_95796166insA	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96799026	96799027	+	IGR	INS	-	AGGA	AGGA			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96799026_96799027insAGGA								C8orf37 (517589 upstream) : GDF6 (355533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96977958	96977958	+	IGR	DEL	G	-	-	rs35277274		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96977958delG								C8orf37 (696521 upstream) : GDF6 (176602 downstream)																																			---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97332635	97332636	+	Intron	INS	-	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97332635_97332636insG	uc003yht.1	+						PTDSS1_uc003yhu.1_Intron	NM_014754	NP_055569			phosphatidylserine synthase 1						phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)													---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100108476	100108476	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100108476delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yit.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yis.2_Intron|VPS13B_uc011lgy.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	102350083	102350083	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102350083delA								ZNF706 (132123 upstream) : NACAP1 (23939 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108315770	108315770	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108315770delA	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_Intron	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	109140114	109140133	+	IGR	DEL	AAGGAAGGAAGGAAGGAAGG	-	-	rs71947791	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109140114_109140133delAAGGAAGGAAGGAAGGAAGG								RSPO2 (44201 upstream) : EIF3E (73840 downstream)																																			---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110460356	110460356	+	Intron	DEL	T	-	-	rs112970760		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110460356delT	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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113402740	113402741	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113402740_113402741insA	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)			---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124708147	124708147	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124708147delC	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297			annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
SQLE	6713	broad.mit.edu	37	8	126019615	126019615	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126019615delT	uc011liq.1	+							NM_003129	NP_003120			squalene epoxidase						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)													---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141843275	141843275	+	Intron	DEL	A	-	-	rs141534503		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141843275delA	uc003yvu.2	-						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)															---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5753519	5753519	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5753519delT	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)														---	---	---	---
ERMP1	79956	broad.mit.edu	37	9	5812235	5812235	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5812235delA	uc003zjm.1	-						ERMP1_uc011lme.1_Intron|ERMP1_uc010mhs.1_Intron	NM_024896	NP_079172			aminopeptidase Fxna						proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)														---	---	---	---
KIAA2026	158358	broad.mit.edu	37	9	5968043	5968044	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5968043_5968044insT	uc003zjq.3	-	3	2403_2404	c.2187_2188insA	c.(2185-2190)AAAGCAfs	p.K729fs		NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358	729_730	Lys-rich.									ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6556451	6556451	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6556451delA	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						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)													---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8526762	8526766	+	Intron	DEL	AAAAG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8526762_8526766delAAAAG	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13217332	13217333	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13217332_13217333insA	uc010mia.1	-						MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820			multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
SMU1	55234	broad.mit.edu	37	9	33071911	33071911	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33071911delA	uc003zsf.1	-						SMU1_uc010mjo.1_Intron|SMU1_uc010mjp.1_Intron|SMU1_uc011lnu.1_Intron	NM_018225	NP_060695			smu-1 suppressor of mec-8 and unc-52 homolog							cytoplasm|nucleus				ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)														---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33115994	33115994	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33115994delA	uc003zsg.2	-	4	1143	c.954delT	c.(952-954)TTTfs	p.F318fs		NM_001497	NP_001488	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	318	Lumenal (Potential).				oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34997369	34997369	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)															---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35725917	35725917	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35725917delT	uc003zxt.2	-						TLN1_uc003zxu.3_Intron	NM_006289	NP_006280			talin 1						axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
MELK	9833	broad.mit.edu	37	9	36642981	36642981	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36642981delT	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	65635539	65635539	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:65635539delT								FAM74A4 (141153 upstream) : LOC442421 (860931 downstream)																																			---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86584096	86584096	+	3'UTR	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
NAA35	60560	broad.mit.edu	37	9	88590183	88590183	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88590183delT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911			corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3																		---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88650552	88650553	+	Intron	DEL	AC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88650552_88650553delAC	uc004aol.2	-						GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
SPIN1	10927	broad.mit.edu	37	9	91026437	91026437	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91026437delT	uc010mqj.2	+						SPIN1_uc004apy.2_Intron|SPIN1_uc004apz.2_Intron|SPIN1_uc010mqk.2_Intron	NM_006717	NP_006708			spindlin						cell cycle|gamete generation|multicellular organismal development	nucleus	methylated histone residue binding				0																		---	---	---	---
SLC35D2	11046	broad.mit.edu	37	9	99098997	99098998	+	Splice_Site	INS	-	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99098997_99098998insC	uc004awc.2	-	9	828	c.752_splice	c.e9+1	p.G251_splice	SLC35D2_uc010msd.2_Splice_Site|SLC35D2_uc010mse.2_Splice_Site_p.G204_splice|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron	NM_007001	NP_008932			solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)																---	---	---	---
TEX10	54881	broad.mit.edu	37	9	103065721	103065721	+	Intron	DEL	C	-	-	rs35109045		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103065721delC	uc004bas.2	-						TEX10_uc011lvf.1_Intron|TEX10_uc011lvg.1_Intron	NM_017746	NP_060216			testis expressed 10 isoform 1							integral to membrane|MLL1 complex|nuclear membrane|nucleolus	binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)														---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119537865	119537868	+	Intron	DEL	AGGG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119537865_119537868delAGGG	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																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130087203	130087203	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130087203delC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	133834286	133834291	+	IGR	DEL	ACCACT	-	-	rs144639279	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133834286_133834291delACCACT								FIBCD1 (19831 upstream) : LAMC3 (50213 downstream)																																			---	---	---	---
SETX	23064	broad.mit.edu	37	9	135221514	135221514	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135221514delA	uc004cbk.2	-							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)														---	---	---	---
GRIN1	2902	broad.mit.edu	37	9	140052735	140052735	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140052735delG	uc004clk.2	+						GRIN1_uc004cli.1_Intron|GRIN1_uc004clj.1_Intron|GRIN1_uc004cll.2_Intron|GRIN1_uc004clm.2_Intron|GRIN1_uc004cln.2_Intron|GRIN1_uc004clo.2_Intron	NM_007327	NP_015566			NMDA receptor 1 isoform NR1-3 precursor						ionotropic glutamate receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|regulation of excitatory postsynaptic membrane potential|response to ethanol|visual learning	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane|synaptic vesicle|synaptosome	calcium ion binding|calmodulin binding|extracellular-glutamate-gated ion channel activity|glutamate binding|glycine binding			skin(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
PFKP	5214	broad.mit.edu	37	10	3155776	3155776	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3155776delG	uc001igp.2	+						PFKP_uc001igq.2_Intron|PFKP_uc009xhr.2_Intron|PFKP_uc009xhs.1_Intron|PFKP_uc009xht.2_Intron|PFKP_uc009xhu.2_Intron	NM_002627	NP_002618			phosphofructokinase, platelet						glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)														---	---	---	---
PITRM1	10531	broad.mit.edu	37	10	3205748	3205748	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3205748delA	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|PITRM1_uc001igw.1_Intron|uc001igx.1_5'Flank					SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	8007107	8007107	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8007107delA	uc010qbd.1	+	3	1634	c.1634delA	c.(1633-1635)GAAfs	p.E545fs		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	545	Lys-rich.				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15256758	15256760	+	Intron	DEL	TTT	-	-	rs79674551		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15256758_15256760delTTT	uc001iob.2	-							NM_001010924	NP_001010924			hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
MRC1	4360	broad.mit.edu	37	10	17875520	17875520	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17875520delA	uc001ipk.2	+							NM_002438	NP_002429			mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0																		---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21875206	21875208	+	Intron	DEL	TTT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21875206_21875208delTTT	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								---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34572884	34572884	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34572884delT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	64005582	64005583	+	Intron	INS	-	A	A	rs145698745	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64005582_64005583insA	uc001jlw.2	-						RTKN2_uc001jlx.2_Intron	NM_145307	NP_660350			rhotekin 2						signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)																	---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70140858	70140858	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70140858delA	uc001job.2	-						RUFY2_uc001jnz.1_Intron|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Intron|RUFY2_uc001jod.1_Intron	NM_017987	NP_060457			RUN and FYVE domain-containing 2 isoform a							nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72288965	72288972	+	Intron	DEL	CCCCCCCC	-	-	rs72290492		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72288965_72288972delCCCCCCCC	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74653469	74653470	+	5'UTR	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74653469_74653470delAA	uc001jte.1	+	1					OIT3_uc009xqs.1_RNA	NM_152635	NP_689848			oncoprotein-induced transcript 3 precursor							nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)																	---	---	---	---
ZNF503	84858	broad.mit.edu	37	10	77160768	77160769	+	Intron	INS	-	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77160768_77160769insC	uc001jxg.2	-						C10orf41_uc010qlf.1_5'Flank|C10orf41_uc010qlg.1_5'Flank	NM_032772	NP_116161			zinc finger protein 503						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1	all_cancers(46;0.105)|all_epithelial(25;0.00449)|Prostate(51;0.0112)|Ovarian(15;0.088)																	---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88559184	88559184	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88559184delT	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				---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89725231	89725231	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89725231delT	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)			---	---	---	---
PCGF5	84333	broad.mit.edu	37	10	93001427	93001427	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93001427delA	uc001khh.2	+						PCGF5_uc010qnk.1_Intron|PCGF5_uc001khi.2_Intron	NM_032373	NP_115749			polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1																		---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93724151	93724151	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93724151delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_5'Flank	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)																---	---	---	---
PDE6C	5146	broad.mit.edu	37	10	95394481	95394481	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95394481delA	uc001kiu.3	+							NM_006204	NP_006195			phosphodiesterase 6C						visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)																---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98714563	98714563	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98714563delT	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)														---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98799862	98799862	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98799862delC	uc001kmw.2	-	21	2432	c.2180delG	c.(2179-2181)GGCfs	p.G727fs	SLIT1_uc009xvh.1_Frame_Shift_Del_p.G737fs	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	727	LRRNT 4.				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)														---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101571087	101571087	+	Intron	DEL	A	-	-	rs112044854		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101571087delA	uc001kqf.2	+							NM_000392	NP_000383			ATP-binding cassette, sub-family C (CFTR/MRP),							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)													---	---	---	---
SEC31B	25956	broad.mit.edu	37	10	102275671	102275672	+	Intron	INS	-	G	G	rs143845466	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102275671_102275672insG	uc001krc.1	-						SEC31B_uc010qpo.1_Intron|SEC31B_uc001krd.1_Intron|SEC31B_uc001krf.1_Intron|SEC31B_uc001kre.1_Intron|SEC31B_uc010qpp.1_Intron|SEC31B_uc009xwn.1_Intron|SEC31B_uc009xwo.1_Intron|SEC31B_uc010qpq.1_Intron|SEC31B_uc010qpr.1_Intron	NM_015490	NP_056305			SEC31 homolog B						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)														---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105179557	105179557	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	107445676	107445676	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107445676delT								SORCS3 (420683 upstream) : SORCS1 (887746 downstream)																																			---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114710910	114710910	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114710910delC	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_5'UTR|TCF7L2_uc010qrs.1_5'UTR|TCF7L2_uc010qrt.1_5'UTR	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114925622	114925622	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114925622delC	uc001lae.3	+	14	2207	c.1700delC	c.(1699-1701)GCCfs	p.A567fs	TCF7L2_uc001lac.3_Frame_Shift_Del_p.A561fs|TCF7L2_uc010qrk.1_3'UTR|TCF7L2_uc010qrl.1_Frame_Shift_Del_p.A544fs|TCF7L2_uc010qrm.1_3'UTR|TCF7L2_uc010qrn.1_3'UTR|TCF7L2_uc001lad.3_3'UTR|TCF7L2_uc001lag.3_3'UTR|TCF7L2_uc001laf.3_Frame_Shift_Del_p.A544fs|TCF7L2_uc010qro.1_3'UTR|TCF7L2_uc001lah.2_3'UTR|TCF7L2_uc010qrp.1_3'UTR|TCF7L2_uc010qrq.1_3'UTR|TCF7L2_uc010qrr.1_Frame_Shift_Del_p.A499fs|TCF7L2_uc010qrs.1_Frame_Shift_Del_p.A455fs|TCF7L2_uc010qrt.1_Frame_Shift_Del_p.A455fs|TCF7L2_uc010qru.1_3'UTR|TCF7L2_uc010qrv.1_3'UTR|TCF7L2_uc010qrw.1_3'UTR|TCF7L2_uc010qrx.1_3'UTR	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1	584					anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
DCLRE1A	9937	broad.mit.edu	37	10	115606848	115606848	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115606848delT	uc001law.2	-							NM_014881	NP_055696			DNA cross-link repair 1A						cell division|mitosis	nucleus	hydrolase activity			skin(2)	2				Epithelial(162;0.0157)|all cancers(201;0.0171)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117228676	117228676	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117228676delT	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)														---	---	---	---
RGS10	6001	broad.mit.edu	37	10	121285672	121285672	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121285672delA	uc001lee.2	-						RGS10_uc001lef.2_Intron|RGS10_uc001leg.2_Intron	NM_002925	NP_002916			regulator of G-protein signaling 10 isoform b						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|protein binding|signal transducer activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)														---	---	---	---
WDR11	55717	broad.mit.edu	37	10	122638065	122638065	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122638065delT	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587			bromodomain and WD repeat domain containing 2							integral to membrane					0																		---	---	---	---
CUZD1	50624	broad.mit.edu	37	10	124596659	124596659	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124596659delT	uc001lgq.2	-						CUZD1_uc001lgp.2_Intron|CUZD1_uc009yad.2_Intron|CUZD1_uc009yaf.2_Intron|CUZD1_uc001lgr.2_Intron|CUZD1_uc010qty.1_Intron|CUZD1_uc009yae.2_Intron|CUZD1_uc001lgs.2_Intron|CUZD1_uc010qtz.1_Intron	NM_022034	NP_071317			CUB and zona pellucida-like domains 1 precursor						cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)														---	---	---	---
PPP2R2D	55844	broad.mit.edu	37	10	133753424	133753424	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133753424delT	uc001lks.2	+						PPP2R2D_uc001lkr.2_Intron|PPP2R2D_uc001lkt.2_Intron|PPP2R2D_uc009yay.2_5'Flank	NM_018461	NP_060931			protein phosphatase 2, regulatory subunit B,						cell division|exit from mitosis|mitosis|signal transduction	cytoplasm|protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			skin(1)	1		all_cancers(35;2.16e-12)|all_epithelial(44;2.77e-09)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Colorectal(31;0.0124)|Breast(234;0.023)|all_neural(114;0.0299)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.86e-05)|Epithelial(32;8.82e-05)|all cancers(32;0.000106)|BRCA - Breast invasive adenocarcinoma(275;0.21)														---	---	---	---
PKP3	11187	broad.mit.edu	37	11	400055	400055	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:400055delC	uc001lpc.2	+	6	1438	c.1362delC	c.(1360-1362)AGCfs	p.S454fs		NM_007183	NP_009114	Q9Y446	PKP3_HUMAN	plakophilin 3	454	ARM 4.				cell adhesion	desmosome|nucleus	binding			skin(1)	1		all_cancers(49;3.02e-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;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)														---	---	---	---
CARS	833	broad.mit.edu	37	11	3063661	3063661	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3063661delT	uc001lxh.2	-						CARS_uc001lxe.2_Intron|CARS_uc001lxf.2_Intron|CARS_uc001lxg.2_Intron|CARS_uc010qxo.1_Intron|CARS_uc010qxp.1_Intron	NM_001751	NP_001742			cysteinyl-tRNA synthetase isoform b						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								---	---	---	---
TUB	7275	broad.mit.edu	37	11	8121984	8121984	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8121984delC	uc001mga.2	+						TUB_uc010rbk.1_Intron|TUB_uc001mfy.2_Intron	NM_177972	NP_813977			tubby isoform b						phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)														---	---	---	---
LMO1	4004	broad.mit.edu	37	11	8246319	8246320	+	Intron	INS	-	G	G	rs142817725	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8246319_8246320insG	uc001mgg.1	-						LMO1_uc009yfo.1_Intron|LMO1_uc001mgh.1_Intron	NM_002315	NP_002306			LIM domain only 1						cell proliferation|multicellular organismal development|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;1.59e-07)|BRCA - Breast invasive adenocarcinoma(625;0.203)				T|A	TRD@	T-ALL|neuroblastoma	neuroblastoma							---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9088129	9088129	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9088129delG	uc001mhh.1	-						SCUBE2_uc001mhi.1_Intron|SCUBE2_uc001mhj.1_Intron	NM_020974	NP_066025			CEGP1 protein precursor							extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9200705	9200705	+	Intron	DEL	T	-	-	rs78862197		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9200705delT	uc001mhl.2	-						DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
FAR1	84188	broad.mit.edu	37	11	13722198	13722199	+	Intron	INS	-	TCT	TCT	rs137872059	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13722198_13722199insTCT	uc001mld.2	+						FAR1_uc009ygp.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	25440621	25440622	+	IGR	INS	-	GAAG	GAAG	rs138519223	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25440621_25440622insGAAG								LUZP2 (336439 upstream) : ANO3 (770207 downstream)																																			---	---	---	---
DEPDC7	91614	broad.mit.edu	37	11	33053862	33053862	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33053862delT	uc001mub.2	+						DEPDC7_uc001muc.2_Intron	NM_001077242	NP_001070710			novel 58.3 KDA protein isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33451556	33451563	+	IGR	DEL	CCTTCCTT	-	-	rs142044105	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33451556_33451563delCCTTCCTT								HIPK3 (75617 upstream) : C11orf41 (112314 downstream)																																			---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35457302	35457302	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35457302delA	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																		---	---	---	---
F2	2147	broad.mit.edu	37	11	46748556	46748556	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46748556delT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46775145	46775145	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46775145delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
MTCH2	23788	broad.mit.edu	37	11	47657242	47657242	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47817976	47817976	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47817976delA	uc001ngm.2	-						NUP160_uc009ylw.2_Intron	NM_015231	NP_056046			nucleoporin 160kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48967951	48967951	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48967951delA								OR4A47 (456679 upstream) : FOLH1 (200237 downstream)																																			---	---	---	---
MS4A7	58475	broad.mit.edu	37	11	60161439	60161439	+	3'UTR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60161439delA	uc001npe.2	+	7					MS4A7_uc001npf.2_3'UTR|MS4A7_uc001npg.2_3'UTR|MS4A7_uc001nph.2_3'UTR|MS4A14_uc001npi.2_Intron	NM_206939	NP_996822			membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CD6	923	broad.mit.edu	37	11	60781260	60781261	+	Intron	DEL	GC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60781260_60781261delGC	uc001nqq.2	+						CD6_uc001nqp.2_Intron|CD6_uc001nqr.2_Intron|CD6_uc001nqs.2_Intron|CD6_uc001nqt.2_Intron	NM_006725	NP_006716			CD6 molecule precursor						cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
FIBP	9158	broad.mit.edu	37	11	65653077	65653077	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65653077delT	uc001ogd.2	-	5	691	c.570delA	c.(568-570)AAAfs	p.K190fs	FIBP_uc009yqu.2_Frame_Shift_Del_p.K187fs|FIBP_uc001oge.2_Frame_Shift_Del_p.K190fs	NM_198897	NP_942600	O43427	FIBP_HUMAN	FGF intracellular binding protein isoform a	190					fibroblast growth factor receptor signaling pathway	endomembrane system|membrane|microsome|mitochondrion|nucleus	fibroblast growth factor binding			ovary(1)	1				READ - Rectum adenocarcinoma(159;0.166)												OREG0021089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CPT1A	1374	broad.mit.edu	37	11	68528892	68528892	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68528892delT	uc001oog.3	-						CPT1A_uc001oof.3_Intron|CPT1A_uc009ysj.2_Intron	NM_001876	NP_001867			carnitine palmitoyltransferase 1A liver isoform						carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)													---	---	---	---
INPPL1	3636	broad.mit.edu	37	11	71948748	71948748	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71948748delC	uc001osf.2	+	26	3607	c.3460delC	c.(3460-3462)CCCfs	p.P1154fs	INPPL1_uc001osg.2_Frame_Shift_Del_p.P912fs	NM_001567	NP_001558	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1154					actin filament organization|cell adhesion|endocytosis	actin cortical patch|cytosol	actin binding|SH2 domain binding|SH3 domain binding			skin(2)|ovary(1)|breast(1)	4																		---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77409841	77409841	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77409841delA	uc001oyn.2	-						RSF1_uc001oym.2_Intron	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)															---	---	---	---
AMOTL1	154810	broad.mit.edu	37	11	94592670	94592670	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94592670delT	uc001pfb.2	+						AMOTL1_uc001pfc.2_Intron	NM_130847	NP_570899			angiomotin like 1							cytoplasm|tight junction	identical protein binding			ovary(1)|breast(1)	2		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)																---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100095272	100095272	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100095272delA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron|CNTN5_uc010ruk.1_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107686334	107686334	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686334delT	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985			solute carrier family 35, member F2						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)														---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108031565	108031566	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108031565_108031566delAA	uc001pjz.3	-						NPAT_uc010rvv.1_Intron	NM_002519	NP_002510			nuclear protein,  ataxia-telangiectasia locus						positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|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)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108098310	108098310	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108098310delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|ATM_uc001pkc.1_Intron	NM_000051	NP_000042			ataxia telangiectasia mutated isoform 1						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)			---	---	---	---
RDX	5962	broad.mit.edu	37	11	110118357	110118357	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110118357delA	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897			radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)														---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118252002	118252002	+	Intron	DEL	T	-	-	rs139803253	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118252002delT	uc001psw.2	+						UBE4A_uc001psv.2_Intron	NM_004788	NP_004779			ubiquitination factor E4A						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	5	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;3.28e-05)														---	---	---	---
TBCEL	219899	broad.mit.edu	37	11	120930918	120930918	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120930918delA	uc009zay.2	+						TBCEL_uc001pxo.2_Intron|TBCEL_uc001pxp.2_Intron|TBCEL_uc001pxq.2_Intron	NM_001130047	NP_001123519			tubulin folding cofactor E-like							cytoplasm|cytoskeleton				skin(1)	1		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)														---	---	---	---
C11orf63	79864	broad.mit.edu	37	11	122775729	122775729	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122775729delT	uc001pym.2	+						C11orf63_uc001pyl.1_Intron	NM_024806	NP_079082			hypothetical protein LOC79864 isoform 1											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)														---	---	---	---
SCN3B	55800	broad.mit.edu	37	11	123509101	123509101	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123509101delT	uc001pza.1	-						SCN3B_uc001pzb.1_Intron	NM_001040151	NP_001035241			voltage-gated sodium channel beta-3 subunit						axon guidance	integral to membrane|plasma membrane	voltage-gated sodium channel activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)														---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133789013	133789014	+	Intron	INS	-	G	G	rs72000603		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133789013_133789014insG	uc001qgx.3	-							NM_014987	NP_055802			immunoglobulin superfamily, member 9B							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)														---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2715986	2715986	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2715986delT	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)													---	---	---	---
PZP	5858	broad.mit.edu	37	12	9313518	9313518	+	Intron	DEL	T	-	-	rs7972015	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9313518delT	uc001qvl.2	-						PZP_uc009zgl.2_Intron|PZP_uc010sgo.1_Intron	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
KCNJ8	3764	broad.mit.edu	37	12	21925909	21925910	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21925909_21925910insT	uc001rff.2	-							NM_004982	NP_004973			potassium inwardly-rectifying channel J8							voltage-gated potassium channel complex					0					Levosimendan(DB00922)													---	---	---	---
TM7SF3	51768	broad.mit.edu	37	12	27152329	27152329	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27152329delA	uc010sjl.1	-							NM_016551	NP_057635			transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)																	---	---	---	---
DDX11	1663	broad.mit.edu	37	12	31256198	31256198	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31256198delG	uc001rjt.1	+						DDX11_uc001rjr.1_Intron|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Intron|DDX11_uc001rjw.1_Intron|DDX11_uc009zjn.1_Intron|DDX11_uc009zjo.1_Intron	NM_152438	NP_689651			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)														Multiple Myeloma(12;0.14)			---	---	---	---
RPAP3	79657	broad.mit.edu	37	12	48061519	48061519	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48061519delA	uc001rpr.2	-						RPAP3_uc010slk.1_Intron|RPAP3_uc001rps.2_Intron	NM_024604	NP_078880			RNA polymerase II associated protein 3 isoform								binding			ovary(1)	1	Lung SC(27;0.192)																	---	---	---	---
HOXC11	3227	broad.mit.edu	37	12	54366916	54366917	+	5'UTR	DEL	AG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54366916_54366917delAG	uc001sem.2	+	1						NM_014212	NP_055027			homeobox C11						endoderm development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1								T	NUP98	AML								---	---	---	---
DNAJC14	85406	broad.mit.edu	37	12	56197268	56197268	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56197268delA	uc001shu.1	-						SARNP_uc009zoa.2_Intron|SARNP_uc001shs.3_Intron|SARNP_uc001sht.2_Intron|SARNP_uc001shv.3_Intron	NM_032364	NP_115740			dopamine receptor interacting protein						protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
ESYT1	23344	broad.mit.edu	37	12	56528386	56528386	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56528386delT	uc001sjq.2	+						ESYT1_uc001sjr.2_Intron	NM_015292	NP_056107			extended synaptotagmin-like protein 1							integral to membrane				ovary(4)|skin(1)	5																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	56999550	56999550	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999550delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|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																		---	---	---	---
ARHGAP9	64333	broad.mit.edu	37	12	57867211	57867211	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57867211delA	uc001sod.2	-						ARHGAP9_uc001sny.2_Intron|ARHGAP9_uc001snz.2_Intron|ARHGAP9_uc001soa.2_Intron|ARHGAP9_uc001sob.2_Intron|ARHGAP9_uc001soc.2_Intron	NM_032496	NP_115885			Rho GTPase activating protein 9 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)															---	---	---	---
MARS	4141	broad.mit.edu	37	12	57905367	57905367	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57905367delA	uc001sog.2	+						MARS_uc001sof.1_Intron|MARS_uc010srp.1_Intron|MARS_uc010srq.1_Intron|MARS_uc001soh.1_5'Flank	NM_004990	NP_004981			methionyl-tRNA synthetase						methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)													---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57975862	57975862	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57975862delA	uc001sor.1	+						KIF5A_uc010srr.1_Intron|uc001sos.2_5'Flank	NM_004984	NP_004975			kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3																		---	---	---	---
GNS	2799	broad.mit.edu	37	12	65113720	65113720	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65113720delA	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067			glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)														---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69020555	69020555	+	Intron	DEL	T	-	-	rs74812051		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69020555delT	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)														---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69036118	69036118	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69036118delA	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)														---	---	---	---
PTPRB	5787	broad.mit.edu	37	12	70949083	70949083	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70949083delG	uc001swb.3	-	18	4376	c.4346delC	c.(4345-4347)CCTfs	p.P1449fs	PTPRB_uc010sto.1_Frame_Shift_Del_p.P1359fs|PTPRB_uc010stp.1_Frame_Shift_Del_p.P1359fs|PTPRB_uc001swc.3_Frame_Shift_Del_p.P1667fs|PTPRB_uc001swa.3_Frame_Shift_Del_p.P1579fs	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1449	Fibronectin type-III 17.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)															---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71526398	71526398	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71526398delT	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	74151336	74151337	+	IGR	INS	-	GAAG	GAAG	rs143357657	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74151336_74151337insGAAG								None (None upstream) : ATXN7L3B (780214 downstream)																																			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78592475	78592475	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78592475delT	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)			---	---	---	---
PAWR	5074	broad.mit.edu	37	12	79988067	79988067	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79988067delA	uc001syx.2	-							NM_002583	NP_002574			PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0																		---	---	---	---
ATP2B1	490	broad.mit.edu	37	12	90010464	90010465	+	Intron	DEL	AA	-	-	rs113951213		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90010464_90010465delAA	uc001tbh.2	-						ATP2B1_uc001tbg.2_Intron|ATP2B1_uc001tbf.2_Intron	NM_001682	NP_001673			plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DCN	1634	broad.mit.edu	37	12	91558363	91558363	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91558363delA	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																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95453642	95453642	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
SCYL2	55681	broad.mit.edu	37	12	100709304	100709304	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100709304delT	uc001thn.2	+						SCYL2_uc009ztw.1_Intron|SCYL2_uc001thm.1_Intron	NM_017988	NP_060458			SCY1-like 2 protein						endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101679516	101679516	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101679516delC	uc001tia.1	+						UTP20_uc009ztz.1_Intron	NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104134268	104134268	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104134268delA	uc001tjw.2	+						STAB2_uc009zug.2_Intron	NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
TCP11L2	255394	broad.mit.edu	37	12	106712021	106712021	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106712021delT	uc001tln.2	+						TCP11L2_uc001tll.2_Intron|TCP11L2_uc001tlm.2_Intron	NM_152772	NP_689985			t-complex 11 (mouse) like 2											ovary(3)	3																		---	---	---	---
POLR3B	55703	broad.mit.edu	37	12	106799414	106799414	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106799414delT	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552			DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
WSCD2	9671	broad.mit.edu	37	12	108625764	108625764	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108625764delA	uc001tms.2	+						WSCD2_uc001tmt.2_Intron|WSCD2_uc001tmu.2_Intron	NM_014653	NP_055468			WSC domain containing 2							integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
RAD9B	144715	broad.mit.edu	37	12	110950776	110950777	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110950776_110950777delTT	uc001trf.3	+						RAD9B_uc001trg.3_Intron|RAD9B_uc010sya.1_Intron|RAD9B_uc001tre.3_Intron|RAD9B_uc001trd.3_Intron	NM_152442	NP_689655			RAD9 homolog B						cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2																		---	---	---	---
PPP1CC	5501	broad.mit.edu	37	12	111158948	111158948	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111158948delT	uc001tru.2	-	7	1150	c.905delA	c.(904-906)AAGfs	p.K302fs		NM_002710	NP_002701	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma	302					cell division|glycogen metabolic process|mitotic prometaphase|triglyceride catabolic process	cleavage furrow|condensed chromosome kinetochore|cytosol|midbody|MLL5-L complex|nuclear speck|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein kinase binding|protein serine/threonine phosphatase activity			lung(2)|central_nervous_system(1)	3																		---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112491483	112491483	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112491483delA	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229			mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
TRAFD1	10906	broad.mit.edu	37	12	112568247	112568247	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112568247delT	uc001ttp.2	+						TRAFD1_uc001tto.2_Intron|TRAFD1_uc009zwb.2_Intron|TRAFD1_uc010syj.1_Intron	NM_006700	NP_006691			TRAF-type zinc finger domain containing 1						negative regulation of innate immune response	intracellular	protein binding|zinc ion binding				0																		---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116418760	116418760	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116418760delA	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)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116420495	116420495	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116420495delC	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)														---	---	---	---
TAOK3	51347	broad.mit.edu	37	12	118615305	118615305	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118615305delA	uc001twx.2	-						TAOK3_uc001twv.2_Intron|TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365			TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120602670	120602670	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120602670delT	uc001txo.2	-							NM_006836	NP_006827			GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
ANAPC5	51433	broad.mit.edu	37	12	121756441	121756441	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121756441delT	uc001uag.2	-						ANAPC5_uc010szu.1_Intron|ANAPC5_uc001uae.2_Intron|ANAPC5_uc010szv.1_Intron|ANAPC5_uc001uaf.2_Intron|ANAPC5_uc001uah.2_Intron|ANAPC5_uc001uai.1_Intron	NM_016237	NP_057321			anaphase-promoting complex subunit 5 isoform a						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			skin(3)|breast(2)|kidney(1)	6	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
TCTN2	79867	broad.mit.edu	37	12	124158006	124158006	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124158006delG	uc001ufp.2	+						TCTN2_uc009zya.2_Intron	NM_024809	NP_079085			tectonic family member 2 isoform 1						cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)														---	---	---	---
FZD10	11211	broad.mit.edu	37	12	130649317	130649318	+	3'UTR	DEL	TT	-	-	rs112714527		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130649317_130649318delTT	uc001uii.2	+	1					uc001uih.1_5'Flank	NM_007197	NP_009128			frizzled 10 precursor						brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)														---	---	---	---
ULK1	8408	broad.mit.edu	37	12	132397937	132397938	+	Intron	DEL	AA	-	-	rs80025522		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132397937_132397938delAA	uc001uje.2	+							NM_003565	NP_003556			Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132474451	132474451	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132474451delT	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron|EP400_uc001ujj.1_Intron|EP400_uc001ujk.2_Intron	NM_015409	NP_056224			E1A binding protein p400						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)														---	---	---	---
NOC4L	79050	broad.mit.edu	37	12	132635788	132635788	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132635788delC	uc001ujz.1	+							NM_024078	NP_076983			nucleolar complex associated 4 homolog						rRNA processing	integral to membrane|nuclear membrane|nucleolus	protein binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	28270838	28270838	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28270838delT								POLR1D (29291 upstream) : GSX1 (95942 downstream)																																			---	---	---	---
C13orf36	400120	broad.mit.edu	37	13	37269030	37269030	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37269030delT	uc001uvt.3	+							NM_203451	NP_982276			hypothetical protein LOC400120							integral to membrane				skin(1)	1																		---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38357012	38357012	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38357012delA	uc001uws.2	-						TRPC4_uc010abv.2_Intron|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263			transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46577610	46577610	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46577610delA	uc010tfw.1	-						ZC3H13_uc001vas.1_Intron|ZC3H13_uc001vat.1_Intron	NM_015070	NP_055885			zinc finger CCCH-type containing 13								nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716269	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269delA	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 								---	---	---	---
RNASEH2B	79621	broad.mit.edu	37	13	51530587	51530587	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51530587delA	uc001vfa.3	+	11	1237	c.916delA	c.(916-918)AAAfs	p.K306fs	RNASEH2B_uc001vfb.3_Intron	NM_024570	NP_078846	Q5TBB1	RNH2B_HUMAN	ribonuclease H2, subunit B isoform 1	306					RNA catabolic process	nucleus|ribonuclease H2 complex					0		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	56363936	56363937	+	IGR	INS	-	TTCC	TTCC			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56363936_56363937insTTCC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59837560	59837560	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59837560delA								None (None upstream) : DIAPH3 (402165 downstream)																																			---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	67840882	67840882	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67840882delT								PCDH9 (36414 upstream) : None (None downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72131053	72131053	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76430509	76430509	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76430509delT	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjx.1_5'Flank	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)														---	---	---	---
SLITRK6	84189	broad.mit.edu	37	13	86370823	86370823	+	Intron	DEL	T	-	-	rs72093623		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86370823delT	uc001vll.1	-						SLITRK6_uc010afe.1_5'Flank	NM_032229	NP_115605			slit and trk like 6 precursor							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	113563486	113563486	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113563486delA	uc001vso.2	+											Homo sapiens cDNA clone IMAGE:5185971, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	19408019	19408019	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19408019delA								OR11H12 (29447 upstream) : POTEG (145346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22675596	22675596	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22675596delA	uc001wbw.2	+						uc010aiv.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|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc001wdk.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22981789	22981789	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22981789delA	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_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|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001weh.1_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001wet.2_Intron|uc001weu.2_Intron|uc001wev.2_Intron|uc001wew.2_Intron|uc010tmv.1_Intron|uc001wez.2_Intron|uc010ajx.1_Intron|uc001wfb.1_Intron|uc001wfd.1_Intron|uc001wfe.2_Intron|uc001wfg.2_Intron|uc001wfh.1_Intron|uc001wfi.2_5'Flank|uc001wfj.1_5'Flank|uc001wfk.2_5'Flank|uc001wfl.2_5'Flank|uc010ajy.1_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31626637	31626637	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31626637delA	uc001wrc.1	-						HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33243111	33243111	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33243111delT	uc001wrq.2	+						uc001wrr.2_5'Flank	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)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33294194	33294194	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33294194delA	uc001wrq.2	+							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35163831	35163831	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35163831delA								SNX6 (64465 upstream) : CFL2 (15757 downstream)																																			---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39734733	39734733	+	5'Flank	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39734733delT	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_5'Flank|CTAGE5_uc001wvc.3_5'Flank|CTAGE5_uc001wva.3_5'Flank|CTAGE5_uc001wve.1_5'Flank|CTAGE5_uc001wvh.3_5'Flank|CTAGE5_uc001wvf.3_5'Flank|CTAGE5_uc001wvi.3_5'Flank|CTAGE5_uc010amz.2_5'Flank	NM_005930	NP_005921			CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	39855714	39855714	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39855714delT								CTAGE5 (35319 upstream) : FBXO33 (11164 downstream)																																			---	---	---	---
PYGL	5836	broad.mit.edu	37	14	51381897	51381897	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51381897delT	uc001wyu.2	-						PYGL_uc010tqq.1_Intron|PYGL_uc001wyv.2_Intron	NM_002863	NP_002854			liver glycogen phosphorylase isoform 1						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)													---	---	---	---
NID2	22795	broad.mit.edu	37	14	52473574	52473574	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52473574delT	uc001wzo.2	-						NID2_uc010tqs.1_Intron|NID2_uc010tqt.1_Intron	NM_007361	NP_031387			nidogen 2 precursor							basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)																	---	---	---	---
PSMC6	5706	broad.mit.edu	37	14	53194281	53194281	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53194281delA	uc010tqx.1	+	14	1158	c.1158delA	c.(1156-1158)AGAfs	p.R386fs	STYX_uc010tqy.1_5'Flank|STYX_uc001xaa.2_5'Flank|PSMC6_uc001wzy.2_RNA	NM_002806	NP_002797	P62333	PRS10_HUMAN	proteasome 26S ATPase subunit 6	372					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|proteasome complex	ATP binding|ATPase activity|protein binding, bridging			lung(1)	1	Breast(41;0.176)																	---	---	---	---
FERMT2	10979	broad.mit.edu	37	14	53386064	53386064	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53386064delT	uc001xad.2	-	3	223	c.168delA	c.(166-168)AAAfs	p.K56fs	FERMT2_uc001xac.2_Frame_Shift_Del_p.K56fs|FERMT2_uc001xae.2_Frame_Shift_Del_p.K56fs|FERMT2_uc001xaf.2_Frame_Shift_Del_p.K56fs	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1	56					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)																	---	---	---	---
DDHD1	80821	broad.mit.edu	37	14	53527795	53527795	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53527795delA	uc001xai.2	-						DDHD1_uc001xaj.2_Intron|DDHD1_uc001xah.2_Intron|DDHD1_uc001xag.2_Intron|DDHD1_uc001xak.1_Intron	NM_001160148	NP_001153620			DDHD domain containing 1 isoform c						lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)																	---	---	---	---
ARID4A	5926	broad.mit.edu	37	14	58827849	58827849	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58827849delA	uc001xdp.2	+						ARID4A_uc001xdo.2_Intron|ARID4A_uc001xdq.2_Intron|ARID4A_uc010apg.1_Intron	NM_002892	NP_002883			retinoblastoma-binding protein 1 isoform I						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																		---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58934755	58934755	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58934755delT	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron|KIAA0586_uc010trt.1_Intron|KIAA0586_uc010tru.1_Intron	NM_014749	NP_055564			talpid3 protein											ovary(1)	1																		---	---	---	---
SNAPC1	6617	broad.mit.edu	37	14	62233907	62233908	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62233907_62233908insT	uc001xft.2	+							NM_003082	NP_003073			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)														---	---	---	---
HEATR4	399671	broad.mit.edu	37	14	73986075	73986075	+	Intron	DEL	A	-	-	rs68181245		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73986075delA	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)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75137972	75137972	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75137972delA	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron|KIAA0317_uc001xqc.2_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)														---	---	---	---
C14orf166B	145497	broad.mit.edu	37	14	77333613	77333614	+	Intron	INS	-	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77333613_77333614insG	uc001xsx.2	+						C14orf166B_uc010asn.1_Intron|C14orf166B_uc001xsw.2_Intron	NM_194287	NP_919263			hypothetical protein LOC145497												0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)														---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88952286	88952286	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88952286delA	uc001xwv.3	-						PTPN21_uc010twc.1_Intron	NM_007039	NP_008970			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89153678	89153678	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89153678delA	uc001xxg.2	-						EML5_uc001xxh.1_Intron	NM_183387	NP_899243			echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
TTC8	123016	broad.mit.edu	37	14	89343511	89343511	+	Intron	DEL	A	-	-	rs34301947		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89343511delA	uc010ath.2	+						TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051			tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
GOLGA5	9950	broad.mit.edu	37	14	93282502	93282502	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93282502delT	uc001yaz.1	+							NM_005113	NP_005104			Golgi autoantigen, golgin subfamily a, 5						Golgi organization	cis-Golgi network|integral to membrane	ATP binding|protein homodimerization activity|protein tyrosine kinase activity|Rab GTPase binding			ovary(2)|lung(1)	3		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)				T	RET	papillary thyroid								---	---	---	---
SERPINA3	12	broad.mit.edu	37	14	95088657	95088657	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95088657delT	uc001ydp.2	+						SERPINA3_uc001ydo.3_Intron|SERPINA3_uc001ydr.2_Intron|SERPINA3_uc001ydq.2_Intron|SERPINA3_uc001yds.2_Intron|SERPINA3_uc010avg.2_Intron	NM_001085	NP_001076			serpin peptidase inhibitor, clade A, member 3						acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1)	6		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)														---	---	---	---
CLMN	79789	broad.mit.edu	37	14	95689917	95689917	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95689917delA	uc001yef.2	-							NM_024734	NP_079010			calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)														---	---	---	---
PAPOLA	10914	broad.mit.edu	37	14	97022124	97022124	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97022124delT	uc001yfq.2	+						PAPOLA_uc001yfr.2_Intron|PAPOLA_uc010twv.1_Intron|PAPOLA_uc010avp.2_Intron	NM_032632	NP_116021			poly(A) polymerase alpha						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)														---	---	---	---
SNORD114-9	767585	broad.mit.edu	37	14	101432277	101432277	+	5'Flank	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101432277delT	uc001yiz.2	+						SNORD114-10_uc001yja.2_5'Flank|SNORD114-11_uc001yjb.2_5'Flank	NR_003201				Homo sapiens small nucleolar RNA, C/D box 114-9 (SNORD114-9), non-coding RNA.												0																		---	---	---	---
MIR376A2	664615	broad.mit.edu	37	14	101506159	101506159	+	5'Flank	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101506159delC	hsa-mir-376a-2|MI0003529	+						MIR654_hsa-mir-654|MI0003676_5'Flank|MIR376B_hsa-mir-376b|MI0002466_5'Flank|uc010awc.1_5'Flank|MIR376A1_hsa-mir-376a-1|MI0000784_5'Flank|MIR300_hsa-mir-300|MI0005525_5'Flank																	0																		---	---	---	---
C14orf2	9556	broad.mit.edu	37	14	104381692	104381692	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104381692delT	uc001yoi.3	-						C14orf2_uc001yoj.3_Intron|C14orf2_uc010aww.1_Intron|C14orf2_uc001yok.2_Intron	NM_004894	NP_004885			6.8 kDa mitochondrial proteolipid isoform 1							mitochondrion					0				Epithelial(152;0.223)														---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23316189	23316189	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23316189delA	uc001yvr.2	-						HERC2P2_uc010ayf.1_Intron|HERC2P2_uc001yvp.3_Intron					RecName: Full=Putative HERC2-like protein 3;												0																		---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25222784	25222784	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25222784delA	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron|SNRPN_uc001ywv.1_Intron|SNRPN_uc001yww.1_Intron|SNRPN_uc001ywx.1_Intron|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_Intron	NM_022807	NP_073718			small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30010055	30010055	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30010055delT	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)														---	---	---	---
LPCAT4	254531	broad.mit.edu	37	15	34656625	34656627	+	Intron	DEL	TTC	-	-	rs60508631	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34656625_34656627delTTC	uc001zig.2	-						LPCAT4_uc010bav.1_Intron	NM_153613	NP_705841			lysophosphatidylcholine acyltransferase 4						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|calcium ion binding				0																		---	---	---	---
THBS1	7057	broad.mit.edu	37	15	39882587	39882587	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39882587delA	uc001zkh.2	+						THBS1_uc010bbi.2_Intron	NM_003246	NP_003237			thrombospondin 1 precursor						activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			ovary(3)|central_nervous_system(3)	6		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Becaplermin(DB00102)													---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40292933	40292933	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40292933delT	uc001zkm.1	+						EIF2AK4_uc010bbj.1_Intron|EIF2AK4_uc001zkn.1_Intron|EIF2AK4_uc001zko.1_5'Flank	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)														---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40895288	40895288	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40895288delT	uc010bbs.1	+						CASC5_uc010ucq.1_Intron|CASC5_uc001zme.2_Intron|CASC5_uc010bbt.1_Intron	NM_170589	NP_733468			cancer susceptibility candidate 5 isoform 1						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)														---	---	---	---
EXD1	161829	broad.mit.edu	37	15	41508186	41508186	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41508186delT	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																		---	---	---	---
GANC	2595	broad.mit.edu	37	15	42579747	42579747	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42579747delT	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)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44789416	44789416	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44789416delT	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
SHC4	399694	broad.mit.edu	37	15	49217160	49217160	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49217160delA	uc001zxb.1	-							NM_203349	NP_976224			rai-like protein						intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)														---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51276506	51276506	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51276506delT	uc001zyx.1	+							NM_007347	NP_031373			adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
TMOD3	29766	broad.mit.edu	37	15	52201131	52201131	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52201131delT	uc002abm.2	+	10					TMOD3_uc010bfc.1_Intron|TMOD3_uc002abn.2_5'Flank	NM_014547	NP_055362			tropomodulin 3 (ubiquitous)							cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	56570157	56570157	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56570157delT								RFX7 (34674 upstream) : TEX9 (87487 downstream)																																			---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57570745	57570746	+	Intron	INS	-	T	T	rs66508689		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57570745_57570746insT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron|TCF12_uc010ugp.1_Intron|TCF12_uc010ugq.1_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59376343	59376343	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59376343delC	uc002afv.2	+	9	2592	c.2313delC	c.(2311-2313)CGCfs	p.R771fs	RNF111_uc002afs.2_Frame_Shift_Del_p.R771fs|RNF111_uc002aft.2_Frame_Shift_Del_p.R780fs|RNF111_uc002afu.2_Frame_Shift_Del_p.R770fs|RNF111_uc002afw.2_Frame_Shift_Del_p.R780fs|RNF111_uc002afx.2_Frame_Shift_Del_p.R297fs|RNF111_uc002afy.2_5'Flank	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	771	Pro-rich.				multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
CCNB2	9133	broad.mit.edu	37	15	59415893	59415893	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59415893delG	uc002afz.2	+						CCNB2_uc010bge.2_Intron	NM_004701	NP_004692			cyclin B2						cell cycle checkpoint|cell division|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	centrosome|cytosol|nucleus	protein kinase binding				0																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62254181	62254181	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62254181delT	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																		---	---	---	---
DENND4A	10260	broad.mit.edu	37	15	65989151	65989151	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65989151delT	uc002aph.2	-						DENND4A_uc002api.2_Intron|DENND4A_uc002apj.3_Intron	NM_005848	NP_005839			DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68649477	68649478	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68649477_68649478insT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	71355369	71355369	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71355369delT								LRRC49 (12935 upstream) : CT62 (47214 downstream)																																			---	---	---	---
HEXA	3073	broad.mit.edu	37	15	72637614	72637615	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72637614_72637615delTT	uc002aun.3	-						uc002aug.2_Intron|CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Intron|HEXA_uc002auo.3_Intron|HEXA_uc010bix.2_3'UTR	NM_000520	NP_000511			hexosaminidase A preproprotein						cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
TMED3	23423	broad.mit.edu	37	15	79606081	79606081	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79606081delT	uc002beu.2	+						TMED3_uc010unj.1_Intron|TMED3_uc002bev.2_Intron	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																		---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86923509	86923509	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86923509delT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88474352	88474353	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88474352_88474353delTT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.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)			---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93489248	93489249	+	Intron	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93489248_93489249insT	uc002bsp.2	+						CHD2_uc002bsn.2_Intron|CHD2_uc002bso.1_Intron|CHD2_uc010urb.1_Intron|CHD2_uc010bof.1_Intron	NM_001271	NP_001262			chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)															---	---	---	---
ALG1	56052	broad.mit.edu	37	16	5121732	5121732	+	5'Flank	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5121732delG	uc002cym.2	+						ALG1_uc002cyj.2_Intron|ALG1_uc002cyn.2_5'Flank|ALG1_uc010bue.2_5'Flank|ALG1_uc010uxy.1_5'Flank	NM_019109	NP_061982			beta-1,4-mannosyltransferase						dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(90;0.0164)																---	---	---	---
USP7	7874	broad.mit.edu	37	16	8988505	8988505	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8988505delA	uc002czl.2	-						USP7_uc002czj.2_Intron|USP7_uc010uyj.1_Intron|USP7_uc002czk.2_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																		---	---	---	---
USP7	7874	broad.mit.edu	37	16	8994680	8994680	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8994680delA	uc002czl.2	-						USP7_uc010uyk.1_Intron|USP7_uc002czj.2_Intron|USP7_uc010uyj.1_Intron|USP7_uc002czk.2_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																		---	---	---	---
USP7	7874	broad.mit.edu	37	16	9014408	9014408	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9014408delT	uc002czl.2	-						USP7_uc010uyk.1_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																		---	---	---	---
RRN3	54700	broad.mit.edu	37	16	15164886	15164886	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15164886delA	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Intron|RRN3_uc010uzq.1_Intron	NM_018427	NP_060897			RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21033225	21033225	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21033225delA	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21469994	21469994	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21469994delA	uc002diq.3	+						LOC100271836_uc002diu.1_Intron|LOC100271836_uc002diz.1_5'Flank					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21712046	21712046	+	Intron	DEL	A	-	-	rs72401968		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21712046delA	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron	NM_144672	NP_653273			otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)														---	---	---	---
EARS2	124454	broad.mit.edu	37	16	23544150	23544150	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23544150delT	uc002dlt.3	-						EARS2_uc002dlr.3_Intron|EARS2_uc002dls.3_Intron|EARS2_uc002dlu.2_Intron	NM_001083614	NP_001077083			glutamyl-tRNA synthetase 2 precursor						glutamyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|glutamate-tRNA ligase activity|RNA binding				0				GBM - Glioblastoma multiforme(48;0.0353)	L-Glutamic Acid(DB00142)													---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24874160	24874160	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24874160delA	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	25300771	25300774	+	IGR	DEL	TTCT	-	-	rs8044599		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25300771_25300774delTTCT								ZKSCAN2 (31916 upstream) : HS3ST4 (402573 downstream)																																			---	---	---	---
FAM57B	83723	broad.mit.edu	37	16	30041821	30041821	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30041821delC	uc002dvt.2	-	1	366	c.28delG	c.(28-30)GTGfs	p.V10fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|FAM57B_uc002dvu.2_5'Flank	NM_031478	NP_113666	Q71RH2	FA57B_HUMAN	hypothetical protein LOC83723	10						endoplasmic reticulum|integral to membrane					0																		---	---	---	---
PPP4C	5531	broad.mit.edu	37	16	30087657	30087657	+	5'UTR	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30087657delG	uc002dwe.2	+	2					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|PPP4C_uc002dwf.2_5'UTR|PPP4C_uc002dwg.2_RNA|PPP4C_uc002dwh.2_5'UTR	NM_002720	NP_002711			protein phosphatase 4, catalytic subunit						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																		---	---	---	---
LOC595101	595101	broad.mit.edu	37	16	30291742	30291742	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30291742delA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0																		---	---	---	---
N4BP1	9683	broad.mit.edu	37	16	48579939	48579939	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48579939delA	uc002efp.2	-							NM_153029	NP_694574			Nedd4 binding protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)																---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58622855	58622855	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58622855delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
CBFB	865	broad.mit.edu	37	16	67070809	67070809	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67070809delT	uc002era.2	+						CBFB_uc002erb.2_Intron|CBFB_uc010vja.1_Intron	NM_001755	NP_001746			core-binding factor, beta subunit isoform 2						transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)				T	MYH11	AML								---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67325658	67325658	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67325658delG	uc002esu.2	-	13	2352	c.2301delC	c.(2299-2301)CCCfs	p.P767fs	KCTD19_uc002est.2_Frame_Shift_Del_p.P539fs|KCTD19_uc010vjj.1_Frame_Shift_Del_p.P510fs	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain	767						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)														---	---	---	---
IL34	146433	broad.mit.edu	37	16	70690422	70690422	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70690422delA	uc002ezh.1	+						IL34_uc002ezi.1_Intron	NM_152456	NP_689669			interleukin 34 precursor						positive regulation of cell proliferation|positive regulation of protein phosphorylation	extracellular space	cytokine activity|growth factor activity|macrophage colony-stimulating factor receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71803440	71803440	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71803440delA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc010vmg.1_Intron|AP1G1_uc010vmh.1_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71808633	71808633	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71808633delT	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc010vmg.1_Intron|AP1G1_uc010vmh.1_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
PMFBP1	83449	broad.mit.edu	37	16	72163921	72163921	+	Intron	DEL	T	-	-	rs67023960		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72163921delT	uc002fcc.3	-						PMFBP1_uc002fcd.2_Intron|PMFBP1_uc002fce.2_Intron|PMFBP1_uc002fcf.2_Intron|PMFBP1_uc010cgo.1_5'Flank	NM_031293	NP_112583			polyamine modulated factor 1 binding protein 1											ovary(2)	2		Ovarian(137;0.179)																---	---	---	---
SCARF1	8578	broad.mit.edu	37	17	1539905	1539906	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1539905_1539906insA	uc002fsz.1	-						SCARF1_uc002fsy.1_Intron|SCARF1_uc002fta.1_Intron|SCARF1_uc010cjv.1_Intron	NM_003693	NP_003684			scavenger receptor class F, member 1 isoform 1						cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1565461	1565461	+	Intron	DEL	A	-	-	rs3814969	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1565461delA	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)														---	---	---	---
POLR2A	5430	broad.mit.edu	37	17	7399697	7399697	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7399697delG	uc002ghf.3	+						POLR2A_uc002ghe.2_Intron	NM_000937	NP_000928			DNA-directed RNA polymerase II A						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)																---	---	---	---
TP53	7157	broad.mit.edu	37	17	7577036	7577036	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577036delG	uc002gim.2	-	8	1096	c.902delC	c.(901-903)CCAfs	p.P301fs	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.P301fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.P169fs|TP53_uc010cng.1_Frame_Shift_Del_p.P169fs|TP53_uc002gii.1_Frame_Shift_Del_p.P169fs|TP53_uc010cnh.1_Frame_Shift_Del_p.P301fs|TP53_uc010cni.1_Frame_Shift_Del_p.P301fs|TP53_uc002gij.2_Frame_Shift_Del_p.P301fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	301	Interaction with HIPK1 (By similarity).|Interaction with CARM1.		P -> T (in a sporadic cancer; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.P301fs*44(9)|p.0?(7)|p.G302fs*4(4)|p.?(3)|p.P301fs*5(3)|p.P301S(3)|p.P301_S303delPGS(1)|p.L299fs*2(1)|p.P301P(1)|p.L265_K305del41(1)|p.P301Q(1)|p.P301fs*45(1)|p.P301T(1)|p.G293fs*1(1)|p.P301L(1)|p.P301A(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7976012	7976013	+	3'UTR	INS	-	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7976012_7976013insT	uc002gjy.1	-	15						NM_001139	NP_001130			arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0															Multiple Myeloma(8;0.094)			---	---	---	---
SLC25A35	399512	broad.mit.edu	37	17	8199740	8199740	+	5'Flank	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8199740delT	uc002gla.3	-						SLC25A35_uc002gku.1_5'Flank|SLC25A35_uc002gkt.2_5'Flank|SLC25A35_uc002gkz.1_5'Flank	NM_201520	NP_958928			solute carrier family 25, member 35						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	18988562	18988562	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18988562delT								GRAP (38226 upstream) : GRAPL (42220 downstream)																																			---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19748828	19748828	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19748828delA	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)																	---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26090966	26090966	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26090966delC	uc002gzu.2	-							NM_000625	NP_000616			nitric oxide synthase 2A						arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)													---	---	---	---
NLK	51701	broad.mit.edu	37	17	26459626	26459626	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26459626delT	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)														---	---	---	---
SEZ6	124925	broad.mit.edu	37	17	27309130	27309130	+	Intron	DEL	G	-	-	rs78209823		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27309130delG	uc002hdp.2	-						SEZ6_uc002hdm.2_5'Flank|SEZ6_uc010cry.1_Intron|SEZ6_uc002hdq.1_Intron|SEZ6_uc010crz.1_Intron	NM_178860	NP_849191			seizure related 6 homolog isoform 1							integral to membrane|plasma membrane				large_intestine(1)|central_nervous_system(1)	2	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)															---	---	---	---
C17orf42	79736	broad.mit.edu	37	17	29231700	29231701	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29231700_29231701delTT	uc002hfu.2	-						C17orf42_uc002hfv.2_Intron|C17orf42_uc002hfw.2_Intron|C17orf42_uc010wbs.1_Intron	NM_024683	NP_078959			hypothetical protein LOC79736						oxidative phosphorylation|regulation of transcription, DNA-dependent|transcription from mitochondrial promoter	mitochondrial nucleoid|ribonucleoprotein complex	DNA polymerase processivity factor activity|nucleic acid binding|protein binding			ovary(1)	1		all_cancers(10;4.64e-07)|all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)																---	---	---	---
ZNF207	7756	broad.mit.edu	37	17	30690056	30690056	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30690056delT	uc002hhh.3	+						ZNF207_uc002hhj.3_Intron|ZNF207_uc002hhi.3_Intron|ZNF207_uc010csz.2_Intron|ZNF207_uc002hhk.1_Intron|ZNF207_uc002hhl.1_Intron	NM_003457	NP_003448			zinc finger protein 207 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
TAF15	8148	broad.mit.edu	37	17	34171886	34171886	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34171886delG	uc002hkd.2	+	15	1669	c.1583delG	c.(1582-1584)CGGfs	p.R528fs	TAF15_uc002hkc.2_Frame_Shift_Del_p.R525fs	NM_139215	NP_631961	Q92804	RBP56_HUMAN	TBP-associated factor 15 isoform 1	528	Arg/Gly-rich.|16.|21 X approximate tandem repeats of D-R- [S,G](0,3)-G-G-Y-G-G.				positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		TAF15/NR4A3(33)	bone(33)|lung(1)|skin(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)				T	TEC|CHN1|ZNF384	extraskeletal myxoid chondrosarcomas|ALL								---	---	---	---
PLEKHH3	79990	broad.mit.edu	37	17	40826040	40826042	+	Intron	DEL	GAG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40826040_40826042delGAG	uc002iau.2	-						PLEKHH3_uc010cyl.1_5'Flank|PLEKHH3_uc002iat.1_Intron|PLEKHH3_uc002iav.2_Intron|PLEKHH3_uc010cym.1_Intron|PLEKHH3_uc002iaw.2_Intron	NM_024927	NP_079203			pleckstrin homology domain containing, family H						signal transduction	cytoskeleton				large_intestine(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)														---	---	---	---
G6PC3	92579	broad.mit.edu	37	17	42151308	42151308	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42151308delA	uc002iex.2	+						G6PC3_uc002iey.2_Intron|G6PC3_uc010czo.2_Intron|G6PC3_uc002iez.2_Intron|G6PC3_uc002ifb.2_5'Flank|G6PC3_uc002ifc.2_5'Flank	NM_138387	NP_612396			glucose-6-phosphatase catalytic subunit 3						gluconeogenesis|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	glucose-6-phosphatase activity			skin(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)														---	---	---	---
RUNDC3A	10900	broad.mit.edu	37	17	42392043	42392046	+	Intron	DEL	GGGG	-	-	rs67278675		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42392043_42392046delGGGG	uc002igl.3	+						RUNDC3A_uc002igi.2_Intron|RUNDC3A_uc002igj.2_Intron|RUNDC3A_uc002igk.2_Intron	NM_001144825	NP_001138297			RUN domain containing 3A isoform 1						small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42552275	42552275	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42552275delA	uc002igw.1	-						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)														---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756539	42756539	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42756539delA	uc002ihc.2	-						CCDC43_uc010czw.1_Intron	NM_144609	NP_653210			coiled-coil domain containing 43 isoform 1												0		Prostate(33;0.0322)																---	---	---	---
CDC27	996	broad.mit.edu	37	17	45249513	45249513	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45249513delA	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247			cell division cycle protein 27 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|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	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5																		---	---	---	---
SLC35B1	10237	broad.mit.edu	37	17	47783739	47783740	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47783739_47783740delAA	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron|SLC35B1_uc010wly.1_Intron	NM_005827	NP_005818			solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0																		---	---	---	---
MYCBPAP	84073	broad.mit.edu	37	17	48599306	48599307	+	Intron	INS	-	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48599306_48599307insA	uc010wmr.1	+						MYCBPAP_uc002iqx.2_Intron|MYCBPAP_uc002iqz.2_Intron	NM_032133	NP_115509			Myc-binding protein-associated protein						cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)															---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54305177	54305177	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54305177delC	uc002iun.1	+						uc002iuo.2_5'Flank	NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57126492	57126492	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57126492delT	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				---	---	---	---
ACE	1636	broad.mit.edu	37	17	61571517	61571518	+	Intron	DEL	GT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61571517_61571518delGT	uc002jau.1	+						ACE_uc002jav.1_Intron|ACE_uc010ddv.1_Intron|ACE_uc010wpj.1_Intron|ACE_uc002jaw.1_Intron|ACE_uc010wpk.1_Intron	NM_000789	NP_000780			angiotensin I converting enzyme 1 isoform 1						arachidonic acid secretion|hormone catabolic process|kidney development|peptide catabolic process|regulation of smooth muscle cell migration	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)													---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61864351	61864351	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61864351delT	uc002jbu.2	+						DDX42_uc002jbv.2_Intron	NM_007372	NP_031398			DEAD box polypeptide 42 protein						protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64125854	64125854	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64125854delT	uc002jfl.2	-						CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
GGA3	23163	broad.mit.edu	37	17	73243032	73243032	+	Intron	DEL	A	-	-	rs75940499		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73243032delA	uc002jni.1	-						GGA3_uc002jnj.1_Intron|GGA3_uc010wrw.1_Intron|GGA3_uc002jnk.1_Intron|GGA3_uc010wrx.1_Intron|GGA3_uc010wry.1_Intron|GGA3_uc010wrz.1_Intron	NM_138619	NP_619525			ADP-ribosylation factor binding protein 3						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|breast(1)	2			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)															---	---	---	---
GAA	2548	broad.mit.edu	37	17	78084942	78084942	+	Intron	DEL	G	-	-	rs4889817	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78084942delG	uc002jxo.2	+						GAA_uc002jxp.2_Intron|GAA_uc002jxq.2_Intron	NM_001079803	NP_001073271			acid alpha-glucosidase preproprotein						cardiac muscle contraction|diaphragm contraction|glycogen catabolic process|lysosome organization|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)													---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78349503	78349503	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78349503delA	uc002jyh.1	+						uc002jyi.1_Intron|RNF213_uc010dhw.1_Intron	NM_020914	NP_065965			ring finger protein 213											ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
C17orf70	80233	broad.mit.edu	37	17	79516068	79516081	+	Intron	DEL	AAAAAAAAAAAAAA	-	-	rs77732926		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79516068_79516081delAAAAAAAAAAAAAA	uc002kaq.2	-						C17orf70_uc002kao.1_5'Flank|C17orf70_uc010wuq.1_Intron|C17orf70_uc002kap.2_Intron	NM_001109760	NP_001103230			Fanconi anemia core complex 100 kDa subunit						DNA repair	cytoplasm|intermediate filament cytoskeleton|nucleoplasm	DNA binding			ovary(1)|skin(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)															---	---	---	---
P4HB	5034	broad.mit.edu	37	17	79803764	79803764	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79803764delT	uc002kbn.1	-	8	1357	c.1160delA	c.(1159-1161)AACfs	p.N387fs	P4HB_uc002kbl.1_Frame_Shift_Del_p.N64fs|P4HB_uc002kbm.1_Frame_Shift_Del_p.N64fs	NM_000918	NP_000909	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta subunit precursor	387	Thioredoxin 2.				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)															---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3134954	3134954	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3134954delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10675298	10675298	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10675298delA	uc002kor.3	-						FAM38B_uc002koq.2_Intron	NM_022068	NP_071351			family with sequence similarity 38, member B							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
OSBPL1A	114876	broad.mit.edu	37	18	21898414	21898414	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21898414delA	uc002kve.2	-						OSBPL1A_uc002kvf.3_Intron	NM_080597	NP_542164			oxysterol-binding protein-like 1A isoform B						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	22774992	22774992	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22774992delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	18	26836674	26836674	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26836674delA								None (None upstream) : None (None downstream)																																			---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29796832	29796832	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29796832delA	uc002kxj.3	+							NM_005925	NP_005916			meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
GALNT1	2589	broad.mit.edu	37	18	33289488	33289488	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33289488delA	uc010dmu.2	+						GALNT1_uc002kyz.3_Intron|GALNT1_uc002kzb.2_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																		---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34465687	34465687	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34465687delT	uc002kzz.2	+							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	46005697	46005697	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46005697delT								ZBTB7C (70034 upstream) : KIAA0427 (59730 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	50589416	50589416	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50589416delT	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)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50848596	50848596	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50848596delA	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)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54385475	54385475	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54385475delA	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)														---	---	---	---
MALT1	10892	broad.mit.edu	37	18	56383323	56383323	+	Intron	DEL	T	-	-	rs9959997	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56383323delT	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776			mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4								T	BIRC3	MALT								---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59954566	59954566	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59954566delT	uc002lil.2	+						KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
SERPINB10	5273	broad.mit.edu	37	18	61584739	61584739	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61584739delA	uc010xev.1	+	3	308	c.218delA	c.(217-219)GAAfs	p.E73fs	SERPINB2_uc002ljp.1_Frame_Shift_Del_p.E214fs|SERPINB2_uc002ljq.1_Frame_Shift_Del_p.E187fs|SERPINB10_uc010xew.1_Frame_Shift_Del_p.E73fs	NM_005024	NP_005015	P48595	SPB10_HUMAN	serine (or cysteine) proteinase inhibitor, clade	73						cytoplasm|nucleus	serine-type endopeptidase inhibitor activity			lung(1)|kidney(1)|skin(1)	3		Esophageal squamous(42;0.131)																---	---	---	---
TMX3	54495	broad.mit.edu	37	18	66381141	66381141	+	Intron	DEL	A	-	-	rs139944394		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66381141delA	uc002lkf.2	-						CCDC102B_uc002lkk.2_5'Flank|TMX3_uc010xez.1_Intron|TMX3_uc010xfa.1_Intron|TMX3_uc002lkg.3_Intron|CCDC102B_uc002lkh.2_5'Flank	NM_019022	NP_061895			thioredoxin domain containing 10 precursor						cell redox homeostasis|glycerol ether metabolic process	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			skin(1)	1																		---	---	---	---
ARID3A	1820	broad.mit.edu	37	19	971614	971614	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:971614delA	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)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3013522	3013522	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3013522delA	uc002lww.2	-						TLE2_uc010xhb.1_Intron|TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_Intron	NM_003260	NP_003251			transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MATK	4145	broad.mit.edu	37	19	3779654	3779654	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3779654delC	uc002lyt.2	-						MATK_uc002lyv.2_Intron|MATK_uc002lyu.2_Intron|MATK_uc010dtq.2_Intron	NM_139355	NP_647612			megakaryocyte-associated tyrosine kinase isoform						cell proliferation|mesoderm development|positive regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(2)|ovary(1)|lung(1)|large_intestine(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
FSD1	79187	broad.mit.edu	37	19	4323505	4323505	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4323505delC	uc002lzy.2	+						FSD1_uc002lzz.2_Intron|FSD1_uc002maa.2_Intron	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)														---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4682879	4682882	+	Intron	DEL	AGAG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4682879_4682882delAGAG	uc002mba.2	-							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)														---	---	---	---
SAFB2	9667	broad.mit.edu	37	19	5587282	5587282	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5587282delG	uc002mcd.2	-	21	3046	c.2834delC	c.(2833-2835)CCGfs	p.P945fs		NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	945	Interacts with SAFB1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)														---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5667205	5667205	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5667205delC	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)														---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5754000	5754001	+	Intron	DEL	AC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5754000_5754001delAC	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997			transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
DENND1C	79958	broad.mit.edu	37	19	6469043	6469043	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6469043delT	uc002mfe.2	-						DENND1C_uc002mfb.2_Intron|DENND1C_uc002mfc.2_Intron|DENND1C_uc002mfd.2_Intron|DENND1C_uc010xje.1_Intron	NM_024898	NP_079174			DENN/MADD domain containing 1C							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1																		---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7512065	7512065	+	Intron	DEL	T	-	-	rs59050162	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)																---	---	---	---
PEX11G	92960	broad.mit.edu	37	19	7551023	7551023	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7551023delT	uc002mgk.1	-						PEX11G_uc002mgl.1_Intron	NM_080662	NP_542393			peroxisomal biogenesis factor 11 gamma							integral to membrane|peroxisomal membrane					0																		---	---	---	---
XAB2	56949	broad.mit.edu	37	19	7685993	7685993	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7685993delC	uc002mgx.2	-							NM_020196	NP_064581			XPA binding protein 2						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					---	---	---	---
C19orf66	55337	broad.mit.edu	37	19	10197480	10197480	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10197480delG	uc002mmu.3	+						C19orf66_uc002mmt.2_Intron|C19orf66_uc002mmv.3_Intron|C19orf66_uc002mmw.3_5'Flank	NM_018381	NP_060851			hypothetical protein LOC55337												0																		---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10477410	10477413	+	Intron	DEL	AAAA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10477410_10477413delAAAA	uc002moc.3	-						TYK2_uc010dxe.2_Intron|TYK2_uc002mod.2_Intron	NM_003331	NP_003322			tyrosine kinase 2						intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)															---	---	---	---
RAB3D	9545	broad.mit.edu	37	19	11447649	11447651	+	Intron	DEL	AGA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11447649_11447651delAGA	uc002mqy.2	-							NM_004283	NP_004274			RAB3D, member RAS oncogene family						exocytosis|protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
EPOR	2057	broad.mit.edu	37	19	11488894	11488894	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11488894delG	uc002mrj.1	-	8	1429	c.1293delC	c.(1291-1293)CCCfs	p.P431fs	EPOR_uc002mrh.2_Frame_Shift_Del_p.P90fs|EPOR_uc002mri.2_Frame_Shift_Del_p.P258fs|EPOR_uc002mrk.1_Frame_Shift_Del_p.P258fs|EPOR_uc002mrl.1_RNA|EPOR_uc010xlx.1_RNA|EPOR_uc010xly.1_Frame_Shift_Del_p.P258fs	NM_000121	NP_000112	P19235	EPOR_HUMAN	erythropoietin receptor precursor	431	Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	erythropoietin receptor activity|identical protein binding			ovary(1)	1					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)											OREG0025254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SYCE2	256126	broad.mit.edu	37	19	13015656	13015656	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13015656delA	uc002mvr.2	-							NM_001105578	NP_001099048			synaptonemal complex central element protein 2						cell division	central element					0																		---	---	---	---
CYP4F11	57834	broad.mit.edu	37	19	16032767	16032767	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16032767delA	uc002nbu.2	-						CYP4F11_uc010eab.1_Intron|CYP4F11_uc002nbt.2_Intron	NM_001128932	NP_001122404			cytochrome P450 family 4 subfamily F polypeptide						inflammatory response|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)	1																		---	---	---	---
CALR3	125972	broad.mit.edu	37	19	16596143	16596143	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16596143delT	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																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17369974	17369974	+	Intron	DEL	A	-	-	rs80351288		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17369974delA	uc002nfs.1	-						USHBP1_uc002nfr.1_5'Flank|USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_Intron	NM_031941	NP_114147			Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1																		---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21239294	21239295	+	Intron	DEL	AA	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21239294_21239295delAA	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	22396263	22396263	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22396263delA								ZNF676 (16510 upstream) : ZNF98 (177636 downstream)																																			---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31041551	31041551	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31041551delG	uc002nsu.1	+						ZNF536_uc010edd.1_Intron	NM_014717	NP_055532			zinc finger protein 536						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33586469	33586469	+	Intron	DEL	T	-	-	rs79024536		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33586469delT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
HPN	3249	broad.mit.edu	37	19	35556034	35556034	+	Intron	DEL	T	-	-	rs113406953		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35556034delT	uc002nxq.1	+						HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_Intron|HPN_uc002nxt.1_Intron|LOC100128675_uc010xsi.1_Intron	NM_002151	NP_002142			hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)													---	---	---	---
LGI4	163175	broad.mit.edu	37	19	35631923	35631923	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35631923delC	uc002nxy.1	-						FXYD1_uc002nyb.1_Intron|FXYD1_uc002nyc.2_Intron|FXYD1_uc002nyd.2_Intron|FXYD7_uc010xsp.1_5'Flank|FXYD7_uc002nye.1_5'Flank|FXYD7_uc002nyf.1_5'Flank	NM_139284	NP_644813			leucine-rich repeat LGI family, member 4							extracellular region				pancreas(1)	1	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
ZNF461	92283	broad.mit.edu	37	19	37155555	37155555	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37155555delA	uc002oem.2	-						ZNF461_uc002oen.2_Intron|ZNF461_uc010xtj.1_Intron	NM_153257	NP_694989			gonadotropin inducible transcription repressor						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)															---	---	---	---
HKR1	284459	broad.mit.edu	37	19	37835534	37835534	+	5'UTR	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37835534delC	uc002ogb.2	+	3					HKR1_uc002ofx.2_Intron|HKR1_uc002ofy.2_Intron|HKR1_uc002ofz.2_Intron|HKR1_uc002oga.2_Intron|HKR1_uc010xto.1_Intron|HKR1_uc002ogc.2_Intron|HKR1_uc010xtp.1_Intron|HKR1_uc002ogd.2_5'Flank	NM_181786	NP_861451			GLI-Kruppel family member HKR1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
PAK4	10298	broad.mit.edu	37	19	39614497	39614500	+	5'Flank	DEL	GAAG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39614497_39614500delGAAG	uc002okj.1	+						PAK4_uc002okl.1_5'Flank|PAK4_uc002okn.1_5'Flank|PAK4_uc002okm.1_5'Flank|PAK4_uc002oko.1_5'Flank|PAK4_uc002okp.1_5'Flank	NM_001014831	NP_001014831			p21-activated kinase 4 isoform 1						cellular component movement|signal transduction	Golgi apparatus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)															---	---	---	---
CEACAM1	634	broad.mit.edu	37	19	43016797	43016797	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43016797delT	uc002otv.2	-						uc010eif.1_Intron|uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron|CEACAM1_uc010eii.2_Intron|CEACAM1_uc002otw.2_Intron|CEACAM1_uc010eij.2_Intron|CEACAM1_uc002otx.2_Intron|CEACAM1_uc002oty.2_Intron|CEACAM1_uc002otz.2_Intron|CEACAM1_uc010eik.2_Intron	NM_001712	NP_001703			carcinoembryonic antigen-related cell adhesion						angiogenesis|cell migration|homophilic cell adhesion|integrin-mediated signaling pathway	extracellular region|integral to plasma membrane|membrane fraction				ovary(1)|central_nervous_system(1)	2		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)													---	---	---	---
PHLDB3	653583	broad.mit.edu	37	19	44005952	44005954	+	In_Frame_Del	DEL	CTC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44005952_44005954delCTC	uc002own.3	-	4	725_727	c.466_468delGAG	c.(466-468)GAGdel	p.E156del	PHLDB3_uc002owo.2_In_Frame_Del_p.E156del	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,	156	Potential.										0		Prostate(69;0.0153)																---	---	---	---
KLC3	147700	broad.mit.edu	37	19	45852955	45852955	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45852955delG	uc002pbf.1	+						KLC3_uc010ejy.1_Intron|KLC3_uc002pbg.1_Intron	NM_177417	NP_803136			kinesin light chain 3							cytoplasm|kinesin complex|microtubule	microtubule motor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)														---	---	---	---
GRIN2D	2906	broad.mit.edu	37	19	48922310	48922310	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48922310delT	uc002pjc.3	+						GRIN2D_uc010elx.2_5'Flank	NM_000836	NP_000827			N-methyl-D-aspartate receptor subunit 2D							cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)													---	---	---	---
KLK1	3816	broad.mit.edu	37	19	51327164	51327165	+	5'Flank	DEL	CC	-	-	rs35641597		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51327164_51327165delCC	uc002ptk.1	-						KLK1_uc010ycg.1_5'Flank	NM_002257	NP_002248			kallikrein 1 preproprotein						proteolysis	nucleus	serine-type endopeptidase activity				0		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57287026	57287026	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57287026delA	uc002qnr.2	-						uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron	NM_015363	NP_056178			zinc finger, imprinted 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)														---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3278632	3278632	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3278632delA	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3577009	3577009	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3577009delT	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
CDS2	8760	broad.mit.edu	37	20	5165756	5165756	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5165756delA	uc002wls.2	+						CDS2_uc002wlr.1_Intron|CDS2_uc010zqt.1_Intron|CDS2_uc002wlu.2_Intron|CDS2_uc010zqu.1_Intron|CDS2_uc002wlv.2_Intron|CDS2_uc010zqv.1_Intron	NM_003818	NP_003809			phosphatidate cytidylyltransferase 2						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphatidate cytidylyltransferase activity				0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5545874	5545874	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5545874delT	uc002wme.3	-						GPCPD1_uc002wmd.3_Intron	NM_019593	NP_062539			hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5579306	5579306	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5579306delA	uc002wme.3	-							NM_019593	NP_062539			hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30365539	30365539	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30365539delA	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244			TPX2, microtubule-associated protein homolog						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)															---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	31022442	31022442	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31022442delG	uc002wxs.2	+	12	2353	c.1927delG	c.(1927-1929)GGGfs	p.G643fs	ASXL1_uc010geb.2_Frame_Shift_Del_p.G534fs	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	643	Gly-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding	p.A640fs*14(2)|p.T639_G659>PPWD(1)|p.A640_S664>PCSGG(1)|p.T639fs*14(1)|p.T639fs*19(1)|p.T639_P647>PPSDGS(1)		haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248								F|N|Mis		MDS|CMML								---	---	---	---
CHMP4B	128866	broad.mit.edu	37	20	32399502	32399502	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32711134	32711134	+	IGR	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32711134delA								EIF2S2 (11049 upstream) : ASIP (137037 downstream)																																			---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33935201	33935201	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33935201delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						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)															---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34389333	34389333	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34389333delT	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron|PHF20_uc002xeh.2_Intron	NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34766817	34766817	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34766817delA	uc002xfb.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xev.2_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)																	---	---	---	---
KIAA0406	9675	broad.mit.edu	37	20	36625458	36625458	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36625458delA	uc002xhl.2	-						KIAA0406_uc002xhm.2_Intron	NM_014657	NP_055472			hypothetical protein LOC9675								binding				0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42233059	42233059	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42233059delA	uc002xkw.2	+						IFT52_uc010zwi.1_Intron|IFT52_uc002xky.2_Intron|IFT52_uc002xkx.2_Intron|IFT52_uc010ggn.2_Intron|IFT52_uc002xkz.2_Intron	NM_016004	NP_057088			intraflagellar transport 52 homolog							intraflagellar transport particle B|microtubule-based flagellum	protein C-terminus binding			ovary(2)	2		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42233603	42233603	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42233603delT	uc002xkw.2	+						IFT52_uc010zwi.1_Intron|IFT52_uc002xky.2_Intron|IFT52_uc002xkx.2_Intron|IFT52_uc010ggn.2_Intron|IFT52_uc002xkz.2_Intron	NM_016004	NP_057088			intraflagellar transport 52 homolog							intraflagellar transport particle B|microtubule-based flagellum	protein C-terminus binding			ovary(2)	2		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45890816	45890816	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45890816delA	uc002xta.1	-						ZMYND8_uc010ghq.1_Intron|ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xtg.2_Intron|ZMYND8_uc010ghs.1_Intron	NM_012408	NP_036540			zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)															---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46281062	46281062	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46281062delA	uc002xtk.2	+						NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron|NCOA3_uc010zyc.1_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																		---	---	---	---
SPO11	23626	broad.mit.edu	37	20	55906733	55906733	+	Intron	DEL	T	-	-	rs67108426		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55906733delT	uc002xye.2	+						SPO11_uc002xyf.2_Intron	NM_012444	NP_036576			meiotic recombination protein SPO11 isoform a						female gamete generation|reciprocal meiotic recombination	chromosome|nucleus	ATP binding|DNA binding|hydrolase activity			breast(2)|skin(1)	3	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)										Editing_and_processing_nucleases					---	---	---	---
NKAIN4	128414	broad.mit.edu	37	20	61874139	61874139	+	Intron	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874139delG	uc002yek.2	-							NM_152864	NP_690603			Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)																	---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62193250	62193251	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62193250_62193251insG	uc002yfm.2	-	12	7508_7509	c.6616_6617insC	c.(6616-6618)CGTfs	p.R2206fs	PRIC285_uc002yfl.1_Frame_Shift_Ins_p.R1637fs	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	2206					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)															---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30318667	30318667	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30318667delA	uc002ymr.2	-							NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
KRTAP12-4	386684	broad.mit.edu	37	21	46074550	46074550	+	5'UTR	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46074550delG	uc002zfs.1	-	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198698	NP_941971			keratin associated protein 12-4							keratin filament				ovary(1)	1																		---	---	---	---
LOC91316	91316	broad.mit.edu	37	22	23981190	23981191	+	Intron	DEL	CT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23981190_23981191delCT	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0																		---	---	---	---
HPS4	89781	broad.mit.edu	37	22	26854625	26854625	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26854625delA	uc003acl.2	-						HPS4_uc003aci.2_Intron|HPS4_uc003acj.2_Intron|HPS4_uc003ack.2_Intron|HPS4_uc003acn.2_Intron|HPS4_uc003ach.2_Intron	NM_022081	NP_071364			light ear protein isoform a						lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														Hermansky-Pudlak_syndrome				---	---	---	---
SRRD	402055	broad.mit.edu	37	22	26885892	26885892	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26885892delT	uc010gve.2	+						SRRD_uc003acp.3_Intron|uc003acu.1_5'Flank	NM_001013694	NP_001013716			SRR1 domain containing						rhythmic process						0																		---	---	---	---
HORMAD2	150280	broad.mit.edu	37	22	30500336	30500336	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30500336delT	uc003agy.2	+							NM_152510	NP_689723			HORMA domain containing 2						meiosis|mitosis	chromosome|nucleus					0			Epithelial(10;0.125)															---	---	---	---
RNF185	91445	broad.mit.edu	37	22	31593111	31593111	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31593111delA	uc003akb.2	+						RNF185_uc010gwh.2_Intron|RNF185_uc011alm.1_Intron|RNF185_uc003akc.2_Intron|RNF185_uc003ake.2_Intron	NM_152267	NP_689480			ring finger protein 185 isoform 1							integral to membrane	zinc ion binding				0																		---	---	---	---
BPIL2	254240	broad.mit.edu	37	22	32843062	32843062	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32843062delA	uc003amn.2	-						BPIL2_uc010gwo.2_Intron|BPIL2_uc011amb.1_Intron	NM_174932	NP_777592			bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2																		---	---	---	---
KCTD17	79734	broad.mit.edu	37	22	37458553	37458553	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37458553delT	uc010gxb.2	+						KCTD17_uc011amv.1_Intron|KCTD17_uc010gxc.2_Intron	NM_024681	NP_078957			potassium channel tetramerisation domain							voltage-gated potassium channel complex	identical protein binding|voltage-gated potassium channel activity				0																		---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42898666	42898666	+	Intron	DEL	C	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42898666delC	uc011apm.1	+						SERHL_uc011apl.1_Intron					RecName: Full=Serine hydrolase-like protein;          EC=3.1.-.-;												0																		---	---	---	---
SAMM50	25813	broad.mit.edu	37	22	44353271	44353271	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44353271delA	uc003bej.2	+						PNPLA3_uc010gzm.1_Intron|SAMM50_uc011aqd.1_Intron	NM_015380	NP_056195			sorting and assembly machinery component 50						protein import into mitochondrial outer membrane	integral to membrane|integral to membrane of membrane fraction|mitochondrial sorting and assembly machinery complex	protein binding			skin(1)	1		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
MIR1249	100302149	broad.mit.edu	37	22	45596846	45596846	+	RNA	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45596846delG	hsa-mir-1249|MI0006384	-			c.55delG			C22orf9_uc003bfx.1_Intron|C22orf9_uc010gzw.1_Intron|C22orf9_uc003bfv.1_Intron|C22orf9_uc003bfw.1_Intron|C22orf9_uc010gzx.2_Intron																	0																		---	---	---	---
CRLF2	64109	broad.mit.edu	37	X	1315128	1315128	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1315128delT	uc004cpm.1	-											Homo sapiens mRNA for IL-XR, complete cds.							extracellular region|integral to membrane|plasma membrane	receptor activity			haematopoietic_and_lymphoid_tissue(7)	7		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)						Mis|T	P2RY8|IGH@	B-ALL|Downs associated ALL								---	---	---	---
GYG2	8908	broad.mit.edu	37	X	2774840	2774841	+	Intron	INS	-	ATCT	ATCT	rs142965389		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2774840_2774841insATCT	uc004cqs.1	+						GYG2_uc004cqt.1_Intron|GYG2_uc004cqu.1_Intron|GYG2_uc004cqv.1_Intron|GYG2_uc004cqw.1_Intron|GYG2_uc004cqx.1_Intron|GYG2_uc010ndc.1_Intron	NM_003918	NP_003909			glycogenin 2 isoform b						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity			ovary(1)|kidney(1)	2		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)																---	---	---	---
KAL1	3730	broad.mit.edu	37	X	8513424	8513427	+	Intron	DEL	GGAA	-	-	rs35347105		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8513424_8513427delGGAA	uc004csf.2	-							NM_000216	NP_000207			Kallmann syndrome 1 protein precursor						axon guidance|cell adhesion|cellular component movement	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|serine-type endopeptidase inhibitor activity			ovary(3)|pancreas(1)	4																		---	---	---	---
GEMIN8	54960	broad.mit.edu	37	X	14039512	14039512	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
REPS2	9185	broad.mit.edu	37	X	17024235	17024235	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17024235delT	uc004cxv.1	+						REPS2_uc004cxw.1_Intron|REPS2_uc011miw.1_Intron	NM_004726	NP_004717			RALBP1 associated Eps domain containing 2						epidermal growth factor receptor signaling pathway|protein complex assembly	cytoplasm	calcium ion binding|protein binding			skin(2)|central_nervous_system(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
PPEF1	5475	broad.mit.edu	37	X	18841807	18841807	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18841807delA	uc004cyq.2	+						PPEF1_uc004cyp.2_Intron|PPEF1_uc004cyr.2_Intron|PPEF1_uc004cys.2_Intron|PPEF1_uc011mja.1_Intron|PPEF1_uc011mjb.1_Intron	NM_006240	NP_006231			protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	19507265	19507265	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19507265delT								MAP3K15 (6871 upstream) : SH3KBP1 (44819 downstream)																																			---	---	---	---
APOO	79135	broad.mit.edu	37	X	23855280	23855280	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23855280delT	uc004dax.2	-						APOO_uc004daw.2_Intron|APOO_uc004day.3_Intron	NM_024122	NP_077027			apolipoprotein O precursor						lipid transport	high-density lipoprotein particle|integral to membrane|low-density lipoprotein particle|very-low-density lipoprotein particle					0																		---	---	---	---
EIF2S3	1968	broad.mit.edu	37	X	24089990	24089991	+	Intron	DEL	TT	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24089990_24089991delTT	uc004dbc.2	+							NM_001415	NP_001406			eukaryotic translation initiation factor 2,							cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1																		---	---	---	---
PDK3	5165	broad.mit.edu	37	X	24517162	24517162	+	Intron	DEL	T	-	-	rs113531183		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24517162delT	uc004dbg.2	+						PDK3_uc004dbh.2_Intron	NM_005391	NP_005382			pyruvate dehydrogenase kinase 3 isoform 2						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|protein binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
GK	2710	broad.mit.edu	37	X	30726104	30726104	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30726104delA	uc004dch.3	+						GK_uc010ngj.2_Intron|GK_uc004dci.3_Intron|GK_uc011mjz.1_Intron|GK_uc011mka.1_Intron|GK_uc010ngk.2_Intron	NM_203391	NP_976325			glycerol kinase isoform a						glycerol-3-phosphate metabolic process|triglyceride biosynthetic process	cytosol|mitochondrial outer membrane	ATP binding|glycerol kinase activity			central_nervous_system(1)	1																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31497362	31497362	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31497362delT	uc004dda.1	-						DMD_uc004dcq.1_Intron|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	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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32381186	32381187	+	Intron	DEL	AG	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32381186_32381187delAG	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32456541	32456541	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32456541delT	uc004dda.1	-						DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.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)																---	---	---	---
MED14	9282	broad.mit.edu	37	X	40552264	40552264	+	Intron	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40552264delA	uc004dex.3	-							NM_004229	NP_004220			mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4																		---	---	---	---
DDX3X	1654	broad.mit.edu	37	X	41207100	41207100	+	3'UTR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41207100delT	uc004dfe.2	+	17					DDX3X_uc004dff.2_3'UTR|DDX3X_uc011mkq.1_3'UTR|DDX3X_uc011mkr.1_3'UTR|DDX3X_uc011mks.1_3'UTR|DDX3X_uc004dfg.2_RNA	NM_001356	NP_001347			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3						interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6															HNSCC(61;0.18)			---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44935952	44935952	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44935952delA	uc004dge.3	+	18	3088	c.2713delA	c.(2713-2715)AAAfs	p.K905fs	KDM6A_uc010nhk.2_Frame_Shift_Del_p.K871fs|KDM6A_uc011mkz.1_Frame_Shift_Del_p.K957fs|KDM6A_uc011mla.1_Frame_Shift_Del_p.K860fs|KDM6A_uc011mlb.1_Frame_Shift_Del_p.K912fs|KDM6A_uc011mlc.1_Frame_Shift_Del_p.K609fs|KDM6A_uc011mld.1_Frame_Shift_Del_p.K544fs	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide	905					histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
CXorf36	79742	broad.mit.edu	37	X	45013524	45013527	+	Intron	DEL	CTAT	-	-	rs72059118		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45013524_45013527delCTAT	uc004dgg.2	-							NM_176819	NP_789789			hypothetical protein LOC79742 isoform 1							extracellular region				lung(1)	1																		---	---	---	---
SSX3	10214	broad.mit.edu	37	X	48213309	48213309	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48213309delT	uc004djd.1	-						SSX3_uc004dje.2_Intron|SSX3_uc010nic.2_Intron	NM_021014	NP_066294			synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54569370	54569370	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54569370delT	uc004dth.1	+						GNL3L_uc004dti.2_Intron	NM_019067	NP_061940			guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	64548439	64548439	+	IGR	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64548439delT								ZC4H2 (293846 upstream) : ZC3H12B (160267 downstream)																																			---	---	---	---
IL2RG	3561	broad.mit.edu	37	X	70327614	70327614	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70327614delG	uc004dyw.1	-	8	1096	c.1082delC	c.(1081-1083)CCAfs	p.P361fs	CXorf65_uc011mpo.1_5'Flank|CXorf65_uc011mpp.1_5'Flank|IL2RG_uc004dyv.1_Frame_Shift_Del_p.P90fs|IL2RG_uc004dyx.1_Frame_Shift_Del_p.P171fs	NM_000206	NP_000197	P31785	IL2RG_HUMAN	interleukin 2 receptor, gamma precursor	361	Cytoplasmic (Potential).				immune response|interleukin-4-mediated signaling pathway|interspecies interaction between organisms	external side of plasma membrane|integral to plasma membrane	cytokine receptor activity|interleukin-2 binding			pancreas(1)	1	Renal(35;0.156)				Aldesleukin(DB00041)|Denileukin diftitox(DB00004)									Severe_Combined_Immunodeficiency_X-linked				---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70626407	70626407	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70626407delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_5'Flank|TAF1_uc010nle.1_5'Flank|TAF1_uc010nlf.1_5'Flank|TAF1_uc004dzx.2_5'Flank|TAF1_uc004dzy.2_5'Flank	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70628174	70628174	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70628174delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
CXorf26	51260	broad.mit.edu	37	X	75393057	75393057	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75393057delT	uc004ecl.1	+						CXorf26_uc004eck.1_Intron	NM_016500	NP_057584			hypothetical protein LOC51260												0																		---	---	---	---
PGK1	5230	broad.mit.edu	37	X	77380774	77380774	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77380774delT	uc004ecz.3	+						PGK1_uc010nlz.2_Intron|PGK1_uc011mqq.1_Intron	NM_000291	NP_000282			phosphoglycerate kinase 1						gluconeogenesis|glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
TRMT2B	79979	broad.mit.edu	37	X	100273946	100273950	+	Intron	DEL	AAGTC	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100273946_100273950delAAGTC	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																		---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	103903558	103903558	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103903558delT	uc004elz.1	+							NM_017416	NP_059112			interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3																		---	---	---	---
NRK	203447	broad.mit.edu	37	X	105150376	105150376	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105150376delT	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)			---	---	---	---
TMEM164	84187	broad.mit.edu	37	X	109387871	109387871	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109387871delT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603			transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3																		---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122599142	122599142	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122599142delT	uc004etq.3	+						GRIA3_uc004etr.3_Intron|GRIA3_uc004ets.3_Intron	NM_007325	NP_015564			glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123663987	123663987	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123663987delT	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																		---	---	---	---
XPNPEP2	7512	broad.mit.edu	37	X	128890517	128890518	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128890517_128890518insG	uc004eut.1	+	14	1597_1598	c.1353_1354insG	c.(1351-1356)TCTGGGfs	p.S451fs		NM_003399	NP_003390	O43895	XPP2_HUMAN	X-prolyl aminopeptidase 2, membrane-bound	451_452					cellular process|proteolysis	anchored to membrane|plasma membrane	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0																		---	---	---	---
UTP14A	10813	broad.mit.edu	37	X	129052864	129052864	+	Intron	DEL	A	-	-	rs11315972		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129052864delA	uc004euz.2	+						UTP14A_uc011mup.1_Intron|UTP14A_uc011muq.1_Intron|UTP14A_uc004eva.1_5'Flank	NM_006649	NP_006640			UTP14, U3 small nucleolar ribonucleoprotein,						rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2																		---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147011446	147011446	+	Intron	DEL	T	-	-			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147011446delT	uc010nst.2	+						FMR1_uc011mwz.1_Intron|FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_5'Flank	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149637907	149637908	+	Intron	INS	-	TC	TC	rs111485700		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149637907_149637908insTC	uc004fee.1	+						MAMLD1_uc011mxt.1_Intron|MAMLD1_uc011mxu.1_Intron|MAMLD1_uc011mxv.1_Intron|MAMLD1_uc011mxw.1_5'Flank	NM_005491	NP_005482			mastermind-like domain containing 1						male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
RERE	473	broad.mit.edu	37	1	8418972	8418972	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8418972G>A	uc001ape.2	-	21	4433	c.3623C>T	c.(3622-3624)GCG>GTG	p.A1208V	RERE_uc001apf.2_Missense_Mutation_p.A1208V|RERE_uc001apd.2_Missense_Mutation_p.A654V	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	1208	Potential.				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
SRM	6723	broad.mit.edu	37	1	11116784	11116784	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11116784G>A	uc001arz.1	-	4	503	c.412C>T	c.(412-414)CCA>TCA	p.P138S	SRM_uc001ary.1_5'UTR	NM_003132	NP_003123	P19623	SPEE_HUMAN	spermidine synthase	138					spermidine biosynthetic process	cytosol	protein homodimerization activity|spermidine synthase activity				0	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)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)|Spermine(DB00127)													---	---	---	---
NPPB	4879	broad.mit.edu	37	1	11918372	11918372	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11918372T>C	uc001atj.2	-	2	389	c.287A>G	c.(286-288)TAC>TGC	p.Y96C		NM_002521	NP_002512	P16860	ANFB_HUMAN	natriuretic peptide precursor B preproprotein	96					body fluid secretion|cGMP biosynthetic process|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation	extracellular space	diuretic hormone activity			ovary(2)	2	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;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	Carvedilol(DB01136)|Nesiritide(DB04899)|Testosterone(DB00624)													---	---	---	---
KIAA0090	23065	broad.mit.edu	37	1	19577930	19577930	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19577930T>A	uc001bbo.2	-	1	117	c.74A>T	c.(73-75)GAC>GTC	p.D25V	KIAA0090_uc001bbp.2_Missense_Mutation_p.D25V|KIAA0090_uc001bbq.2_Missense_Mutation_p.D25V|KIAA0090_uc001bbr.2_Missense_Mutation_p.D25V|MRTO4_uc001bbs.2_5'Flank	NM_015047	NP_055862	Q8N766	K0090_HUMAN	hypothetical protein LOC23065 precursor	25	Extracellular (Potential).					integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
PINK1	65018	broad.mit.edu	37	1	20964564	20964564	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20964564A>C	uc001bdm.2	+	2	711	c.617A>C	c.(616-618)GAG>GCG	p.E206A		NM_032409	NP_115785	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1 precursor	206	Protein kinase.|Cytoplasmic (Potential).				cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress	cytosol|integral to membrane|mitochondrial outer membrane	ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding			ovary(2)|central_nervous_system(1)	3		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21599193	21599193	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21599193G>A	uc001bek.2	-	4	567	c.492C>T	c.(490-492)CTC>CTT	p.L164L	ECE1_uc001bem.2_Silent_p.L148L|ECE1_uc001bej.2_Silent_p.L152L|ECE1_uc001bei.2_Silent_p.L161L|ECE1_uc010odl.1_Silent_p.L164L|ECE1_uc009vqa.1_Silent_p.L164L	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	164	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)														---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29581889	29581889	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29581889G>T	uc001bru.2	+	2	286	c.176G>T	c.(175-177)GGC>GTC	p.G59V	PTPRU_uc001brv.2_Missense_Mutation_p.G59V|PTPRU_uc001brw.2_Missense_Mutation_p.G59V|PTPRU_uc009vtq.2_Missense_Mutation_p.G59V|PTPRU_uc009vtr.2_Missense_Mutation_p.G59V	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	59	Extracellular (Potential).|MAM.				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)														---	---	---	---
RBBP4	5928	broad.mit.edu	37	1	33134451	33134451	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33134451A>G	uc001bvr.2	+	5	755	c.596A>G	c.(595-597)GAC>GGC	p.D199G	RBBP4_uc001bvs.2_Missense_Mutation_p.D198G|RBBP4_uc010ohj.1_5'UTR|RBBP4_uc010ohk.1_Missense_Mutation_p.D164G	NM_005610	NP_005601	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4 isoform a	199	WD 2.				cell cycle|CenH3-containing nucleosome assembly at centromere|DNA replication|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|ESC/E(Z) complex|NuRD complex|NURF complex|Sin3 complex	histone binding|histone deacetylase binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)																---	---	---	---
EPHA10	284656	broad.mit.edu	37	1	38227120	38227120	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38227120G>A	uc009vvi.2	-	3	893	c.807C>T	c.(805-807)TGC>TGT	p.C269C	EPHA10_uc001cbw.3_Silent_p.C269C	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	269	Extracellular (Potential).					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
RLF	6018	broad.mit.edu	37	1	40705156	40705156	+	Silent	SNP	C	T	T	rs145611435	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40705156C>T	uc001cfc.3	+	8	4813	c.4782C>T	c.(4780-4782)TAC>TAT	p.Y1594Y	RLF_uc001cfd.3_Silent_p.Y1285Y	NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	1594					chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)															---	---	---	---
SLFNL1	200172	broad.mit.edu	37	1	41483496	41483496	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41483496G>A	uc001cgm.1	-	3	988	c.768C>T	c.(766-768)GGC>GGT	p.G256G	SLFNL1_uc009vwf.1_Silent_p.G256G|SLFNL1_uc001cgn.1_Silent_p.G197G|SLFNL1_uc009vwg.1_Silent_p.G256G	NM_144990	NP_659427	Q499Z3	SLNL1_HUMAN	schlafen-like 1	256							ATP binding			skin(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
TIE1	7075	broad.mit.edu	37	1	43772883	43772883	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43772883C>T	uc001ciu.2	+	5	790	c.711C>T	c.(709-711)TGC>TGT	p.C237C	TIE1_uc010okd.1_Silent_p.C237C|TIE1_uc010oke.1_Silent_p.C192C|TIE1_uc009vwq.2_Intron|TIE1_uc010okf.1_5'UTR|TIE1_uc010okg.1_5'UTR|TIE1_uc010okc.1_Silent_p.C237C	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	237	Extracellular (Potential).|EGF-like 1.				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
DMRTB1	63948	broad.mit.edu	37	1	53927224	53927224	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53927224C>T	uc001cvq.1	+	2	711	c.656C>T	c.(655-657)CCG>CTG	p.P219L		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	219	Pro-rich.				sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
BRDT	676	broad.mit.edu	37	1	92428391	92428391	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92428391G>A	uc001dok.3	+	2	429	c.80G>A	c.(79-81)CGA>CAA	p.R27Q	BRDT_uc001dol.3_Missense_Mutation_p.R27Q|BRDT_uc010osz.1_Missense_Mutation_p.R27Q|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Missense_Mutation_p.R27Q|BRDT_uc010otb.1_Missense_Mutation_p.R27Q|BRDT_uc001dom.3_Missense_Mutation_p.R27Q	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	27					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94502716	94502716	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94502716G>A	uc001dqh.2	-	25	3902	c.3798C>T	c.(3796-3798)GAC>GAT	p.D1266D		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1266	Cytoplasmic.				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)														---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107866901	107866901	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107866901T>C	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_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)														---	---	---	---
GPR61	83873	broad.mit.edu	37	1	110085827	110085827	+	Silent	SNP	C	T	T	rs138020817	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110085827C>T	uc001dxy.2	+	2	866	c.183C>T	c.(181-183)GCC>GCT	p.A61A		NM_031936	NP_114142	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	61	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(2)	2		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)														---	---	---	---
SLC6A17	388662	broad.mit.edu	37	1	110740193	110740193	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110740193C>A	uc009wfq.2	+	11	2248	c.1787C>A	c.(1786-1788)CCG>CAG	p.P596Q		NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN	solute carrier family 6, member 17	596	Extracellular (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)												OREG0013652	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC16A4	9122	broad.mit.edu	37	1	110921593	110921593	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110921593A>G	uc001dzo.1	-	6	1094	c.912T>C	c.(910-912)TTT>TTC	p.F304F	SLC16A4_uc009wfs.1_Silent_p.F256F|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Silent_p.F242F|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Silent_p.F194F	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4	304	Helical; (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)													---	---	---	---
HIPK1	204851	broad.mit.edu	37	1	114483597	114483597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114483597C>T	uc001eem.2	+	2	753	c.592C>T	c.(592-594)CGG>TGG	p.R198W	HIPK1_uc001eel.2_Missense_Mutation_p.R198W|HIPK1_uc001een.2_Missense_Mutation_p.R198W	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	198	Protein kinase.|ATP (Probable).				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)														---	---	---	---
ATP1A1	476	broad.mit.edu	37	1	116931263	116931263	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116931263G>A	uc001ege.2	+	6	844	c.505G>A	c.(505-507)GCC>ACC	p.A169T	ATP1A1_uc010owv.1_Missense_Mutation_p.A138T|ATP1A1_uc010oww.1_Missense_Mutation_p.A169T|ATP1A1_uc010owx.1_Missense_Mutation_p.A138T	NM_000701	NP_000692	P05023	AT1A1_HUMAN	Na+/K+ -ATPase alpha 1 subunit isoform a	169	Cytoplasmic (Potential).				ATP biosynthetic process	melanosome|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Captopril(DB01197)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Esomeprazole(DB00736)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Ouabain(DB01092)|Pantoprazole(DB00213)|Trichlormethiazide(DB01021)													---	---	---	---
TTF2	8458	broad.mit.edu	37	1	117632754	117632754	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117632754A>G	uc001egy.2	+	14	2440	c.2420A>G	c.(2419-2421)GAA>GGA	p.E807G		NM_003594	NP_003585	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase	807					mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)														---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144881535	144881535	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144881535A>G	uc001elw.3	-	25	3952	c.3661T>C	c.(3661-3663)TCA>CCA	p.S1221P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.S1177P|PDE4DIP_uc001elv.3_Missense_Mutation_p.S228P	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1221	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144915576	144915576	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144915576A>G	uc001elw.3	-	14	2140	c.1849T>C	c.(1849-1851)TGC>CGC	p.C617R	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.C683R|PDE4DIP_uc001emc.1_Missense_Mutation_p.C617R|PDE4DIP_uc001emd.1_Missense_Mutation_p.C617R|PDE4DIP_uc001emb.1_Missense_Mutation_p.C780R|PDE4DIP_uc001eme.1_Missense_Mutation_p.C146R|PDE4DIP_uc001emf.1_Missense_Mutation_p.C402R	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	617	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PI4KB	5298	broad.mit.edu	37	1	151288916	151288916	+	Silent	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151288916A>C	uc001ext.2	-	2	457	c.42T>G	c.(40-42)ACT>ACG	p.T14T	PI4KB_uc001exr.2_Silent_p.T26T|PI4KB_uc001exs.2_Silent_p.T14T|PI4KB_uc001exu.2_Silent_p.T14T|PI4KB_uc010pcw.1_Intron|PI4KB_uc009wmq.1_Silent_p.T26T	NM_002651	NP_002642	Q9UBF8	PI4KB_HUMAN	catalytic phosphatidylinositol 4-kinase beta	14					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)															---	---	---	---
TDRKH	11022	broad.mit.edu	37	1	151747603	151747603	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151747603C>T	uc009wnb.1	-	11	1656	c.1474G>A	c.(1474-1476)GCA>ACA	p.A492T	TDRKH_uc001eyy.2_Missense_Mutation_p.A268T|TDRKH_uc001ezb.3_Missense_Mutation_p.A488T|TDRKH_uc001ezc.3_Missense_Mutation_p.A447T|TDRKH_uc001eza.3_Missense_Mutation_p.A492T|TDRKH_uc001ezd.3_Missense_Mutation_p.A492T|TDRKH_uc010pdn.1_Missense_Mutation_p.A268T	NM_006862	NP_006853	Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing isoform a	492							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)															---	---	---	---
S100A8	6279	broad.mit.edu	37	1	153362988	153362988	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153362988G>T	uc001fbs.2	-	2	79	c.24C>A	c.(22-24)GCC>GCA	p.A8A		NM_002964	NP_002955	P05109	S10A8_HUMAN	S100 calcium-binding protein A8	8					chemotaxis	cytoplasm|cytoskeleton|plasma membrane	calcium ion binding|protein binding				0	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
CHRNB2	1141	broad.mit.edu	37	1	154543725	154543725	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154543725C>T	uc001ffg.2	+	5	690	c.426C>T	c.(424-426)AGC>AGT	p.S142S		NM_000748	NP_000739	P17787	ACHB2_HUMAN	neuronal nicotinic acetylcholine receptor beta 2	142	Extracellular (Potential).				B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)													---	---	---	---
RUSC1	23623	broad.mit.edu	37	1	155294263	155294263	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155294263T>C	uc001fkj.2	+						RAG1AP1_uc010pey.1_Intron|C1orf104_uc001fkh.1_5'Flank|C1orf104_uc001fki.2_5'Flank|RUSC1_uc001fkk.2_Intron|RUSC1_uc009wqn.1_Intron|RUSC1_uc009wqo.1_Intron|RUSC1_uc001fkl.2_Missense_Mutation_p.C19R|RUSC1_uc001fkp.2_5'UTR|RUSC1_uc001fkq.2_5'UTR|RUSC1_uc010pgb.1_5'UTR|RUSC1_uc009wqp.1_5'UTR|RUSC1_uc001fkn.2_5'Flank|RUSC1_uc001fko.2_5'Flank|RUSC1_uc001fkr.2_5'Flank|RUSC1_uc001fks.2_5'Flank	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	155450332	155450332	+	Missense_Mutation	SNP	G	A	A	rs150671158	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155450332G>A	uc009wqq.2	-	3	2809	c.2329C>T	c.(2329-2331)CGC>TGC	p.R777C	ASH1L_uc001fkt.2_Missense_Mutation_p.R777C|ASH1L_uc009wqr.1_Missense_Mutation_p.R777C	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	777					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)															---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156918025	156918025	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156918025G>A	uc001fqo.2	-						ARHGEF11_uc010phu.1_Intron|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)																	---	---	---	---
IFI16	3428	broad.mit.edu	37	1	158988127	158988127	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158988127A>G	uc001ftf.1	+	6	1265	c.658A>G	c.(658-660)ACC>GCC	p.T220A	IFI16_uc001ftg.2_Missense_Mutation_p.T220A|IFI16_uc010pis.1_Missense_Mutation_p.T164A	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	220	HIN-200 1.				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)																	---	---	---	---
CCDC19	25790	broad.mit.edu	37	1	159846359	159846359	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159846359C>T	uc001fui.2	-	10	1357	c.1339G>A	c.(1339-1341)GAG>AAG	p.E447K	CCDC19_uc009wtb.2_RNA|CCDC19_uc001fuj.2_RNA|CCDC19_uc001fuk.2_Missense_Mutation_p.E362K|CCDC19_uc001ful.2_Missense_Mutation_p.E362K|CCDC19_uc009wtc.1_3'UTR	NM_012337	NP_036469	Q9UL16	CCD19_HUMAN	nasopharyngeal epithelium specific protein 1	447	Potential.					mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)															---	---	---	---
NR1I3	9970	broad.mit.edu	37	1	161201029	161201029	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161201029G>T	uc001fzx.2	-	7	904	c.701C>A	c.(700-702)CCC>CAC	p.P234H	TOMM40L_uc009wuf.1_Intron|NR1I3_uc001fzf.2_Intron|NR1I3_uc001fzg.2_Intron|NR1I3_uc001fzh.2_Intron|NR1I3_uc001fzi.2_Intron|NR1I3_uc001fzj.2_Intron|NR1I3_uc001fzk.2_Intron|NR1I3_uc001fzl.2_Intron|NR1I3_uc001fzm.2_Intron|NR1I3_uc001fzn.2_Intron|NR1I3_uc009wug.2_Intron|NR1I3_uc001fzp.2_Missense_Mutation_p.P234H|NR1I3_uc001fzo.2_Intron|NR1I3_uc001fzq.2_Intron|NR1I3_uc001fzr.2_Intron|NR1I3_uc001fzs.2_Intron|NR1I3_uc001fzt.2_Intron|NR1I3_uc001fzu.2_Intron|NR1I3_uc001fzv.2_Intron|NR1I3_uc001fzw.2_Missense_Mutation_p.P234H|NR1I3_uc001fzy.2_Intron|NR1I3_uc001fzz.2_Intron|NR1I3_uc001gaa.2_Intron|NR1I3_uc001gab.2_Intron|NR1I3_uc001gac.2_Missense_Mutation_p.P205H|NR1I3_uc010pkm.1_Intron|NR1I3_uc010pkn.1_3'UTR	NM_001077480	NP_001070948	Q14994	NR1I3_HUMAN	constitutive androstane receptor isoform 2	234					regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	androgen receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(1)|skin(1)	2	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
ALDH9A1	223	broad.mit.edu	37	1	165638534	165638534	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165638534G>A	uc001gdh.1	-	7	1189	c.1084C>T	c.(1084-1086)CGA>TGA	p.R362*	ALDH9A1_uc010pky.1_Nonsense_Mutation_p.R268*|ALDH9A1_uc010pkz.1_Nonsense_Mutation_p.R352*|ALDH9A1_uc010pla.1_Nonsense_Mutation_p.R268*	NM_000696	NP_000687	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9A1	338					carnitine biosynthetic process|cellular aldehyde metabolic process|hormone metabolic process|neurotransmitter biosynthetic process	cytosol|plasma membrane	3-chloroallyl aldehyde dehydrogenase activity|4-trimethylammoniobutyraldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aminobutyraldehyde dehydrogenase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				NADH(DB00157)													---	---	---	---
KLHL20	27252	broad.mit.edu	37	1	173720977	173720977	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173720977C>T	uc001gjc.2	+	4	851	c.672C>T	c.(670-672)AAC>AAT	p.N224N	KLHL20_uc010pmr.1_Silent_p.N35N|KLHL20_uc009wwf.2_Silent_p.N206N	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	224	BACK.				cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173912759	173912759	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173912759G>A	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																		---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176926923	176926923	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176926923A>G	uc001glc.2	-	11	1990	c.1778T>C	c.(1777-1779)GTT>GCT	p.V593A	ASTN1_uc001glb.1_Missense_Mutation_p.V593A|ASTN1_uc001gld.1_Missense_Mutation_p.V593A|ASTN1_uc009wwx.1_Missense_Mutation_p.V593A	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	601					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178854243	178854243	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178854243C>T	uc001glz.2	+	12	1275	c.937C>T	c.(937-939)CGA>TGA	p.R313*	RALGPS2_uc010pnb.1_Nonsense_Mutation_p.R313*	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	313					small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0																		---	---	---	---
LAMC1	3915	broad.mit.edu	37	1	183111832	183111832	+	Silent	SNP	C	T	T	rs139212722		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183111832C>T	uc001gpy.3	+	28	4994	c.4737C>T	c.(4735-4737)ATC>ATT	p.I1579I		NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor	1579	Potential.|Domain II and I.				axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
RGS13	6003	broad.mit.edu	37	1	192628502	192628502	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192628502T>C	uc001gsj.2	+	7	610	c.329T>C	c.(328-330)ATC>ACC	p.I110T	RGS13_uc001gsk.2_Missense_Mutation_p.I110T	NM_002927	NP_002918	O14921	RGS13_HUMAN	regulator of G-protein signalling 13	110	RGS.					plasma membrane	GTPase activator activity|signal transducer activity				0																		---	---	---	---
CFHR1	3078	broad.mit.edu	37	1	196799764	196799764	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196799764C>T	uc001gtn.2	+	5	856	c.742C>T	c.(742-744)CGA>TGA	p.R248*	CFHR1_uc001gtm.2_Nonsense_Mutation_p.R152*	NM_002113	NP_002104	Q03591	FHR1_HUMAN	complement factor H-related 1 precursor	248	Sushi 4.				complement activation	extracellular space					0																		---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197060039	197060039	+	Missense_Mutation	SNP	G	A	A	rs140679756		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197060039G>A	uc001gtu.2	-	23	9834	c.9577C>T	c.(9577-9579)CGC>TGC	p.R3193C	ASPM_uc001gtv.2_Missense_Mutation_p.R1608C|ASPM_uc001gtw.3_Missense_Mutation_p.R1041C	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	3193	IQ 38.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
C1orf106	55765	broad.mit.edu	37	1	200880598	200880598	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200880598C>T	uc001gvo.2	+	9	1262	c.1232C>T	c.(1231-1233)GCG>GTG	p.A411V	C1orf106_uc010ppm.1_Missense_Mutation_p.A326V	NM_018265	NP_060735	Q3KP66	CA106_HUMAN	hypothetical protein LOC55765 isoform 1	411										skin(2)|ovary(1)	3																		---	---	---	---
UBE2T	29089	broad.mit.edu	37	1	202304780	202304780	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202304780G>A	uc001gxx.3	-	2	239	c.103C>T	c.(103-105)CGA>TGA	p.R35*		NM_014176	NP_054895	Q9NPD8	UBE2T_HUMAN	ubiquitin-conjugating enzyme E2T	35					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																		---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204413529	204413529	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204413529C>T	uc001haw.2	-	18	3181	c.2702G>A	c.(2701-2703)CGT>CAT	p.R901H	PIK3C2B_uc010pqv.1_Missense_Mutation_p.R873H	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	901					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)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204949561	204949561	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204949561C>T	uc001hbj.2	+	20	2568	c.2240C>T	c.(2239-2241)ACG>ATG	p.T747M	NFASC_uc010pra.1_Missense_Mutation_p.T743M|NFASC_uc001hbi.2_Missense_Mutation_p.T743M|NFASC_uc010prb.1_Missense_Mutation_p.T758M|NFASC_uc010prc.1_Missense_Mutation_p.T314M|NFASC_uc001hbk.1_Missense_Mutation_p.T553M|NFASC_uc001hbl.1_5'Flank	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	747	Extracellular (Potential).|Fibronectin type-III 2.				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)															---	---	---	---
C1orf107	27042	broad.mit.edu	37	1	210006641	210006641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210006641G>A	uc001hhr.1	+	4	576	c.500G>A	c.(499-501)AGC>AAC	p.S167N	C1orf107_uc009xcu.1_5'UTR	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	167	Glu-rich.				multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)														---	---	---	---
NVL	4931	broad.mit.edu	37	1	224495799	224495799	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224495799T>C	uc001hok.2	-	6	552	c.509A>G	c.(508-510)GAA>GGA	p.E170G	NVL_uc001hol.2_Missense_Mutation_p.E64G|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_RNA	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1	170						aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
JMJD4	65094	broad.mit.edu	37	1	227920368	227920368	+	Silent	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227920368T>G	uc001hrb.2	-	6	1117	c.1117A>C	c.(1117-1119)AGG>CGG	p.R373R	SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|LOC100130093_uc001hqx.3_RNA|LOC100130093_uc001hqy.3_RNA|JMJD4_uc001hrc.2_Silent_p.R357R	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1	373											0		Prostate(94;0.0885)																---	---	---	---
PRSS38	339501	broad.mit.edu	37	1	228003829	228003829	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228003829G>A	uc001hrh.2	+	2	187	c.187G>A	c.(187-189)GGC>AGC	p.G63S		NM_183062	NP_898885	A1L453	PRS38_HUMAN	marapsin 2 precursor	63	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2																		---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228404718	228404718	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228404718C>T	uc009xez.1	+	8	2426	c.2382C>T	c.(2380-2382)CTC>CTT	p.L794L	OBSCN_uc001hsn.2_Silent_p.L794L	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	794					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)																---	---	---	---
ABCB10	23456	broad.mit.edu	37	1	229685122	229685122	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229685122C>T	uc001htp.3	-	2	620	c.577G>A	c.(577-579)GGG>AGG	p.G193R		NM_012089	NP_036221	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B, member 10	193	Mitochondrial intermembrane (Potential).|Mitochondrial matrix (Potential).|ABC transmembrane type-1.					integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(2)	2	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
C1orf198	84886	broad.mit.edu	37	1	230979323	230979323	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230979323G>A	uc001hub.2	-	3	748	c.704C>T	c.(703-705)CCG>CTG	p.P235L	C1orf198_uc009xfh.1_Missense_Mutation_p.P105L|C1orf198_uc001huc.1_Missense_Mutation_p.P18L|C1orf198_uc001hud.1_Missense_Mutation_p.P197L	NM_032800	NP_116189	Q9H425	CA198_HUMAN	hypothetical protein LOC84886 isoform 1	235											0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237666765	237666765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237666765C>T	uc001hyl.1	+	22	2693	c.2573C>T	c.(2572-2574)ACG>ATG	p.T858M		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	858	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)															---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240254991	240254991	+	5'Flank	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240254991T>A	uc010pyd.1	+						FMN2_uc010pye.1_5'Flank	NM_020066	NP_064450			formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245848974	245848974	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245848974C>T	uc001ibf.1	+	12	3129	c.2689C>T	c.(2689-2691)CAG>TAG	p.Q897*	KIF26B_uc001ibg.1_Nonsense_Mutation_p.Q515*|KIF26B_uc001ibh.1_Nonsense_Mutation_p.Q139*	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	897					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
ZNF669	79862	broad.mit.edu	37	1	247267342	247267342	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247267342G>C	uc001ice.2	-	1	333	c.160C>G	c.(160-162)CGG>GGG	p.R54G	ZNF669_uc001icf.2_Intron	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	54					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)															---	---	---	---
OR2G3	81469	broad.mit.edu	37	1	247769005	247769005	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247769005G>A	uc010pyz.1	+	1	118	c.118G>A	c.(118-120)GTG>ATG	p.V40M		NM_001001914	NP_001001914	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)															---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17847726	17847726	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17847726C>T	uc002rco.2	-	27	3418	c.3122G>A	c.(3121-3123)CGT>CAT	p.R1041H	SMC6_uc010exo.2_Missense_Mutation_p.R1041H|SMC6_uc002rcn.2_Missense_Mutation_p.R1041H	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	1041					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)																	---	---	---	---
C2orf43	60526	broad.mit.edu	37	2	20990057	20990057	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20990057C>T	uc002rec.2	-	3	289	c.256G>A	c.(256-258)GCG>ACG	p.A86T	C2orf43_uc002rea.1_Missense_Mutation_p.A86T|C2orf43_uc002reb.1_RNA|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_5'UTR|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Missense_Mutation_p.A86T|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526	86											0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf43	60526	broad.mit.edu	37	2	21001136	21001136	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21001136G>A	uc002rec.2	-	2	121	c.88C>T	c.(88-90)CCC>TCC	p.P30S	C2orf43_uc002rea.1_Missense_Mutation_p.P30S|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Missense_Mutation_p.P30S|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Missense_Mutation_p.P30S|C2orf43_uc010ykd.1_Missense_Mutation_p.P30S|C2orf43_uc010yke.1_Missense_Mutation_p.P30S|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526	30											0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26174773	26174773	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26174773A>G	uc002rgu.2	-	5	2548	c.1891T>C	c.(1891-1893)TAC>CAC	p.Y631H	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Missense_Mutation_p.Y631H	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	631	Globular (Potential).				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)																	---	---	---	---
IFT172	26160	broad.mit.edu	37	2	27695182	27695182	+	Missense_Mutation	SNP	G	A	A	rs143520040		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27695182G>A	uc002rku.2	-	15	1510	c.1459C>T	c.(1459-1461)CGT>TGT	p.R487C	IFT172_uc002rkw.2_Missense_Mutation_p.R487C|IFT172_uc010yls.1_Missense_Mutation_p.R466C|IFT172_uc010ezc.2_Missense_Mutation_p.R487C|IFT172_uc002rkv.2_Missense_Mutation_p.R461C	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	487	WD 8.				cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31154985	31154985	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31154985C>T	uc002rnr.2	-	10	1626	c.1007G>A	c.(1006-1008)CGG>CAG	p.R336Q	GALNT14_uc002rnq.2_Missense_Mutation_p.R316Q|GALNT14_uc002rns.2_Missense_Mutation_p.R341Q|GALNT14_uc010ymr.1_Missense_Mutation_p.R301Q|GALNT14_uc010ezo.1_Missense_Mutation_p.R303Q|GALNT14_uc010ezp.1_3'UTR	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	336	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)																	---	---	---	---
RASGRP3	25780	broad.mit.edu	37	2	33783395	33783395	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33783395T>C	uc002rox.2	+	17	2324	c.1697T>C	c.(1696-1698)CTG>CCG	p.L566P	RASGRP3_uc010ync.1_Missense_Mutation_p.L566P|RASGRP3_uc002roy.2_Missense_Mutation_p.L565P	NM_170672	NP_733772	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and	566					MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)																	---	---	---	---
OXER1	165140	broad.mit.edu	37	2	42990108	42990108	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42990108T>C	uc002rss.2	-	1	1294	c.1212A>G	c.(1210-1212)ATA>ATG	p.I404M		NM_148962	NP_683765	Q8TDS5	OXER1_HUMAN	G-protein coupled receptor TG1019	404	Cytoplasmic (Potential).				regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding|G-protein coupled receptor activity			breast(1)	1																		---	---	---	---
GPR75	10936	broad.mit.edu	37	2	54081206	54081206	+	Missense_Mutation	SNP	G	A	A	rs143781055		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54081206G>A	uc002rxo.3	-	2	959	c.688C>T	c.(688-690)CGG>TGG	p.R230W	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	230	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61416142	61416142	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61416142T>C	uc002sbe.2	-	79	9958	c.9936A>G	c.(9934-9936)CTA>CTG	p.L3312L	USP34_uc002sbd.2_Silent_p.L114L	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3312					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)															---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70392254	70392254	+	Silent	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70392254C>A	uc002sgh.2	-	8	1651	c.1323G>T	c.(1321-1323)CTG>CTT	p.L441L		NM_017880	NP_060350	Q9NWW7	CB042_HUMAN	hypothetical protein LOC54980	441											0																		---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70408792	70408792	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70408792T>C	uc002sgh.2	-	3	654	c.326A>G	c.(325-327)CAG>CGG	p.Q109R		NM_017880	NP_060350	Q9NWW7	CB042_HUMAN	hypothetical protein LOC54980	109											0																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71766292	71766292	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71766292G>A	uc002sie.2	+	16	1779	c.1403G>A	c.(1402-1404)CGC>CAC	p.R468H	DYSF_uc010feg.2_Missense_Mutation_p.R499H|DYSF_uc010feh.2_Missense_Mutation_p.R468H|DYSF_uc002sig.3_Missense_Mutation_p.R468H|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Missense_Mutation_p.R468H|DYSF_uc010fef.2_Missense_Mutation_p.R499H|DYSF_uc010fei.2_Missense_Mutation_p.R499H|DYSF_uc010fek.2_Missense_Mutation_p.R500H|DYSF_uc010fej.2_Missense_Mutation_p.R469H|DYSF_uc010fel.2_Missense_Mutation_p.R469H|DYSF_uc010feo.2_Missense_Mutation_p.R500H|DYSF_uc010fem.2_Missense_Mutation_p.R469H|DYSF_uc010fen.2_Missense_Mutation_p.R500H|DYSF_uc002sif.2_Missense_Mutation_p.R469H	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	468	Cytoplasmic (Potential).|C2 3.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86683981	86683981	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86683981C>T	uc002sri.3	+	7	1062	c.735C>T	c.(733-735)CAC>CAT	p.H245H	KDM3A_uc010ytj.1_Silent_p.H245H|KDM3A_uc010ytk.1_Silent_p.H193H	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	245					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109116015	109116015	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109116015A>G	uc002tec.2	+	22	4943	c.4789A>G	c.(4789-4791)AAA>GAA	p.K1597E	GCC2_uc002ted.2_Missense_Mutation_p.K1496E	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1597	Mediates interaction with RAB6A.|Potential.|Mediates interaction with RAB9A.				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																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112614266	112614266	+	Intron	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112614266C>A	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	112832491	112832491	+	Silent	SNP	T	C	C	rs141654814		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112832491T>C	uc002thm.2	+	5	822	c.453T>C	c.(451-453)AAT>AAC	p.N151N	TMEM87B_uc010fkg.2_Intron|TMEM87B_uc010fkh.2_Intron	NM_032824	NP_116213	Q96K49	TM87B_HUMAN	transmembrane protein 87B precursor	151						integral to membrane					0																		---	---	---	---
TMEM177	80775	broad.mit.edu	37	2	120438597	120438597	+	Silent	SNP	G	A	A	rs116090839	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120438597G>A	uc010flg.1	+	2	641	c.168G>A	c.(166-168)CCG>CCA	p.P56P	TMEM177_uc002tme.2_Intron|TMEM177_uc002tmc.1_Silent_p.P56P|TMEM177_uc002tmd.2_Silent_p.P56P|TMEM177_uc010flh.2_Silent_p.P56P	NM_001105198	NP_001098668	Q53S58	TM177_HUMAN	transmembrane protein 177	56						integral to membrane				ovary(1)	1	Colorectal(110;0.196)																	---	---	---	---
BIN1	274	broad.mit.edu	37	2	127806129	127806129	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127806129G>T	uc002tns.1	-	19	2100	c.1755C>A	c.(1753-1755)CCC>CCA	p.P585P	BIN1_uc010yzf.1_Silent_p.P377P|BIN1_uc010yzg.1_Silent_p.P462P|BIN1_uc002tnu.1_Silent_p.P416P|BIN1_uc002toa.1_Silent_p.P474P|BIN1_uc002tnt.1_Silent_p.P401P|BIN1_uc002tnv.1_Silent_p.P542P|BIN1_uc002tnw.1_Silent_p.P489P|BIN1_uc002tnx.1_Silent_p.P446P|BIN1_uc002tny.1_Silent_p.P498P|BIN1_uc002tnz.1_Silent_p.P510P|BIN1_uc002tob.1_Silent_p.P431P|BIN1_uc002toc.1_Silent_p.P467P	NM_139343	NP_647593	O00499	BIN1_HUMAN	bridging integrator 1 isoform 1	585	SH3.				cell proliferation|endocytosis|interspecies interaction between organisms|multicellular organismal development	actin cytoskeleton|nucleus				ovary(2)|central_nervous_system(2)|skin(2)|lung(1)	7	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)														---	---	---	---
CCDC115	84317	broad.mit.edu	37	2	131096756	131096756	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131096756C>A	uc002tqy.1	-	5	704	c.480G>T	c.(478-480)TGG>TGT	p.W160C	CCDC115_uc002tqw.1_3'UTR|CCDC115_uc010zaf.1_3'UTR|CCDC115_uc002tqx.2_Missense_Mutation_p.W155C|CCDC115_uc002tqz.1_3'UTR	NM_032357	NP_115733	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	160	Potential.					endosome|lysosome					0	Colorectal(110;0.1)																	---	---	---	---
TUBA3D	113457	broad.mit.edu	37	2	132237023	132237023	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132237023C>T	uc002tsu.3	+	3	476	c.369C>T	c.(367-369)CGC>CGT	p.R123R		NM_080386	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	123					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)														---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136393550	136393550	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136393550T>C	uc002tuo.2	+	10	1159	c.789T>C	c.(787-789)TTT>TTC	p.F263F	R3HDM1_uc010fni.2_Silent_p.F261F|R3HDM1_uc002tup.2_Silent_p.F207F|R3HDM1_uc010zbh.1_Silent_p.F95F	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	263							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
MCM6	4175	broad.mit.edu	37	2	136602247	136602247	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136602247G>A	uc002tuw.2	-	16	2293	c.2217C>T	c.(2215-2217)GAC>GAT	p.D739D		NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	739					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)													---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152324577	152324577	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152324577C>T	uc002txm.2	+	31	6794	c.6664C>T	c.(6664-6666)CGG>TGG	p.R2222W	RIF1_uc002txl.2_Missense_Mutation_p.R2222W|RIF1_uc002txn.2_Missense_Mutation_p.R2222W|RIF1_uc002txo.2_Missense_Mutation_p.R2222W|RIF1_uc002txp.2_RNA	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	2222	Interaction with condensed chromosomes in telophase.				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)														---	---	---	---
NR4A2	4929	broad.mit.edu	37	2	157186441	157186441	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157186441C>T	uc002tyz.3	-	3	680	c.258G>A	c.(256-258)CAG>CAA	p.Q86Q	NR4A2_uc002tyx.3_Silent_p.Q23Q|NR4A2_uc010zcf.1_Silent_p.Q86Q|NR4A2_uc010zcg.1_5'Flank	NM_006186	NP_006177	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	86	Gln-rich.				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																		---	---	---	---
PLA2R1	22925	broad.mit.edu	37	2	160798419	160798419	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160798419T>C	uc002ube.1	-	30	4469	c.4262A>G	c.(4261-4263)TAC>TGC	p.Y1421C	PLA2R1_uc010zcp.1_Missense_Mutation_p.Y1419C	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	1421	Cytoplasmic (Potential).				endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168100214	168100214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168100214G>A	uc002udx.2	+	8	2330	c.2312G>A	c.(2311-2313)CGG>CAG	p.R771Q	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.R596Q|XIRP2_uc010fpq.2_Missense_Mutation_p.R549Q|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	596	Xin 7.				actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170059292	170059292	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170059292C>A	uc002ues.2	-	43	8396	c.8183G>T	c.(8182-8184)GGC>GTC	p.G2728V		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2728	LDL-receptor class A 16.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
TTN	7273	broad.mit.edu	37	2	179395182	179395182	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179395182G>A	uc010zfg.1	-	307	98680	c.98456C>T	c.(98455-98457)TCA>TTA	p.S32819L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.S26514L|TTN_uc010zfi.1_Missense_Mutation_p.S26447L|TTN_uc010zfj.1_Missense_Mutation_p.S26322L|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33746							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	179580341	179580341	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179580341G>A	uc010zfg.1	-	86	22292	c.22068C>T	c.(22066-22068)TTC>TTT	p.F7356F	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.F4017F	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	8283							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	179667001	179667001	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179667001G>A	uc002und.2	-	3	384	c.159C>T	c.(157-159)GGC>GGT	p.G53G	TTN_uc010zfg.1_Silent_p.G53G|TTN_uc010zfh.1_Silent_p.G53G|TTN_uc010zfi.1_Silent_p.G53G|TTN_uc010zfj.1_Silent_p.G53G|TTN_uc002unb.2_Silent_p.G53G			Q8WZ42	TITIN_HUMAN	Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.	53							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)															---	---	---	---
SPATS2L	26010	broad.mit.edu	37	2	201284108	201284108	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201284108G>A	uc002uvn.3	+	6	686	c.334G>A	c.(334-336)GAG>AAG	p.E112K	SPATS2L_uc010fst.2_Missense_Mutation_p.E112K|SPATS2L_uc002uvo.3_Missense_Mutation_p.E52K|SPATS2L_uc002uvp.3_Missense_Mutation_p.E112K|SPATS2L_uc002uvq.3_Missense_Mutation_p.E112K|SPATS2L_uc002uvr.3_Missense_Mutation_p.E112K|SPATS2L_uc010zhc.1_Missense_Mutation_p.E142K	NM_015535	NP_056350	Q9NUQ6	SPS2L_HUMAN	SPATS2-like protein isoform a	112						cytoplasm|nucleolus				ovary(2)|pancreas(1)	3																		---	---	---	---
CASP8	841	broad.mit.edu	37	2	202131514	202131514	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202131514G>T	uc002uxr.1	+	3	514	c.305G>T	c.(304-306)AGG>ATG	p.R102M	CASP8_uc010ftc.1_Missense_Mutation_p.R102M|CASP8_uc002uxo.1_Missense_Mutation_p.R102M|CASP8_uc002uxp.1_Missense_Mutation_p.R102M|CASP8_uc002uxq.1_Missense_Mutation_p.R102M|CASP8_uc002uxs.1_Missense_Mutation_p.R102M|CASP8_uc002uxt.1_Missense_Mutation_p.R161M|CASP8_uc002uxu.1_RNA|CASP8_uc010ftd.1_Intron|CASP8_uc002uxv.1_Missense_Mutation_p.R102M|CASP8_uc002uxw.1_Missense_Mutation_p.R102M|CASP8_uc002uxy.1_Missense_Mutation_p.R102M|CASP8_uc002uxx.1_Missense_Mutation_p.R102M|CASP8_uc010ftf.2_Missense_Mutation_p.R102M	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor	102	DED 2.				activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5															HNSCC(4;0.00038)			---	---	---	---
IHH	3549	broad.mit.edu	37	2	219920518	219920518	+	Missense_Mutation	SNP	G	A	A	rs142245478		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219920518G>A	uc002vjo.1	-	3	647	c.647C>T	c.(646-648)GCG>GTG	p.A216V		NM_002181	NP_002172	Q14623	IHH_HUMAN	Indian hedgehog homolog precursor	216					cell-cell signaling|intein-mediated protein splicing|proteolysis	extracellular space|plasma membrane	cholesterol binding|patched binding|peptidase activity			breast(1)	1		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220344783	220344783	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220344783T>C	uc010fwg.2	+	25	5263	c.5263T>C	c.(5263-5265)TAC>CAC	p.Y1755H		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1755	Protein kinase 1.				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)														---	---	---	---
OBSL1	23363	broad.mit.edu	37	2	220420875	220420875	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220420875G>A	uc010fwk.2	-	14	4533	c.4476C>T	c.(4474-4476)CAC>CAT	p.H1492H	OBSL1_uc002vmh.1_Silent_p.H391H|OBSL1_uc010zli.1_Silent_p.H299H|OBSL1_uc010fwl.1_Silent_p.H967H	NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1	1492	Ig-like 12.				cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)														---	---	---	---
MOGAT1	116255	broad.mit.edu	37	2	223553100	223553100	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223553100A>G	uc010fws.1	+	2	180	c.132A>G	c.(130-132)ATA>ATG	p.I44M	MOGAT1_uc010fwt.1_Missense_Mutation_p.I4M	NM_058165	NP_477513	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	44	Helical; (Potential).				glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			breast(1)	1		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	233113941	233113941	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233113941A>G	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596			DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
ANO7	50636	broad.mit.edu	37	2	242129505	242129505	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242129505G>T	uc002wax.2	+	2	292	c.189G>T	c.(187-189)GAG>GAT	p.E63D	ANO7_uc002waw.2_Missense_Mutation_p.E63D	NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	63	Cytoplasmic (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3																		---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4706906	4706906	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4706906G>A	uc003bqa.2	+	17	1987	c.1639G>A	c.(1639-1641)GCT>ACT	p.A547T	ITPR1_uc010hca.1_Missense_Mutation_p.A532T|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Missense_Mutation_p.A532T	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	547	Cytoplasmic (Potential).				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)														---	---	---	---
THUMPD3	25917	broad.mit.edu	37	3	9412739	9412739	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9412739T>C	uc003bro.3	+						LOC440944_uc003brm.2_Intron|THUMPD3_uc003brn.3_Intron	NM_001114092	NP_001107564			THUMP domain containing 3								methyltransferase activity|protein binding|RNA binding			ovary(1)	1	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)														---	---	---	---
TATDN2	9797	broad.mit.edu	37	3	10312453	10312453	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10312453A>T	uc003bvg.2	+	4	2168	c.1587A>T	c.(1585-1587)GAA>GAT	p.E529D	TATDN2_uc003bvf.2_Missense_Mutation_p.E529D|TATDN2_uc011atr.1_Missense_Mutation_p.E529D|TATDN2_uc011ats.1_RNA|TATDN2_uc011att.1_RNA	NM_014760	NP_055575	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	529						nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding			pancreas(2)	2																		---	---	---	---
GHRL	51738	broad.mit.edu	37	3	10328491	10328491	+	Silent	SNP	G	A	A	rs149447194	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10328491G>A	uc010hdf.2	-	4	366	c.231C>T	c.(229-231)AAC>AAT	p.N77N	GHRLOS_uc011atw.1_Intron|GHRLOS_uc011atx.1_Intron|GHRLOS_uc011aty.1_Intron|GHRLOS_uc011atz.1_Intron|GHRLOS_uc011aua.1_Intron|GHRLOS_uc010hdl.2_Intron|GHRLOS_uc011aub.1_Intron|GHRLOS_uc010hdm.2_Intron|GHRLOS_uc011auc.1_Intron|GHRLOS_uc011aud.1_Intron|GHRLOS_uc011aue.1_Intron|GHRLOS_uc011auf.1_Intron|GHRLOS_uc011aug.1_Intron|GHRLOS_uc011auh.1_Intron|GHRLOS_uc011aui.1_Intron|GHRLOS_uc011auj.1_Intron|GHRLOS_uc010hdn.2_Intron|GHRL_uc010hda.1_RNA|GHRL_uc010hdb.1_RNA|GHRL_uc003bvj.1_Intron|GHRL_uc003bvk.3_RNA|GHRL_uc010hdk.2_Silent_p.N64N|GHRL_uc010hdc.2_Silent_p.N26N|GHRL_uc010hdd.2_Intron|GHRL_uc010hde.2_Silent_p.N76N|GHRL_uc010hdi.2_Silent_p.N77N|GHRL_uc010hdh.2_Silent_p.N77N|GHRL_uc010hdj.2_Silent_p.N65N|GHRLOS_uc011auk.1_5'Flank	NM_016362	NP_057446	Q9UBU3	GHRL_HUMAN	ghrelin/obestatin isoform 1 preproprotein	77					actin polymerization or depolymerization|activation of MAPK activity|adult feeding behavior|cartilage development|cortisol secretion|decidualization|dendrite development|elevation of cytosolic calcium ion concentration|G-protein coupled receptor protein signaling pathway|glucose metabolic process|growth hormone secretion|hormone-mediated signaling pathway|negative regulation of angiogenesis|negative regulation of circadian sleep/wake cycle, REM sleep|negative regulation of endothelial cell proliferation|negative regulation of inflammatory response|negative regulation of interleukin-1 beta production|negative regulation of interleukin-6 biosynthetic process|negative regulation of tumor necrosis factor biosynthetic process|positive regulation of appetite|positive regulation of circadian sleep/wake cycle, non-REM sleep|positive regulation of corticotropin secretion|positive regulation of cortisol secretion|positive regulation of growth hormone secretion|positive regulation of insulin secretion|positive regulation of synaptogenesis|response to estrogen stimulus	axon|endoplasmic reticulum lumen|extracellular space|stored secretory granule	ghrelin receptor binding|growth hormone-releasing hormone activity|protein tyrosine kinase activator activity			ovary(1)	1																OREG0015386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10442673	10442673	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10442673G>A	uc003bvt.2	-	5	1184	c.745C>T	c.(745-747)CGC>TGC	p.R249C	ATP2B2_uc003bvv.2_Missense_Mutation_p.R249C|ATP2B2_uc003bvw.2_Missense_Mutation_p.R249C|ATP2B2_uc010hdp.2_Missense_Mutation_p.R249C|ATP2B2_uc010hdo.2_5'UTR	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	249	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12645699	12645699	+	Missense_Mutation	SNP	G	A	A	rs80338796		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12645699G>A	uc003bxf.3	-	7	1185	c.770C>T	c.(769-771)TCG>TTG	p.S257L	RAF1_uc011aut.1_Missense_Mutation_p.S42L|RAF1_uc011auu.1_Missense_Mutation_p.S175L	NM_002880	NP_002871	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog	257			S -> L (in NS5 and LEOPARD2; shows in vitro greater kinase activity and enhanced ERK activation than wild-type).		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				---	---	---	---
FBLN2	2199	broad.mit.edu	37	3	13679190	13679190	+	Missense_Mutation	SNP	C	T	T	rs112412824		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13679190C>T	uc011avb.1	+	17	3451	c.3326C>T	c.(3325-3327)GCG>GTG	p.A1109V	FBLN2_uc011auz.1_Missense_Mutation_p.A1135V|FBLN2_uc011ava.1_Missense_Mutation_p.A1156V|FBLN2_uc011avc.1_Missense_Mutation_p.A1156V	NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor	1109	Domain III.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)															---	---	---	---
OXSM	54995	broad.mit.edu	37	3	25835771	25835771	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25835771C>T	uc003cdn.2	+	3	1273	c.1166C>T	c.(1165-1167)GCT>GTT	p.A389V	OXSM_uc011awp.1_Missense_Mutation_p.A114V|OXSM_uc010hfh.2_Missense_Mutation_p.A306V	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	389					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2																		---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38936341	38936341	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38936341G>A	uc011ays.1	-	15	2717	c.2518C>T	c.(2518-2520)CGC>TGC	p.R840C	SCN11A_uc010hhn.1_5'UTR	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	840					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49568877	49568877	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49568877G>A	uc003cxc.3	+	3	1351	c.933G>A	c.(931-933)CGG>CGA	p.R311R		NM_004393	NP_004384	Q14118	DAG1_HUMAN	dystroglycan 1 preproprotein	311	Required for laminin recognition.				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)														---	---	---	---
HYAL3	8372	broad.mit.edu	37	3	50332546	50332546	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50332546T>G	uc003czd.1	-	2	761	c.488A>C	c.(487-489)CAG>CCG	p.Q163P	HYAL3_uc003czc.1_Missense_Mutation_p.Q163P|HYAL3_uc003cze.1_Intron|HYAL3_uc003czf.1_Intron|HYAL3_uc003czg.1_Missense_Mutation_p.Q163P	NM_003549	NP_003540	O43820	HYAL3_HUMAN	hyaluronoglucosaminidase 3 precursor	163					carbohydrate metabolic process	extracellular region|lysosome	hyalurononglucosaminidase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)														---	---	---	---
TLR9	54106	broad.mit.edu	37	3	52257641	52257641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52257641G>A	uc003dda.1	-	2	1325	c.691C>T	c.(691-693)CGC>TGC	p.R231C	TLR9_uc003ddb.2_Missense_Mutation_p.R328C	NM_017442	NP_059138	Q9NR96	TLR9_HUMAN	toll-like receptor 9 isoform A precursor	231	LRR 7.|Extracellular (Potential).				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity			large_intestine(2)|skin(2)	4				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)													---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57493550	57493550	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57493550A>G	uc003dit.2	-	8	898	c.717T>C	c.(715-717)ATT>ATC	p.I239I	DNAH12_uc003diu.2_Silent_p.I239I	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1	239	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
NFKBIZ	64332	broad.mit.edu	37	3	101574616	101574616	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101574616C>A	uc003dvp.2	+	9	1809	c.1694C>A	c.(1693-1695)GCT>GAT	p.A565D	NFKBIZ_uc003dvo.2_Missense_Mutation_p.A465D|NFKBIZ_uc010hpo.2_Missense_Mutation_p.A465D|NFKBIZ_uc003dvq.2_Missense_Mutation_p.A443D	NM_031419	NP_113607	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene	565	Interaction with NFKB1/p50 (By similarity).|ANK 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2																		---	---	---	---
GUCA1C	9626	broad.mit.edu	37	3	108634981	108634981	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108634981G>A	uc003dxj.2	-	3	503	c.435C>T	c.(433-435)AAC>AAT	p.N145N	GUCA1C_uc003dxk.2_Silent_p.N145N	NM_005459	NP_005450	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	145	3.|EF-hand 4.				signal transduction|visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0																		---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111766802	111766802	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111766802G>A	uc010hqb.2	+	5	739	c.569G>A	c.(568-570)AGC>AAC	p.S190N	TMPRSS7_uc011bhr.1_Missense_Mutation_p.S45N	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	316	Extracellular (Potential).|CUB 1.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
CASR	846	broad.mit.edu	37	3	121981056	121981056	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121981056C>T	uc003eev.3	+	4	1546	c.1174C>T	c.(1174-1176)CGA>TGA	p.R392*	CASR_uc003eew.3_Nonsense_Mutation_p.R392*	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	392	Extracellular (Potential).				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)													---	---	---	---
HEG1	57493	broad.mit.edu	37	3	124732092	124732092	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124732092G>A	uc003ehs.3	-	6	2399	c.2331C>T	c.(2329-2331)GAC>GAT	p.D777D	HEG1_uc011bke.1_Silent_p.D877D	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	777	Extracellular (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(2)	2																		---	---	---	---
KY	339855	broad.mit.edu	37	3	134348463	134348463	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134348463G>A	uc010hty.2	-	4	399	c.337C>T	c.(337-339)CGT>TGT	p.R113C	KY_uc011blw.1_Missense_Mutation_p.R113C|KY_uc011blx.1_Missense_Mutation_p.R92C|KY_uc003eqs.1_Missense_Mutation_p.R133C	NM_178554	NP_848649	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	113						cytoskeleton|Z disc	peptidase activity			ovary(2)	2																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134960059	134960059	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134960059G>A	uc003eqt.2	+	13	2636	c.2416G>A	c.(2416-2418)GAC>AAC	p.D806N	EPHB1_uc003equ.2_Missense_Mutation_p.D367N	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	806	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
PLSCR5	389158	broad.mit.edu	37	3	146307501	146307501	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146307501T>C	uc003ewb.2	-	6	1720	c.716A>G	c.(715-717)CAT>CGT	p.H239R	PLSCR5_uc010hvb.2_Missense_Mutation_p.H227R|PLSCR5_uc010hvc.2_Missense_Mutation_p.H239R	NM_001085420	NP_001078889	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	239											0																		---	---	---	---
ZIC1	7545	broad.mit.edu	37	3	147128660	147128660	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147128660C>T	uc003ewe.2	+	1	1480	c.761C>T	c.(760-762)ACG>ATG	p.T254M		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	254	C2H2-type 1; atypical.				behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151093846	151093846	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151093846T>C	uc003eyp.2	+	26	3830	c.3792T>C	c.(3790-3792)CCT>CCC	p.P1264P	MED12L_uc011bnz.1_Silent_p.P1124P|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Silent_p.P427P	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1264					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155206450	155206450	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155206450A>G	uc011bok.1	-	19	2779	c.2502T>C	c.(2500-2502)CCT>CCC	p.P834P	PLCH1_uc011boj.1_Silent_p.P834P|PLCH1_uc011bol.1_Silent_p.P816P	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	834					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)															---	---	---	---
LRRC31	79782	broad.mit.edu	37	3	169572662	169572662	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169572662C>A	uc003fgc.1	-	6	1007	c.930G>T	c.(928-930)AAG>AAT	p.K310N	LRRC31_uc010hwp.1_Missense_Mutation_p.K254N	NM_024727	NP_079003	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	310										ovary(2)|skin(1)	3	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)															---	---	---	---
IGF2BP2	10644	broad.mit.edu	37	3	185407313	185407313	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185407313G>T	uc003fpo.2	-	6	586	c.507C>A	c.(505-507)GCC>GCA	p.A169A	IGF2BP2_uc010hyi.2_Silent_p.A112A|IGF2BP2_uc010hyj.2_Silent_p.A106A|IGF2BP2_uc010hyk.2_Silent_p.A33A|IGF2BP2_uc010hyl.2_Silent_p.A106A|IGF2BP2_uc003fpp.2_Silent_p.A169A|IGF2BP2_uc003fpq.2_Silent_p.A174A	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	169					anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
HTT	3064	broad.mit.edu	37	4	3136230	3136230	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3136230A>G	uc011bvq.1	+	20	2747	c.2602A>G	c.(2602-2604)ACA>GCA	p.T868A		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	866					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)														---	---	---	---
TADA2B	93624	broad.mit.edu	37	4	7056038	7056038	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7056038G>A	uc003gjw.3	+	2	671	c.520G>A	c.(520-522)GAG>AAG	p.E174K	TADA2B_uc010idi.2_Missense_Mutation_p.E99K	NM_152293	NP_689506	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2 (ADA2 homolog,	174					regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|zinc ion binding				0																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47695111	47695111	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47695111A>G	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																		---	---	---	---
SRP72	6731	broad.mit.edu	37	4	57354156	57354156	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57354156G>T	uc003hbv.2	+	12	1241	c.1201G>T	c.(1201-1203)GAG>TAG	p.E401*	SRP72_uc010ihe.2_Nonsense_Mutation_p.E340*|SRP72_uc003hbw.1_Nonsense_Mutation_p.E162*	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa	401					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)																	---	---	---	---
REST	5978	broad.mit.edu	37	4	57797557	57797557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57797557G>A	uc003hch.2	+	4	2880	c.2533G>A	c.(2533-2535)GTT>ATT	p.V845I	REST_uc003hci.2_Missense_Mutation_p.V845I|REST_uc010ihf.2_Missense_Mutation_p.V519I	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	845					cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	74005551	74005551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74005551G>A	uc003hgp.2	-	15	2899	c.2782C>T	c.(2782-2784)CGG>TGG	p.R928W	ANKRD17_uc003hgo.2_Missense_Mutation_p.R815W|ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Missense_Mutation_p.R928W|ANKRD17_uc011cbd.1_Missense_Mutation_p.R493W	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	928	Gln-rich.				interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
HELQ	113510	broad.mit.edu	37	4	84370031	84370031	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84370031T>G	uc003hom.2	-	3	1275	c.1096A>C	c.(1096-1098)ACC>CCC	p.T366P	HELQ_uc010ikb.2_Missense_Mutation_p.T366P|HELQ_uc003hol.3_RNA|HELQ_uc010ikc.2_RNA|HELQ_uc003hon.1_Missense_Mutation_p.T260P	NM_133636	NP_598375	Q8TDG4	HELQ_HUMAN	DNA helicase HEL308	366	ATP (By similarity).|Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|breast(1)|skin(1)	3													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
NKX6-1	4825	broad.mit.edu	37	4	85414492	85414492	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85414492C>T	uc003hpa.1	-	3	1060	c.1054G>A	c.(1054-1056)GGC>AGC	p.G352S		NM_006168	NP_006159	P78426	NKX61_HUMAN	NK6 transcription factor related, locus 1	352	Poly-Gly.|Involved in DNA-binding (By similarity).				detection of glucose|negative regulation of transcription from RNA polymerase II promoter|organ morphogenesis|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|type B pancreatic cell maturation	nucleus					0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)														---	---	---	---
SPARCL1	8404	broad.mit.edu	37	4	88414917	88414917	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88414917G>A	uc010ikm.2	-	5	1607	c.1035C>T	c.(1033-1035)GGC>GGT	p.G345G	SPARCL1_uc011cdc.1_Silent_p.G220G|SPARCL1_uc003hqs.3_Silent_p.G345G|SPARCL1_uc011cdd.1_Silent_p.G220G|SPARCL1_uc003hqt.2_Silent_p.G345G	NM_001128310	NP_001121782	Q14515	SPRL1_HUMAN	SPARC-like 1 precursor	345					signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00118)														---	---	---	---
DMP1	1758	broad.mit.edu	37	4	88583274	88583274	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88583274G>A	uc003hqv.2	+	6	448	c.344G>A	c.(343-345)GGT>GAT	p.G115D	DMP1_uc003hqw.2_Missense_Mutation_p.G99D	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1	115					biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)														---	---	---	---
RG9MTD2	93587	broad.mit.edu	37	4	100479282	100479282	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100479282C>T	uc003huy.2	-	3	585	c.272G>A	c.(271-273)CGT>CAT	p.R91H	RG9MTD2_uc003huz.3_Missense_Mutation_p.R91H|RG9MTD2_uc003hva.3_Missense_Mutation_p.R91H	NM_152292	NP_689505	Q8TBZ6	RG9D2_HUMAN	RNA (guanine-9-) methyltransferase domain	91							methyltransferase activity			ovary(2)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.7e-08)														---	---	---	---
MTTP	4547	broad.mit.edu	37	4	100521713	100521713	+	Intron	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100521713T>G	uc003hvc.3	+						MTTP_uc011cej.1_Intron	NM_000253	NP_000244			microsomal triglyceride transfer protein large						lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)													---	---	---	---
CFI	3426	broad.mit.edu	37	4	110681532	110681532	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110681532G>A	uc003hzr.3	-	6	985	c.777C>T	c.(775-777)TGC>TGT	p.C259C	CFI_uc003hzq.2_Silent_p.C56C|CFI_uc011cft.1_Silent_p.C259C|CFI_uc003hzs.3_Silent_p.C259C	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein	259	LDL-receptor class A 2.				complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)														---	---	---	---
QRFPR	84109	broad.mit.edu	37	4	122257967	122257967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122257967G>A	uc010inj.1	-	3	935	c.556C>T	c.(556-558)CTT>TTT	p.L186F	QRFPR_uc010ink.1_RNA|QRFPR_uc003ids.2_Missense_Mutation_p.L186F	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	186	Extracellular (Potential).					plasma membrane	neuropeptide Y receptor activity				0																		---	---	---	---
ANXA5	308	broad.mit.edu	37	4	122602903	122602903	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122602903T>C	uc003idu.3	-	5	387	c.317A>G	c.(316-318)AAT>AGT	p.N106S	ANXA5_uc003idv.3_Missense_Mutation_p.N106S|ANXA5_uc003idw.3_RNA|ANXA5_uc010inm.2_Missense_Mutation_p.N106S|ANXA5_uc010inn.2_Missense_Mutation_p.N46S|ANXA5_uc010ino.2_Intron	NM_001154	NP_001145	P08758	ANXA5_HUMAN	annexin 5	106	Annexin 2.				anti-apoptosis|blood coagulation|negative regulation of coagulation|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity			ovary(1)	1																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123192637	123192637	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123192637G>A	uc003ieh.2	+	45	8003	c.7958G>A	c.(7957-7959)CGA>CAA	p.R2653Q	KIAA1109_uc003iel.1_Missense_Mutation_p.R588Q|KIAA1109_uc003iek.2_Missense_Mutation_p.R1272Q	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	2653					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	142950071	142950071	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142950071G>A	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143094842	143094842	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143094842A>G	uc003iix.3	-	17	1897	c.1302T>C	c.(1300-1302)TCT>TCC	p.S434S	INPP4B_uc003iiw.3_Silent_p.S434S|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Silent_p.S249S|INPP4B_uc011cho.1_RNA|INPP4B_uc011chp.1_Silent_p.S305S	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	434					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149356493	149356493	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149356493C>T	uc003ilj.3	-	2	1854	c.1520G>A	c.(1519-1521)AGC>AAC	p.S507N	NR3C2_uc003ilk.3_Missense_Mutation_p.S507N|NR3C2_uc010iph.2_RNA	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	507	Modulating.				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)													---	---	---	---
RBM46	166863	broad.mit.edu	37	4	155720669	155720669	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155720669T>C	uc003ioo.2	+	4	1528	c.1355T>C	c.(1354-1356)TTA>TCA	p.L452S	RBM46_uc011cim.1_Missense_Mutation_p.L452S|RBM46_uc003iop.1_Missense_Mutation_p.L452S	NM_144979	NP_659416	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	452							nucleotide binding|RNA binding			central_nervous_system(1)|skin(1)	2	all_hematologic(180;0.24)	Renal(120;0.0854)																---	---	---	---
CPE	1363	broad.mit.edu	37	4	166388881	166388881	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166388881C>T	uc003irg.3	+	3	823	c.546C>T	c.(544-546)GCC>GCT	p.A182A		NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein	182					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)													---	---	---	---
PDLIM3	27295	broad.mit.edu	37	4	186429447	186429447	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186429447T>C	uc003ixw.3	-						PDLIM3_uc003ixx.3_Intron|PDLIM3_uc010isi.2_Intron	NM_014476	NP_055291			PDZ and LIM domain protein 3 isoform a							sarcomere	zinc ion binding			ovary(2)	2		all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171)														---	---	---	---
TLR3	7098	broad.mit.edu	37	4	186997931	186997931	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186997931T>C	uc003iyq.2	+	2	259	c.158T>C	c.(157-159)ATA>ACA	p.I53T		NM_003265	NP_003256	O15455	TLR3_HUMAN	toll-like receptor 3 precursor	53	LRR 1.|Lumenal (Potential).				activation of NF-kappaB-inducing kinase activity|cellular response to mechanical stimulus|defense response to bacterium|defense response to virus|detection of virus|hyperosmotic response|I-kappaB phosphorylation|inflammatory response|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of osteoclast differentiation|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|toll-like receptor 3 signaling pathway	endoplasmic reticulum membrane|endosome membrane|integral to plasma membrane	double-stranded RNA binding|transmembrane receptor activity			ovary(2)|prostate(1)|lung(1)|breast(1)	5		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;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)														---	---	---	---
PLEKHG4B	153478	broad.mit.edu	37	5	144953	144953	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144953G>T	uc003jak.2	+	4	805	c.755G>T	c.(754-756)CGG>CTG	p.R252L		NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G	252					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(2)	2			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)														---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13928247	13928247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13928247C>T	uc003jfd.2	-	3	275	c.233G>A	c.(232-234)CGA>CAA	p.R78Q	DNAH5_uc003jfe.1_RNA	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	78	Stem (By similarity).				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				---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15936714	15936714	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15936714C>T	uc003jfn.1	+	4	1376	c.895C>T	c.(895-897)CAG>TAG	p.Q299*		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	299	LRR 5.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
AMACR	23600	broad.mit.edu	37	5	34004802	34004802	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34004802C>T	uc003jig.2	-	3	511	c.429G>A	c.(427-429)CCG>CCA	p.P143P	AMACR_uc003jih.2_Intron|AMACR_uc003jii.2_Silent_p.P143P|AMACR_uc003jij.2_Silent_p.P143P|AMACR_uc003jil.1_Silent_p.P143P|AMACR_uc003jik.1_Intron	NM_014324	NP_055139	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase isoform 1	143					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0																		---	---	---	---
CKMT2	1160	broad.mit.edu	37	5	80550869	80550869	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80550869C>T	uc003khc.3	+	6	747	c.505C>T	c.(505-507)CGC>TGC	p.R169C	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Missense_Mutation_p.R169C|CKMT2_uc003khd.3_Missense_Mutation_p.R169C|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	169	Phosphagen kinase C-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)													---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90000297	90000297	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90000297G>T	uc003kju.2	+	36	8474	c.8378G>T	c.(8377-8379)AGG>ATG	p.R2793M	GPR98_uc003kjt.2_Missense_Mutation_p.R499M|GPR98_uc003kjv.2_Missense_Mutation_p.R393M	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2793	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)														---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132560966	132560966	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132560966G>A	uc003kyn.1	-	10	1406	c.1188C>T	c.(1186-1188)AGC>AGT	p.S396S	FSTL4_uc003kym.1_Missense_Mutation_p.A3V	NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor	396	Ig-like 2.					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)															---	---	---	---
VDAC1	7416	broad.mit.edu	37	5	133316414	133316414	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133316414A>G	uc003kyp.1	-						VDAC1_uc003kyq.1_Intron|VDAC1_uc003kyr.1_Intron	NM_003374	NP_003365			voltage-dependent anion channel 1						apoptosis|interspecies interaction between organisms	mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex	porin activity|protein binding|voltage-gated anion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)													---	---	---	---
NEUROG1	4762	broad.mit.edu	37	5	134871302	134871302	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134871302T>C	uc003lax.2	-	1	338	c.79A>G	c.(79-81)ACC>GCC	p.T27A		NM_006161	NP_006152	Q92886	NGN1_HUMAN	neurogenin 1	27					positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter	nucleus	chromatin binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
IL9	3578	broad.mit.edu	37	5	135231384	135231384	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135231384C>T	uc003lbb.1	-							NM_000590	NP_000581			interleukin 9 precursor						immune response|inflammatory response|positive regulation of cell proliferation|positive regulation of interleukin-5 biosynthetic process	extracellular space	cytokine activity|cytokine receptor binding|growth factor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KLHL3	26249	broad.mit.edu	37	5	136964109	136964109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136964109C>T	uc010jek.2	-	13	1912	c.1468G>A	c.(1468-1470)GGA>AGA	p.G490R	KLHL3_uc011cyc.1_Missense_Mutation_p.G225R|KLHL3_uc003lbr.3_Missense_Mutation_p.G408R|KLHL3_uc011cyd.1_RNA	NM_017415	NP_059111	Q9UH77	KLHL3_HUMAN	kelch-like 3	490	Kelch 4.					cytoplasm|cytoskeleton	actin binding|structural molecule activity				0		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)														---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140182453	140182453	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182453C>T	uc003lhf.2	+	1	1671	c.1671C>T	c.(1669-1671)GAC>GAT	p.D557D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.D557D	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	557	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)															---	---	---	---
PCDHA11	56138	broad.mit.edu	37	5	140250586	140250586	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140250586C>T	uc003lia.2	+	1	2756	c.1898C>T	c.(1897-1899)ACG>ATG	p.T633M	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_uc011dae.1_Missense_Mutation_p.T633M	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	633	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140264030	140264030	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140264030C>T	uc003lif.2	+	1	2177	c.2177C>T	c.(2176-2178)CCG>CTG	p.P726L	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_Missense_Mutation_p.P726L|PCDHA13_uc003lid.2_Missense_Mutation_p.P726L	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	726	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB3	56132	broad.mit.edu	37	5	140482030	140482030	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140482030C>T	uc003lio.2	+	1	1797	c.1797C>T	c.(1795-1797)AAC>AAT	p.N599N	uc003lin.2_5'Flank	NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	599	Extracellular (Potential).|Cadherin 6.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB5	26167	broad.mit.edu	37	5	140515675	140515675	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140515675C>T	uc003liq.2	+	1	876	c.659C>T	c.(658-660)CCG>CTG	p.P220L		NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5 precursor	220	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB16	57717	broad.mit.edu	37	5	140563517	140563517	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140563517C>T	uc003liv.2	+	1	2538	c.1383C>T	c.(1381-1383)CGC>CGT	p.R461R	PCDHB16_uc010jfw.1_Silent_p.R133R	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	461	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding	p.R461H(1)		ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB10	56126	broad.mit.edu	37	5	140573508	140573508	+	Silent	SNP	C	T	T	rs112214830	byFrequency;by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573508C>T	uc003lix.2	+	1	1557	c.1383C>T	c.(1381-1383)CGC>CGT	p.R461R		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	461	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB14	56122	broad.mit.edu	37	5	140604527	140604527	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140604527G>A	uc003ljb.2	+	1	1450	c.1450G>A	c.(1450-1452)GCC>ACC	p.A484T	PCDHB14_uc011dal.1_Missense_Mutation_p.A331T	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	484	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140724254	140724254	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140724254C>T	uc003ljm.1	+	1	654	c.654C>T	c.(652-654)GGC>GGT	p.G218G	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Silent_p.G218G	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	218	Extracellular (Potential).|Cadherin 2.				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)															---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140724659	140724659	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140724659A>G	uc003ljm.1	+	1	1059	c.1059A>G	c.(1057-1059)ACA>ACG	p.T353T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Silent_p.T113T|PCDHGA3_uc011dap.1_Silent_p.T353T	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	353	Cadherin 4.|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)															---	---	---	---
TCERG1	10915	broad.mit.edu	37	5	145838686	145838686	+	Silent	SNP	G	A	A	rs143032772		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145838686G>A	uc003lob.2	+	4	718	c.678G>A	c.(676-678)CAG>CAA	p.Q226Q	TCERG1_uc003loc.2_Silent_p.Q226Q|TCERG1_uc011dbt.1_Silent_p.Q226Q	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1	226	Potential.|Ala/Gln-rich.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
ARHGEF37	389337	broad.mit.edu	37	5	148980674	148980674	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148980674C>T	uc003lra.1	+	3	254	c.190C>T	c.(190-192)CCG>TCG	p.P64S		NM_001001669	NP_001001669	A1IGU5	ARH37_HUMAN	hypothetical protein LOC389337	64	DH.				regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
GABRA6	2559	broad.mit.edu	37	5	161113339	161113339	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161113339C>T	uc003lyu.2	+	2	480	c.142C>T	c.(142-144)CGG>TGG	p.R48W		NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	48	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)										TCGA Ovarian(5;0.080)			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167673994	167673994	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167673994A>G	uc010jjd.2	+	27	6023	c.6023A>G	c.(6022-6024)CAG>CGG	p.Q2008R	ODZ2_uc003lzr.3_Missense_Mutation_p.Q1778R|ODZ2_uc003lzt.3_Missense_Mutation_p.Q1381R|ODZ2_uc010jje.2_Missense_Mutation_p.Q1272R	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)														---	---	---	---
KCNMB1	3779	broad.mit.edu	37	5	169805926	169805926	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169805926C>T	uc003maq.1	-	4	758	c.358G>A	c.(358-360)GTG>ATG	p.V120M	KCNIP1_uc003map.2_Intron	NM_004137	NP_004128	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated	120	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)														---	---	---	---
CPEB4	80315	broad.mit.edu	37	5	173359456	173359456	+	Missense_Mutation	SNP	G	A	A	rs142106976		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173359456G>A	uc003mcs.3	+	3	2617	c.1211G>A	c.(1210-1212)CGT>CAT	p.R404H	CPEB4_uc010jju.1_Intron|CPEB4_uc010jjv.2_Intron|CPEB4_uc011dfg.1_Intron|CPEB4_uc003mct.3_Missense_Mutation_p.R22H|CPEB4_uc003mcu.3_Intron	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding	404							nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
MAML1	9794	broad.mit.edu	37	5	179195922	179195922	+	Silent	SNP	C	T	T	rs141541345	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179195922C>T	uc003mkm.2	+	3	2066	c.1803C>T	c.(1801-1803)TCC>TCT	p.S601S	MAML1_uc003mkn.1_Silent_p.S601S	NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1	601					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12122268	12122268	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12122268G>A	uc003nac.2	+	4	2419	c.2240G>A	c.(2239-2241)CGG>CAG	p.R747Q	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	747					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	21231094	21231094	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21231094C>T	uc003ndc.1	+	16	1738	c.1564C>T	c.(1564-1566)CTT>TTT	p.L522F	CDKAL1_uc003ndd.1_Missense_Mutation_p.L522F|CDKAL1_uc003nde.1_Missense_Mutation_p.L431F|CDKAL1_uc003ndf.1_Missense_Mutation_p.L35F|CDKAL1_uc003ndg.2_RNA	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein	522					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)															---	---	---	---
HIST1H4F	8361	broad.mit.edu	37	6	26240923	26240923	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26240923G>A	uc003nhe.1	+	1	270	c.270G>A	c.(268-270)GCG>GCA	p.A90A		NM_003540	NP_003531	P62805	H4_HUMAN	histone cluster 1, H4f	90					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)																---	---	---	---
FKSG83	83954	broad.mit.edu	37	6	27293382	27293382	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27293382C>T	uc010jqt.2	+	1	805	c.321C>T	c.(319-321)AAC>AAT	p.N107N	FKSG83_uc010jqs.1_3'UTR	NM_032030	NP_114419	Q3KNW7	Q3KNW7_HUMAN	FKSG83	107						integral to membrane	pheromone receptor activity				0																		---	---	---	---
OR10C1	442194	broad.mit.edu	37	6	29408587	29408587	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29408587C>T	uc011dlp.1	+	1	795	c.795C>T	c.(793-795)TAC>TAT	p.Y265Y	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C,	265	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
TRIM10	10107	broad.mit.edu	37	6	30128498	30128498	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30128498T>C	uc003npo.3	-	1	214	c.138A>G	c.(136-138)ATA>ATG	p.I46M	TRIM10_uc003npn.2_Missense_Mutation_p.I46M|TRIM15_uc010jrx.2_5'Flank	NM_006778	NP_006769	Q9UDY6	TRI10_HUMAN	tripartite motif-containing 10 isoform 1	46	RING-type.					cytoplasm	zinc ion binding				0																		---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31324494	31324494	+	Missense_Mutation	SNP	A	G	G	rs9266161		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31324494A>G	uc003nth.2	-	2	368	c.314T>C	c.(313-315)CTG>CCG	p.L105P	HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_Missense_Mutation_p.L105P|HLA-B_uc003ntg.1_5'Flank|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_5'Flank|HLA-B_uc010jso.2_Missense_Mutation_p.L77P	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B	105	Alpha-1.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34029800	34029800	+	Missense_Mutation	SNP	C	T	T	rs144674222		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34029800C>T	uc003oir.3	-	3	912	c.742G>A	c.(742-744)GTG>ATG	p.V248M	GRM4_uc011dsn.1_Missense_Mutation_p.V248M|GRM4_uc010jvh.2_Missense_Mutation_p.V248M|GRM4_uc010jvi.2_Translation_Start_Site|GRM4_uc003oio.2_Translation_Start_Site|GRM4_uc003oip.2_RNA|GRM4_uc011dsl.1_Missense_Mutation_p.V108M|GRM4_uc003oiq.2_Missense_Mutation_p.V115M|GRM4_uc011dsm.1_Missense_Mutation_p.V79M	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	248	Extracellular (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	54095592	54095592	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54095592G>A	uc003pcg.3	+	11	1307	c.1194G>A	c.(1192-1194)CTG>CTA	p.L398L	C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Silent_p.L933L	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523	398						nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)																	---	---	---	---
DDX43	55510	broad.mit.edu	37	6	74111617	74111617	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74111617A>C	uc003pgw.2	+	4	816	c.472A>C	c.(472-474)AGC>CGC	p.S158R	DDX43_uc011dyn.1_RNA	NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	158						intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75853001	75853001	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75853001A>G	uc003phs.2	-	26	4960	c.4794T>C	c.(4792-4794)GTT>GTC	p.V1598V	COL12A1_uc003pht.2_Silent_p.V434V	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	1598	Fibronectin type-III 11.				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																		---	---	---	---
MCHR2	84539	broad.mit.edu	37	6	100368816	100368816	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100368816C>T	uc003pqh.1	-	6	1338	c.1023G>A	c.(1021-1023)TAG>TAA	p.*341*	MCHR2_uc003pqi.1_Silent_p.*341*	NM_001040179	NP_001035269	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	341						integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
PREP	5550	broad.mit.edu	37	6	105825262	105825262	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105825262G>A	uc003prc.2	-	3	456	c.253C>T	c.(253-255)CGG>TGG	p.R85W		NM_002726	NP_002717	P48147	PPCE_HUMAN	prolyl endopeptidase	85					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)													---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107956521	107956521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107956521G>A	uc003prx.2	+	6	2977	c.2473G>A	c.(2473-2475)GGC>AGC	p.G825S		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	825							metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
FYN	2534	broad.mit.edu	37	6	111995792	111995792	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111995792G>T	uc003pvj.2	-	12	1655	c.1315C>A	c.(1315-1317)CTG>ATG	p.L439M	FYN_uc003pvi.2_Missense_Mutation_p.L384M|FYN_uc003pvk.2_Missense_Mutation_p.L439M|FYN_uc003pvh.2_Missense_Mutation_p.L436M	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a	439	Protein kinase.				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)													---	---	---	---
RSPH4A	345895	broad.mit.edu	37	6	116949263	116949263	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116949263C>T	uc003pxe.2	+	3	1538	c.1393C>T	c.(1393-1395)CGA>TGA	p.R465*	RSPH4A_uc010kee.2_Nonsense_Mutation_p.R465*	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1	465					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0														Kartagener_syndrome				---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119345681	119345681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119345681T>C	uc003pyj.2	-	2	805	c.457A>G	c.(457-459)ACC>GCC	p.T153A	FAM184A_uc003pyk.3_Missense_Mutation_p.T33A|FAM184A_uc003pyl.3_Missense_Mutation_p.T33A	NM_024581	NP_078857	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 1	153	Potential.									ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
GJA1	2697	broad.mit.edu	37	6	121768435	121768435	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121768435C>T	uc003pyr.2	+	2	692	c.442C>T	c.(442-444)CGA>TGA	p.R148*	GJA1_uc011ebo.1_Nonsense_Mutation_p.R49*|GJA1_uc011ebp.1_Intron	NM_000165	NP_000156	P17302	CXA1_HUMAN	connexin 43	148	Cytoplasmic (Potential).				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)													---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132185669	132185669	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132185669T>G	uc011ecf.1	+	10	1069	c.1049T>G	c.(1048-1050)ATT>AGT	p.I350S	ENPP1_uc003qcy.2_5'UTR	NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	350	Phosphodiesterase.|Extracellular (Potential).				3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)													---	---	---	---
TAAR1	134864	broad.mit.edu	37	6	132966641	132966641	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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)													---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146673425	146673425	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146673425A>T	uc010khw.1	+	5	1696	c.1226A>T	c.(1225-1227)AAG>ATG	p.K409M	GRM1_uc010khv.1_Missense_Mutation_p.K409M|GRM1_uc003qll.2_Missense_Mutation_p.K409M|GRM1_uc011edz.1_Missense_Mutation_p.K409M|GRM1_uc011eea.1_Missense_Mutation_p.K409M	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	409	Extracellular (Potential).	Glutamate (By similarity).			synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152740715	152740715	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152740715T>A	uc010kiw.2	-	40	6012	c.5410A>T	c.(5410-5412)ACT>TCT	p.T1804S	SYNE1_uc003qot.3_Missense_Mutation_p.T1811S|SYNE1_uc003qou.3_Missense_Mutation_p.T1804S|SYNE1_uc010kjb.1_Missense_Mutation_p.T1787S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1804	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152740727	152740727	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152740727G>A	uc010kiw.2	-	40	6000	c.5398C>T	c.(5398-5400)CAA>TAA	p.Q1800*	SYNE1_uc003qot.3_Nonsense_Mutation_p.Q1807*|SYNE1_uc003qou.3_Nonsense_Mutation_p.Q1800*|SYNE1_uc010kjb.1_Nonsense_Mutation_p.Q1783*	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1800	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SNX9	51429	broad.mit.edu	37	6	158349639	158349639	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158349639A>C	uc003qqv.1	+	12	1366	c.1193A>C	c.(1192-1194)AAG>ACG	p.K398T		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	398	BAR.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)														---	---	---	---
UNC93A	54346	broad.mit.edu	37	6	167721271	167721271	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167721271G>A	uc003qvq.2	+	7	1156	c.981G>A	c.(979-981)GCG>GCA	p.A327A	UNC93A_uc003qvr.2_Silent_p.A285A	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	327	Helical; (Potential).					integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168294542	168294542	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168294542G>A	uc003qwd.2	+	9	1317	c.1175G>A	c.(1174-1176)GGG>GAG	p.G392E	MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Missense_Mutation_p.G393E|MLLT4_uc003qwf.2_Intron	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	393					adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
SUN1	23353	broad.mit.edu	37	7	889612	889612	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:889612G>A	uc011jvp.1	+						GET4_uc003sjj.1_5'Flank|SUN1_uc003sje.1_3'UTR|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron|SUN1_uc003sjg.2_Intron|SUN1_uc011jvr.1_Intron|SUN1_uc003sji.2_Silent_p.S38S|SUN1_uc003sjk.2_5'Flank	NM_001130965	NP_001124437			unc-84 homolog A isoform a						cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1525090	1525090	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1525090G>A	uc003skn.2	-	23	3093	c.2992C>T	c.(2992-2994)CTT>TTT	p.L998F	INTS1_uc003skp.1_Missense_Mutation_p.L345F	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	998					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5269378	5269378	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5269378C>T	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron|WIPI2_uc003soa.2_Intron|WIPI2_uc003sob.2_Intron	NM_015610	NP_056425			WD repeat domain, phosphoinositide interacting 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)														---	---	---	---
USP42	84132	broad.mit.edu	37	7	6196693	6196693	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6196693G>T	uc011jwo.1	+	16	4073	c.3950G>T	c.(3949-3951)AGG>ATG	p.R1317M	USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1317					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)														---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21939646	21939646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21939646C>T	uc003svc.2	+	82	13263	c.13232C>T	c.(13231-13233)ACG>ATG	p.T4411M		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	4411					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				---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30088859	30088859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30088859C>T	uc003tam.1	+	5	549	c.458C>T	c.(457-459)ACT>ATT	p.T153I	PLEKHA8_uc003tao.2_Missense_Mutation_p.T37I|PLEKHA8_uc003tap.1_Missense_Mutation_p.T153I|PLEKHA8_uc003tan.2_Missense_Mutation_p.T153I	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A	153					protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4																		---	---	---	---
SFRP4	6424	broad.mit.edu	37	7	37956066	37956066	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37956066T>A	uc003tfo.3	-	1	460	c.74A>T	c.(73-75)GAG>GTG	p.E25V		NM_003014	NP_003005	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related  protein 4 precursor	25	FZ.				brain development|cell differentiation|decidualization|embryo development|epithelium development|gonad development|mammary gland involution|menstrual cycle phase|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell proliferation|negative regulation of JNK cascade|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of sodium-dependent phosphate transport|phosphate ion homeostasis|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epidermal cell differentiation|positive regulation of gene expression|positive regulation of receptor internalization|vasculature development|Wnt receptor signaling pathway	cell surface|cytoplasm|extracellular space|nucleus	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(1)	1																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43532713	43532713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43532713G>A	uc003tid.1	+	19	3976	c.3371G>A	c.(3370-3372)CGC>CAC	p.R1124H	HECW1_uc011kbi.1_Missense_Mutation_p.R1090H	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	1124					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity	p.R1103H(1)		ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
STK17A	9263	broad.mit.edu	37	7	43664348	43664348	+	Silent	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43664348T>A	uc003tih.2	+	7	1303	c.1152T>A	c.(1150-1152)TCT>TCA	p.S384S	C7orf44_uc003til.2_Intron|C7orf44_uc003tii.2_Intron|C7orf44_uc003tij.2_Intron|C7orf44_uc010kxu.1_Intron|C7orf44_uc003tik.2_Intron	NM_004760	NP_004751	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	384					apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			skin(2)	2																		---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47408673	47408673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47408673C>T	uc003tnv.2	-	17	1937	c.1570G>A	c.(1570-1572)GGT>AGT	p.G524S	TNS3_uc003tnw.2_Missense_Mutation_p.G524S	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	524						focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
POM121L12	285877	broad.mit.edu	37	7	53104085	53104085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53104085G>A	uc003tpz.2	+	1	737	c.721G>A	c.(721-723)GGC>AGC	p.G241S		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	241											0																		---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66648139	66648139	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66648139G>A	uc003tvn.2	+	14	1874	c.1725G>A	c.(1723-1725)ACG>ACA	p.T575T	TYW1_uc010lai.2_RNA|TYW1_uc011kef.1_Silent_p.T189T	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	575					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
WBSCR28	135886	broad.mit.edu	37	7	73279550	73279550	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73279550T>C	uc003tzk.2	+	2	336	c.300T>C	c.(298-300)GCT>GCC	p.A100A	RFC2_uc011kfa.1_Intron|WBSCR28_uc003tzl.2_5'UTR	NM_182504	NP_872310	Q6UE05	WBS28_HUMAN	hypothetical protein LOC135886	100						integral to membrane				breast(1)	1		Lung NSC(55;0.159)																---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98581951	98581951	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98581951A>G	uc003upp.2	+	60	9479	c.9270A>G	c.(9268-9270)GCA>GCG	p.A3090A	TRRAP_uc011kis.1_Silent_p.A3061A|TRRAP_uc003upr.2_Silent_p.A2778A	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3090	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
MEPCE	56257	broad.mit.edu	37	7	100028448	100028448	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100028448C>T	uc003uuw.2	+	1	920	c.807C>T	c.(805-807)CAC>CAT	p.H269H	ZCWPW1_uc003uut.2_5'Flank|ZCWPW1_uc011kjr.1_5'Flank|ZCWPW1_uc003uuu.1_5'Flank|ZCWPW1_uc011kjt.1_5'Flank|ZCWPW1_uc011kju.1_5'Flank|MEPCE_uc003uuv.2_5'UTR	NM_019606	NP_062552	Q7L2J0	MEPCE_HUMAN	bin3, bicoid-interacting 3	269							methyltransferase activity			upper_aerodigestive_tract(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
AGFG2	3268	broad.mit.edu	37	7	100162615	100162615	+	3'UTR	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100162615C>T	uc003uvf.2	+	12					AGFG2_uc010lgy.2_3'UTR	NM_006076	NP_006067			ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
GIGYF1	64599	broad.mit.edu	37	7	100281778	100281778	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100281778C>T	uc003uwg.1	-	15	2742	c.1733G>A	c.(1732-1734)CGC>CAC	p.R578H		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	578	Gln-rich.									large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)																	---	---	---	---
SLC12A9	56996	broad.mit.edu	37	7	100463572	100463572	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100463572T>C	uc003uwp.2	+	14	2232	c.2090T>C	c.(2089-2091)GTG>GCG	p.V697A	SLC12A9_uc011kki.1_Missense_Mutation_p.V228A|SLC12A9_uc003uwr.2_Missense_Mutation_p.V433A|SLC12A9_uc003uws.2_Missense_Mutation_p.V228A|SLC12A9_uc003uwt.2_Missense_Mutation_p.V433A|SLC12A9_uc003uwv.2_Missense_Mutation_p.V228A|TRIP6_uc010lhk.1_5'Flank|TRIP6_uc003uww.2_5'Flank	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride	697	Extracellular (Potential).					integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
RELN	5649	broad.mit.edu	37	7	103293015	103293015	+	Silent	SNP	C	T	T	rs138532222		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103293015C>T	uc003vca.2	-	14	1906	c.1746G>A	c.(1744-1746)ACG>ACA	p.T582T	RELN_uc010liz.2_Silent_p.T582T	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	582					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)														---	---	---	---
ORC5L	5001	broad.mit.edu	37	7	103844608	103844608	+	Silent	SNP	C	T	T	rs142978774		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103844608C>T	uc003vcb.2	-	2	258	c.147G>A	c.(145-147)ACG>ACA	p.T49T	ORC5L_uc011klp.1_5'UTR|ORC5L_uc003vcc.2_Silent_p.T49T|ORC5L_uc003vcd.2_Silent_p.T49T	NM_002553	NP_002544	O43913	ORC5_HUMAN	origin recognition complex subunit 5 isoform 1	49					cell cycle checkpoint|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	cytoplasm|nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|identical protein binding				0																		---	---	---	---
NAMPT	10135	broad.mit.edu	37	7	105891627	105891627	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105891627T>C	uc003vdq.2	-	11	1686	c.1378A>G	c.(1378-1380)ACT>GCT	p.T460A		NM_005746	NP_005737	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	460					cell-cell signaling|NAD biosynthetic process|nicotinamide metabolic process|positive regulation of cell proliferation|positive regulation of nitric-oxide synthase biosynthetic process|signal transduction|water-soluble vitamin metabolic process	cytosol	cytokine activity|nicotinamide phosphoribosyltransferase activity|nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			large_intestine(1)	1																		---	---	---	---
RBM28	55131	broad.mit.edu	37	7	127953322	127953322	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127953322C>T	uc003vmp.2	-	18	2166	c.2051G>A	c.(2050-2052)CGG>CAG	p.R684Q	RBM28_uc003vmo.2_Missense_Mutation_p.R226Q|RBM28_uc011koj.1_Missense_Mutation_p.R543Q	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	684					mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
ZYX	7791	broad.mit.edu	37	7	143079975	143079975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143079975G>A	uc003wcw.2	+	5	738	c.583G>A	c.(583-585)GCA>ACA	p.A195T	ZYX_uc011ktd.1_Missense_Mutation_p.A38T|ZYX_uc003wcx.2_Missense_Mutation_p.A195T|ZYX_uc011kte.1_Missense_Mutation_p.A164T|ZYX_uc011ktf.1_Missense_Mutation_p.A38T	NM_001010972	NP_001010972	Q15942	ZYX_HUMAN	zyxin	195					cell adhesion|cell-cell signaling|interspecies interaction between organisms|signal transduction	cell-cell adherens junction|cytoplasm|focal adhesion|integral to plasma membrane|nucleus|stress fiber	protein binding|zinc ion binding				0	Melanoma(164;0.205)																	---	---	---	---
EPHA1	2041	broad.mit.edu	37	7	143091370	143091370	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143091370T>C	uc003wcz.2	-	15	2506	c.2419A>G	c.(2419-2421)AGC>GGC	p.S807G		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1 precursor	807	Protein kinase.|Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)																---	---	---	---
OR2F1	26211	broad.mit.edu	37	7	143658000	143658000	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143658000T>C	uc003wds.1	+	1	981	c.937T>C	c.(937-939)TCA>CCA	p.S313P		NM_012369	NP_036501	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F,	313	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	Melanoma(164;0.0903)																	---	---	---	---
ZNF862	643641	broad.mit.edu	37	7	149544928	149544928	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149544928A>G	uc010lpn.2	+	4	538	c.346A>G	c.(346-348)AGT>GGT	p.S116G	ZNF862_uc003wgm.2_RNA	NM_001099220	NP_001092690	O60290	ZN862_HUMAN	zinc finger protein 862	116					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|nucleic acid binding|protein dimerization activity			skin(1)	1																		---	---	---	---
ZNF775	285971	broad.mit.edu	37	7	150094965	150094965	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150094965C>T	uc003whf.1	+	3	1521	c.1396C>T	c.(1396-1398)CGC>TGC	p.R466C	LOC728743_uc003whg.2_5'Flank	NM_173680	NP_775951	Q96BV0	ZN775_HUMAN	zinc finger protein 775	466	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
ASB10	136371	broad.mit.edu	37	7	150878058	150878058	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150878058C>T	uc003wjm.1	-	3	1333	c.1207G>A	c.(1207-1209)GCC>ACC	p.A403T	ASB10_uc003wjl.1_Missense_Mutation_p.A403T|ASB10_uc003wjn.1_Missense_Mutation_p.A343T	NM_001142459	NP_001135931	Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box-containing 10	358	ANK 7.				intracellular signal transduction						0			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
SMARCD3	6604	broad.mit.edu	37	7	150937306	150937306	+	Silent	SNP	C	T	T	rs1050109		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150937306C>T	uc003wjs.2	-	10	1166	c.1065G>A	c.(1063-1065)ACG>ACA	p.T355T	SMARCD3_uc003wjt.2_Silent_p.T342T|SMARCD3_uc003wju.2_Silent_p.T342T	NM_001003801	NP_001003801	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin	355					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)														---	---	---	---
NOM1	64434	broad.mit.edu	37	7	156762298	156762298	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156762298C>T	uc003wmy.2	+	11	2499	c.2484C>T	c.(2482-2484)AAC>AAT	p.N828N		NM_138400	NP_612409	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	828					RNA metabolic process	nucleolus	protein binding				0	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)														---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8176270	8176270	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8176270C>T	uc003wsh.3	-	5	3615	c.3615G>A	c.(3613-3615)CTG>CTA	p.L1205L		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	1205	Protein kinase.						ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11282089	11282089	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11282089G>A	uc010lry.1	-	3	1058	c.438C>T	c.(436-438)GGC>GGT	p.G146G	C8orf12_uc003wtu.2_Intron|C8orf12_uc003wtv.2_Intron|FAM167A_uc003wtw.2_Silent_p.G146G	NM_053279	NP_444509	Q96KS9	F167A_HUMAN	hypothetical protein LOC83648	146	Potential.										0																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12957700	12957700	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12957700T>G	uc003wwm.2	-	9	2590	c.2146A>C	c.(2146-2148)ATC>CTC	p.I716L	DLC1_uc003wwk.1_Missense_Mutation_p.I279L|DLC1_uc003wwl.1_Missense_Mutation_p.I313L|DLC1_uc011kxx.1_Missense_Mutation_p.I205L	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	716					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
VPS37A	137492	broad.mit.edu	37	8	17125856	17125856	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17125856A>G	uc003wxj.2	+	3	643	c.290A>G	c.(289-291)TAT>TGT	p.Y97C	VPS37A_uc003wxk.2_Missense_Mutation_p.Y72C	NM_152415	NP_689628	Q8NEZ2	VP37A_HUMAN	hepatocellular carcinoma related protein 1	97					cellular membrane organization|endosome transport|protein transport	centrosome|late endosome membrane|nucleus					0				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)														---	---	---	---
SLC18A1	6570	broad.mit.edu	37	8	20008200	20008200	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20008200A>G	uc011kyq.1	-	12	1542	c.1071T>C	c.(1069-1071)GGT>GGC	p.G357G	SLC18A1_uc003wzl.2_Silent_p.G144G|SLC18A1_uc003wzm.2_Silent_p.G357G|SLC18A1_uc011kyr.1_Silent_p.G357G|SLC18A1_uc003wzn.2_Silent_p.G325G|SLC18A1_uc010ltf.2_RNA|SLC18A1_uc003wzo.2_Silent_p.G325G	NM_001135691	NP_001129163	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine),	357	Helical; (Potential).				neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25199933	25199933	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25199933T>G	uc003xeg.2	+	25	2664	c.2527T>G	c.(2527-2529)TTC>GTC	p.F843V	DOCK5_uc010luf.1_RNA|DOCK5_uc003xeh.1_Missense_Mutation_p.F557V|DOCK5_uc003xei.2_Missense_Mutation_p.F413V|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	843						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)														---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56435947	56435947	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56435947G>A	uc003xsf.2	+	3	1146	c.1114G>A	c.(1114-1116)GTC>ATC	p.V372I		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	372	Helical; (Potential).					integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
VCPIP1	80124	broad.mit.edu	37	8	67547095	67547095	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67547095C>T	uc003xwn.2	-	3	3569	c.3310G>A	c.(3310-3312)GCC>ACC	p.A1104T		NM_025054	NP_079330	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex	1104					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)															---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72184073	72184073	+	Missense_Mutation	SNP	G	A	A	rs142104253		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72184073G>A	uc003xys.3	-	9	1173	c.886C>T	c.(886-888)CGT>TGT	p.R296C	EYA1_uc003xyr.3_Missense_Mutation_p.R291C|EYA1_uc003xyt.3_Missense_Mutation_p.R263C|EYA1_uc010lzf.2_Missense_Mutation_p.R223C|EYA1_uc003xyu.2_Missense_Mutation_p.R296C|EYA1_uc011lfe.1_Missense_Mutation_p.R290C|EYA1_uc003xyv.2_Missense_Mutation_p.R174C	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	296					double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|protein sumoylation|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)															---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76456180	76456180	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76456180C>T	uc003yaq.2	+	3	382	c.112C>T	c.(112-114)CGC>TGC	p.R38C	HNF4G_uc003yap.1_Missense_Mutation_p.R38C|HNF4G_uc003yar.2_Missense_Mutation_p.R75C	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	38	Nuclear receptor.				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)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77764274	77764274	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77764274C>A	uc003yav.2	+	10	5369	c.4982C>A	c.(4981-4983)GCC>GAC	p.A1661D	ZFHX4_uc003yau.1_Missense_Mutation_p.A1706D|ZFHX4_uc003yaw.1_Missense_Mutation_p.A1661D	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1661	Gln-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
CPNE3	8895	broad.mit.edu	37	8	87560586	87560586	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87560586T>C	uc003ydv.2	+	12	1099	c.937T>C	c.(937-939)TAC>CAC	p.Y313H	CPNE3_uc003ydw.1_Missense_Mutation_p.Y29H	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III	313	VWFA.				lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
PDP1	54704	broad.mit.edu	37	8	94934286	94934286	+	5'UTR	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94934286C>T	uc003yge.2	+	2					PDP1_uc003ygf.2_Missense_Mutation_p.A25V|PDP1_uc010max.2_Missense_Mutation_p.A25V|PDP1_uc011lgm.1_5'UTR|PDP1_uc011lgn.1_Missense_Mutation_p.A59V	NM_018444	NP_060914			pyruvate dehyrogenase phosphatase catalytic						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106573672	106573672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106573672C>T	uc003ymd.2	+	4	406	c.383C>T	c.(382-384)CCG>CTG	p.P128L		NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	128					blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110453038	110453038	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110453038T>C	uc003yne.2	+	33	4160	c.4056T>C	c.(4054-4056)GGT>GGC	p.G1352G		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1352	Extracellular (Potential).|IPT/TIG 7.				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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114186058	114186058	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114186058C>T	uc003ynu.2	-	4	761	c.602G>A	c.(601-603)CGC>CAC	p.R201H	CSMD3_uc003ynt.2_Missense_Mutation_p.R161H|CSMD3_uc011lhx.1_Missense_Mutation_p.R201H|CSMD3_uc010mcx.1_Missense_Mutation_p.R201H	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	201	Extracellular (Potential).|Sushi 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)			---	---	---	---
TNFRSF11B	4982	broad.mit.edu	37	8	119945336	119945336	+	Silent	SNP	G	A	A	rs144654126	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119945336G>A	uc003yon.3	-	2	557	c.234C>T	c.(232-234)GAC>GAT	p.D78D	TNFRSF11B_uc010mdc.1_RNA	NM_002546	NP_002537	O00300	TR11B_HUMAN	osteoprotegerin precursor	78	TNFR-Cys 2.				apoptosis|skeletal system development		cytokine activity|receptor activity			central_nervous_system(2)	2	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)															---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122627103	122627103	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122627103T>C	uc003yph.2	-	4	1443	c.905A>G	c.(904-906)CAA>CGA	p.Q302R		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	302	Cytoplasmic (Potential).					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)															---	---	---	---
FAM83A	84985	broad.mit.edu	37	8	124195533	124195533	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124195533A>G	uc003ypv.2	+	2	2451	c.437A>G	c.(436-438)AAC>AGC	p.N146S	FAM83A_uc003ypw.2_Missense_Mutation_p.N146S|FAM83A_uc003ypy.2_Missense_Mutation_p.N146S|FAM83A_uc003ypx.2_Missense_Mutation_p.N146S|FAM83A_uc003ypz.2_Missense_Mutation_p.N146S	NM_032899	NP_116288	Q86UY5	FA83A_HUMAN	hypothetical protein LOC84985 isoform a	146										ovary(3)|skin(1)	4	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139158276	139158276	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139158276G>A	uc003yuy.2	-	15	3637	c.3466C>T	c.(3466-3468)CGG>TGG	p.R1156W	FAM135B_uc003yux.2_Missense_Mutation_p.R1057W|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.R718W|FAM135B_uc003yvb.2_Missense_Mutation_p.P683L	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1156										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)			---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144663405	144663405	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144663405G>A	uc011lki.1	-	4	552	c.283C>T	c.(283-285)CGT>TGT	p.R95C	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.R437C|EEF1D_uc003yyq.1_Missense_Mutation_p.R511C|EEF1D_uc011lkj.1_Missense_Mutation_p.R460C|EEF1D_uc003yyr.2_Missense_Mutation_p.R461C|EEF1D_uc003yyt.2_Missense_Mutation_p.R461C|EEF1D_uc011lkk.1_Missense_Mutation_p.R95C|EEF1D_uc003yys.2_Missense_Mutation_p.R95C|EEF1D_uc003yyv.2_Missense_Mutation_p.R71C|EEF1D_uc003yyu.2_Missense_Mutation_p.R95C|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	95					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)															---	---	---	---
VPS28	51160	broad.mit.edu	37	8	145649364	145649364	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145649364C>T	uc003zcr.1	-						VPS28_uc003zcs.1_Intron|VPS28_uc003zct.1_Missense_Mutation_p.R203Q	NM_016208	NP_057292			vacuolar protein sorting 28 isoform 1						cellular membrane organization|endosome transport|negative regulation of protein ubiquitination|protein transport	cytosol|late endosome membrane|plasma membrane	protein binding				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;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)															---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	332451	332451	+	Silent	SNP	G	A	A	rs139297216		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:332451G>A	uc003zgf.2	+	10	1210	c.1098G>A	c.(1096-1098)ACG>ACA	p.T366T	DOCK8_uc011lls.1_Silent_p.T366T|DOCK8_uc010mgu.2_5'UTR|DOCK8_uc010mgv.2_Silent_p.T298T|DOCK8_uc003zgg.2_Silent_p.T298T|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	366	DHR-1.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	414890	414890	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:414890C>T	uc003zgf.2	+	29	3751	c.3639C>T	c.(3637-3639)GCC>GCT	p.A1213A	DOCK8_uc010mgu.2_Silent_p.A515A|DOCK8_uc010mgv.2_Silent_p.A1113A|DOCK8_uc003zgk.2_Silent_p.A671A	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1213					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
INSL6	11172	broad.mit.edu	37	9	5185595	5185595	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5185595C>T	uc003zix.2	-	1	24	c.8G>A	c.(7-9)CGG>CAG	p.R3Q		NM_007179	NP_009110	Q9Y581	INSL6_HUMAN	insulin-like 6 precursor	3						extracellular region	hormone activity				0	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)														---	---	---	---
PSIP1	11168	broad.mit.edu	37	9	15468838	15468838	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15468838G>A	uc003zlv.3	-	14	1540	c.1210C>T	c.(1210-1212)CGG>TGG	p.R404W	PSIP1_uc003zlw.3_Missense_Mutation_p.R404W	NM_033222	NP_150091	O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1 isoform 2	404					initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent	cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin	activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity			breast(1)	1				GBM - Glioblastoma multiforme(50;2.38e-06)														---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17462902	17462902	+	Intron	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17462902T>G	uc003zmz.2	+						CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208			centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
CNTFR	1271	broad.mit.edu	37	9	34564807	34564807	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34564807G>A	uc003zup.1	-	4	390	c.109C>T	c.(109-111)CGC>TGC	p.R37C	CNTFR_uc003zuq.1_Missense_Mutation_p.R37C	NM_147164	NP_671693	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	37	Ig-like C2-type.				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)														---	---	---	---
KIAA1539	80256	broad.mit.edu	37	9	35105674	35105674	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35105674C>T	uc003zwl.2	-						STOML2_uc003zwh.2_5'Flank|STOML2_uc003zwi.2_5'Flank|STOML2_uc003zwj.2_5'Flank|STOML2_uc011lou.1_5'Flank|STOML2_uc003zwk.2_5'Flank|KIAA1539_uc003zwm.2_Intron|KIAA1539_uc003zwn.2_Intron|KIAA1539_uc003zwo.2_Intron	NM_025182	NP_079458			hypothetical protein LOC80256							nucleus				ovary(2)	2	all_epithelial(49;0.217)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
RUSC2	9853	broad.mit.edu	37	9	35557979	35557979	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35557979G>A	uc003zww.2	+	6	3307	c.3052G>A	c.(3052-3054)GGG>AGG	p.G1018R	RUSC2_uc010mkq.2_RNA|RUSC2_uc003zwx.3_Missense_Mutation_p.G1018R	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1018						cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35717226	35717226	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35717226G>A	uc003zxt.2	-	19	2729	c.2375C>T	c.(2374-2376)GCT>GTT	p.A792V		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	792					axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
FGD3	89846	broad.mit.edu	37	9	95738590	95738590	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95738590G>T	uc004asw.2	+	3	680	c.52G>T	c.(52-54)GGG>TGG	p.G18W	FGD3_uc004asx.2_Missense_Mutation_p.G18W|FGD3_uc004asz.2_Missense_Mutation_p.G18W	NM_001083536	NP_001077005	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	18					actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(1)|breast(1)	2																		---	---	---	---
C9orf129	445577	broad.mit.edu	37	9	96080715	96080715	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96080715C>T	uc010mre.2	-	5	920	c.556G>A	c.(556-558)GCC>ACC	p.A186T	WNK2_uc011lud.1_3'UTR|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_3'UTR	NM_001098808	NP_001092278	Q5T035	CI129_HUMAN	hypothetical protein LOC445577	186										ovary(1)	1																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96437269	96437269	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96437269G>T	uc004aub.2	+	19	2834	c.2687G>T	c.(2686-2688)AGG>ATG	p.R896M	PHF2_uc011lug.1_Missense_Mutation_p.R779M|PHF2_uc004auc.2_Missense_Mutation_p.R316M	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	896					liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107581856	107581856	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107581856A>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)													---	---	---	---
PTPN3	5774	broad.mit.edu	37	9	112207535	112207535	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112207535A>T	uc004bed.2	-	7	563	c.451T>A	c.(451-453)TCC>ACC	p.S151T	PTPN3_uc004beb.2_Missense_Mutation_p.S20T|PTPN3_uc004bec.2_Missense_Mutation_p.S20T|PTPN3_uc010mtu.2_RNA|PTPN3_uc011lwg.1_Missense_Mutation_p.S151T|PTPN3_uc011lwh.1_Missense_Mutation_p.S42T	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type	151	FERM.				negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114159310	114159310	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114159310C>A	uc004bfe.1	-	26	3310	c.3310G>T	c.(3310-3312)GGA>TGA	p.G1104*		NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124441061	124441061	+	Splice_Site	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124441061G>A	uc004bln.2	+	2	213	c.144_splice	c.e2+1	p.T48_splice		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																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124535255	124535255	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124535255G>A	uc004bln.2	+	12	2433	c.2364G>A	c.(2362-2364)GCG>GCA	p.A788A	DAB2IP_uc004blo.2_Silent_p.A692A|DAB2IP_uc004blp.2_Silent_p.A221A	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	816					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																		---	---	---	---
SH2D3C	10044	broad.mit.edu	37	9	130502091	130502091	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130502091T>C	uc004bsc.2	-	11	2419	c.2277A>G	c.(2275-2277)CCA>CCG	p.P759P	SH2D3C_uc010mxo.2_Silent_p.P599P|SH2D3C_uc004bry.2_Silent_p.P601P|SH2D3C_uc004brz.3_Silent_p.P405P|SH2D3C_uc011mak.1_Silent_p.P405P|SH2D3C_uc004bsa.2_Silent_p.P602P|SH2D3C_uc004bsb.2_Silent_p.P691P	NM_170600	NP_733745	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C isoform a	759	Ras-GEF.				JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
WDR34	89891	broad.mit.edu	37	9	131396974	131396974	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131396974A>G	uc004bvq.1	-	7	1332	c.1208T>C	c.(1207-1209)TTC>TCC	p.F403S	WDR34_uc004bvs.1_Missense_Mutation_p.F394S|WDR34_uc004bvr.1_Missense_Mutation_p.F375S	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34	403	WD 3.					cytoplasm				central_nervous_system(2)|skin(1)	3																		---	---	---	---
UCK1	83549	broad.mit.edu	37	9	134400578	134400578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134400578T>C	uc004cay.2	-	7	784	c.683A>G	c.(682-684)CAG>CGG	p.Q228R	UCK1_uc010mzk.2_Missense_Mutation_p.Q219R|UCK1_uc004cba.2_Silent_p.P196P|UCK1_uc004caz.2_RNA	NM_031432	NP_113620	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1 isoform a	228					pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137710590	137710590	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137710590G>A	uc004cfe.2	+	55	4701	c.4319G>A	c.(4318-4320)CGA>CAA	p.R1440Q		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1440	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137716476	137716476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137716476C>T	uc004cfe.2	+	62	5111	c.4729C>T	c.(4729-4731)CCA>TCA	p.P1577S	uc004cff.2_Intron	NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1577	Nonhelical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137727007	137727007	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137727007A>G	uc004cfe.2	+	65	5709	c.5327A>G	c.(5326-5328)TAT>TGT	p.Y1776C	uc004cff.2_Intron	NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1776	Fibrillar collagen NC1.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
ZMYND11	10771	broad.mit.edu	37	10	298390	298390	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:298390A>G	uc010pzt.1	+	15	2217	c.1789A>G	c.(1789-1791)ACC>GCC	p.T597A	ZMYND11_uc010pzu.1_Missense_Mutation_p.T597A|ZMYND11_uc010pzv.1_Missense_Mutation_p.T542A|ZMYND11_uc010pzw.1_Missense_Mutation_p.T512A|ZMYND11_uc001ifm.2_Missense_Mutation_p.T543A|ZMYND11_uc009xhg.2_Missense_Mutation_p.T580A|ZMYND11_uc009xhh.2_Missense_Mutation_p.T471A|ZMYND11_uc010pzy.1_Missense_Mutation_p.T449A	NM_006624	NP_006615	Q15326	ZMY11_HUMAN	zinc finger, MYND domain containing 11 isoform	557	MYND-type.				cell cycle|cell proliferation|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
PFKP	5214	broad.mit.edu	37	10	3155656	3155656	+	Silent	SNP	C	T	T	rs148946725		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3155656C>T	uc001igp.2	+	13	1353	c.1317C>T	c.(1315-1317)GAC>GAT	p.D439D	PFKP_uc001igq.2_Silent_p.D431D|PFKP_uc009xhr.2_Silent_p.D401D|PFKP_uc009xhs.1_Silent_p.D223D|PFKP_uc009xht.2_Silent_p.D177D|PFKP_uc009xhu.2_Translation_Start_Site	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	439					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)														---	---	---	---
UPF2	26019	broad.mit.edu	37	10	11997436	11997436	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11997436C>T	uc001ila.2	-	13	3119	c.2645G>A	c.(2644-2646)CGA>CAA	p.R882Q	UPF2_uc001ilb.2_Missense_Mutation_p.R882Q|UPF2_uc001ilc.2_Missense_Mutation_p.R882Q|UPF2_uc009xiz.1_Missense_Mutation_p.R882Q	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	882	Sufficient for interaction with UPF3A and UPF3B.|MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
CDC123	8872	broad.mit.edu	37	10	12291660	12291660	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12291660C>T	uc001ill.2	+	12	1211	c.927C>T	c.(925-927)GAC>GAT	p.D309D	CDC123_uc001ilm.2_Silent_p.D321D	NM_006023	NP_006014	O75794	CD123_HUMAN	cell division cycle 123	309					cell cycle arrest|cell division|positive regulation of cell proliferation|regulation of mitotic cell cycle	cytoplasm				central_nervous_system(1)	1																		---	---	---	---
BEND7	222389	broad.mit.edu	37	10	13541863	13541863	+	Silent	SNP	C	T	T	rs113945389	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13541863C>T	uc001imm.2	-	3	504	c.207G>A	c.(205-207)CCG>CCA	p.P69P	BEND7_uc001imo.3_Silent_p.P69P	NM_152751	NP_689964	Q8N7W2	BEND7_HUMAN	BEN domain containing 7 isoform 1	121							protein binding			ovary(1)|breast(1)	2																		---	---	---	---
PRPF18	8559	broad.mit.edu	37	10	13639639	13639639	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13639639C>T	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																		---	---	---	---
HSPA14	51182	broad.mit.edu	37	10	14896175	14896175	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14896175G>A	uc001inf.2	+	9	927	c.786G>A	c.(784-786)ACG>ACA	p.T262T		NM_016299	NP_057383	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14 isoform 1	262					'de novo' cotranslational protein folding	cytosol	ATP binding|protein binding			ovary(2)|breast(2)|lung(1)	5																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20290849	20290849	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20290849T>C	uc001iqg.1	+	2	895	c.258T>C	c.(256-258)TCT>TCC	p.S86S	PLXDC2_uc001iqh.1_Silent_p.S86S	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor	86	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29811362	29811362	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29811362G>A	uc001iut.1	-	16	4119	c.3366C>T	c.(3364-3366)AGC>AGT	p.S1122S	SVIL_uc010qdw.1_Silent_p.S20S|SVIL_uc001iuu.1_Silent_p.S696S	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1122					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)																---	---	---	---
GPRIN2	9721	broad.mit.edu	37	10	47000018	47000018	+	Missense_Mutation	SNP	C	T	T	rs114077038	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47000018C>T	uc001jec.2	+	3	1273	c.1138C>T	c.(1138-1140)CGG>TGG	p.R380W	GPRIN2_uc010qfq.1_Missense_Mutation_p.R143W	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth	380											0																		---	---	---	---
GDF10	2662	broad.mit.edu	37	10	48429407	48429407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48429407C>T	uc001jfb.2	-	2	935	c.479G>A	c.(478-480)CGC>CAC	p.R160H	GDF10_uc009xnp.2_Missense_Mutation_p.R159H|GDF10_uc009xnq.1_Missense_Mutation_p.R160H	NM_004962	NP_004953	P55107	BMP3B_HUMAN	growth differentiation factor 10 precursor	160					growth|skeletal system development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			lung(1)|central_nervous_system(1)	2																		---	---	---	---
C10orf128	170371	broad.mit.edu	37	10	50374941	50374941	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50374941G>T	uc001jhn.3	-	3	237	c.211C>A	c.(211-213)CTG>ATG	p.L71M	C10orf128_uc001jhl.3_RNA|C10orf128_uc001jhm.3_Missense_Mutation_p.L71M|C10orf128_uc010qgo.1_Missense_Mutation_p.L71M|C10orf128_uc001jho.3_Missense_Mutation_p.L71M	NM_001010863	NP_001010863	Q5T292	CJ128_HUMAN	hypothetical protein LOC170371 precursor	71	Cytoplasmic (Potential).					integral to membrane				lung(1)	1																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	62021641	62021641	+	Silent	SNP	C	T	T	rs146748344		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62021641C>T	uc001jky.2	-	7	966	c.774G>A	c.(772-774)GCG>GCA	p.A258A	ANK3_uc010qih.1_Silent_p.A241A|ANK3_uc001jkz.3_Silent_p.A252A|ANK3_uc001jlb.1_5'UTR	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	258	ANK 6.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64136621	64136621	+	Silent	SNP	C	T	T	rs150802191		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64136621C>T	uc001jmc.2	+	2	984	c.669C>T	c.(667-669)GAC>GAT	p.D223D	ZNF365_uc001jly.3_Silent_p.D238D|ZNF365_uc001jmb.3_Silent_p.D223D|ZNF365_uc001jlz.3_Silent_p.D223D|ZNF365_uc001jma.3_Intron	NM_199451	NP_955523	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform C	Error:Variant_position_missing_in_Q70YC4_after_alignment										ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70525719	70525719	+	Silent	SNP	G	A	A	rs149316365		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70525719G>A	uc001joo.2	+	17	2300	c.2181G>A	c.(2179-2181)CCG>CCA	p.P727P	CCAR1_uc001jol.1_RNA|CCAR1_uc001jom.1_Silent_p.P532P|CCAR1_uc009xpx.1_Silent_p.P701P|CCAR1_uc001jon.1_Silent_p.P673P|CCAR1_uc010qiz.1_Silent_p.P712P|CCAR1_uc010qja.1_Silent_p.P712P|CCAR1_uc010qjb.1_RNA	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1	727	Glu-rich.				apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
VCL	7414	broad.mit.edu	37	10	75877825	75877825	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75877825T>C	uc001jwd.2	+	22	3397	c.3303T>C	c.(3301-3303)TCT>TCC	p.S1101S	VCL_uc009xrr.2_Silent_p.S782S|VCL_uc001jwe.2_Silent_p.S1033S|VCL_uc010qkz.1_Silent_p.S294S	NM_014000	NP_054706	P18206	VINC_HUMAN	vinculin isoform meta-VCL	1101	C-terminal tail.				adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
LRIT2	340745	broad.mit.edu	37	10	85984651	85984651	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85984651C>T	uc001kcy.2	-	2	338	c.330G>A	c.(328-330)CTG>CTA	p.L110L	LRIT2_uc010qmc.1_Silent_p.L110L	NM_001017924	NP_001017924	A6NDA9	LRIT2_HUMAN	leucine rich repeat containing 22 precursor	110	LRR 2.					integral to membrane				ovary(2)	2																		---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93622745	93622745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93622745G>A	uc001khp.2	+	27	3787	c.3490G>A	c.(3490-3492)GTC>ATC	p.V1164I		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1164	PARP catalytic.				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)																---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98764484	98764484	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98764484C>A	uc001kmw.2	-	33	3928	c.3676G>T	c.(3676-3678)GAC>TAC	p.D1226Y		NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	1226	Laminin G-like.				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)														---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99683148	99683148	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99683148G>A	uc001kou.1	-	4	787	c.431C>T	c.(430-432)ACG>ATG	p.T144M	CRTAC1_uc001kov.2_Missense_Mutation_p.T133M|CRTAC1_uc001kot.1_Translation_Start_Site	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	144	FG-GAP 2; atypical.					proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)														---	---	---	---
SEC31B	25956	broad.mit.edu	37	10	102247423	102247423	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102247423T>G	uc001krc.1	-	26	3592	c.3490A>C	c.(3490-3492)ATG>CTG	p.M1164L	SEC31B_uc010qpo.1_Missense_Mutation_p.M1163L|SEC31B_uc001krd.1_Missense_Mutation_p.M701L|SEC31B_uc001krf.1_Missense_Mutation_p.M597L|SEC31B_uc001kre.1_Missense_Mutation_p.M595L	NM_015490	NP_056305	Q9NQW1	SC31B_HUMAN	SEC31 homolog B	1164					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104356986	104356986	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104356986C>T	uc001kvy.1	+	7	992	c.846C>T	c.(844-846)CCC>CCT	p.P282P	SUFU_uc001kvw.1_Silent_p.P282P|SUFU_uc001kvx.2_Silent_p.P282P|SUFU_uc009xxe.1_RNA|SUFU_uc009xxf.1_RNA	NM_016169	NP_057253	Q9UMX1	SUFU_HUMAN	suppressor of fused	282					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		OREG0020482	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105362278	105362278	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105362278G>A	uc001kxj.1	-	14	2753	c.2613C>T	c.(2611-2613)AAC>AAT	p.N871N	SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Silent_p.N706N|SH3PXD2A_uc010qqt.1_Silent_p.N748N|SH3PXD2A_uc009xxn.1_Silent_p.N706N|SH3PXD2A_uc010qqu.1_Silent_p.N814N	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1	899	SH3 4.				cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115364629	115364629	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115364629G>T	uc001laj.2	-	35	4130	c.3966C>A	c.(3964-3966)CCC>CCA	p.P1322P	NRAP_uc009xyb.2_Silent_p.P111P|NRAP_uc001lak.2_Silent_p.P1287P|NRAP_uc001lal.3_Silent_p.P1322P	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1322	Nebulin 35.					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)														---	---	---	---
RIC8A	60626	broad.mit.edu	37	11	212613	212613	+	Splice_Site	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:212613A>G	uc001log.2	+	7	1391	c.1066_splice	c.e7-2	p.V356_splice	RIC8A_uc001lof.2_Missense_Mutation_p.Q361R|RIC8A_uc001loh.2_Splice_Site_p.V349_splice	NM_021932	NP_068751			resistance to inhibitors of cholinesterase 8							cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity				0		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
ANO9	338440	broad.mit.edu	37	11	428612	428612	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:428612C>T	uc001lpi.2	-	13	1133	c.1048G>A	c.(1048-1050)GTC>ATC	p.V350I	ANO9_uc001lph.2_Missense_Mutation_p.V43I|ANO9_uc010qvv.1_Missense_Mutation_p.V206I	NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN	tumor protein p53 inducible protein 5	350	Helical; (Potential).					chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
TRPM5	29850	broad.mit.edu	37	11	2434825	2434825	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2434825T>C	uc001lwm.3	-						TRPM5_uc010qxl.1_Intron|TRPM5_uc009ydn.2_Intron	NM_014555	NP_055370			transient receptor potential cation channel,							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)														---	---	---	---
OR51G2	81282	broad.mit.edu	37	11	4936206	4936206	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4936206C>T	uc001lzr.1	-	1	688	c.688G>A	c.(688-690)GTG>ATG	p.V230M		NM_001005238	NP_001005238	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G,	230	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
UBQLNL	143630	broad.mit.edu	37	11	5536466	5536466	+	Silent	SNP	A	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5536466A>T	uc001maz.3	-	1	1491	c.1206T>A	c.(1204-1206)TCT>TCA	p.S402S	HBG2_uc001mak.1_Intron	NM_145053	NP_659490	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	402										large_intestine(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)														---	---	---	---
OR52L1	338751	broad.mit.edu	37	11	6007639	6007639	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6007639A>G	uc001mcd.2	-	1	577	c.522T>C	c.(520-522)CTT>CTC	p.L174L		NM_001005173	NP_001005173	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L,	174	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
CNGA4	1262	broad.mit.edu	37	11	6261463	6261463	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6261463G>A	uc001mco.2	+	4	546	c.439G>A	c.(439-441)GCG>ACG	p.A147T	CNGA4_uc010raa.1_Intron|CNGA4_uc001mcn.2_Missense_Mutation_p.A107T	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	147	Extracellular (Potential).				response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
ILK	3611	broad.mit.edu	37	11	6630785	6630785	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6630785C>T	uc001mee.2	+	9	906	c.771C>T	c.(769-771)TGC>TGT	p.C257C	ILK_uc001mef.2_Silent_p.C257C|ILK_uc010rap.1_Silent_p.C123C|ILK_uc010raq.1_Silent_p.C196C|ILK_uc001meg.2_Silent_p.C103C|ILK_uc001meh.2_Silent_p.C257C|ILK_uc001mei.2_5'Flank	NM_001014794	NP_001014794	Q13418	ILK_HUMAN	integrin-linked kinase	257	Protein kinase.				cell junction assembly|cell proliferation|cell-matrix adhesion|integrin-mediated signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent	cytosol|focal adhesion	ATP binding|protein serine/threonine kinase activity			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)														---	---	---	---
ZNF215	7762	broad.mit.edu	37	11	6953704	6953704	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6953704C>A	uc001mey.2	+	3	789	c.201C>A	c.(199-201)AGC>AGA	p.S67R	ZNF215_uc010raw.1_Missense_Mutation_p.S67R|ZNF215_uc010rax.1_5'UTR|ZNF215_uc001mez.1_Missense_Mutation_p.S67R	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	67	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)														---	---	---	---
MICALCL	84953	broad.mit.edu	37	11	12315408	12315408	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12315408C>T	uc001mkg.1	+	3	721	c.430C>T	c.(430-432)CAA>TAA	p.Q144*		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	144					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)														---	---	---	---
FBXO3	26273	broad.mit.edu	37	11	33773099	33773099	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33773099C>T	uc001muz.2	-	7	807	c.779G>A	c.(778-780)GGC>GAC	p.G260D	FBXO3_uc010rej.1_5'UTR|FBXO3_uc001muy.2_Missense_Mutation_p.G147D|FBXO3_uc009ykb.2_RNA|FBXO3_uc001mva.1_Missense_Mutation_p.G260D|FBXO3_uc001mvb.1_Missense_Mutation_p.G255D|FBXO3_uc010rek.1_RNA	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1	260					proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)														---	---	---	---
CAT	847	broad.mit.edu	37	11	34485651	34485651	+	Splice_Site	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34485651G>T	uc001mvm.2	+	10	1279	c.1196_splice	c.e10-1	p.G399_splice	CAT_uc009ykc.1_Splice_Site|CAT_uc001mvn.2_Splice_Site_p.G8_splice	NM_001752	NP_001743			catalase						hydrogen peroxide catabolic process|negative regulation of apoptosis|positive regulation of cell division|protein tetramerization|purine base metabolic process|purine nucleotide catabolic process|UV protection	peroxisomal matrix|peroxisomal membrane	catalase activity|heme binding|NADP binding|protein homodimerization activity			ovary(2)|pancreas(1)	3		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)													---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671729	45671729	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671729C>T	uc001mys.1	-	4	1416	c.745G>A	c.(745-747)GAC>AAC	p.D249N		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	249	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)														---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46842731	46842731	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46842731G>A	uc001ndi.1	-	2	162	c.52C>T	c.(52-54)CAC>TAC	p.H18Y	CKAP5_uc009ylg.1_5'Flank|CKAP5_uc001ndj.1_Missense_Mutation_p.H18Y	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	18					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
KBTBD4	55709	broad.mit.edu	37	11	47599113	47599113	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47599113A>G	uc001nfx.2	-	2	610	c.439T>C	c.(439-441)TGC>CGC	p.C147R	NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Missense_Mutation_p.C172R|KBTBD4_uc001nfz.2_Missense_Mutation_p.C163R|KBTBD4_uc001nfy.2_Missense_Mutation_p.C147R|NDUFS3_uc010rhn.1_5'Flank|NDUFS3_uc001nga.2_5'Flank	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	147	BACK.									ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									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																		---	---	---	---
SLC29A2	3177	broad.mit.edu	37	11	66135294	66135294	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66135294G>T	uc001oht.2	-	6	826	c.597C>A	c.(595-597)CCC>CCA	p.P199P	SLC29A2_uc001ohs.2_Silent_p.P79P|SLC29A2_uc010rpb.1_RNA|SLC29A2_uc009yrf.2_Silent_p.P79P|SLC29A2_uc001ohu.2_Silent_p.P199P|SLC29A2_uc001ohv.2_Silent_p.P199P|uc001ohw.1_5'Flank	NM_001532	NP_001523	Q14542	S29A2_HUMAN	solute carrier family 29 (nucleoside	199	Helical; (Potential).				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																		---	---	---	---
MRGPRD	116512	broad.mit.edu	37	11	68747740	68747740	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68747740A>G	uc010rqf.1	-	1	716	c.716T>C	c.(715-717)ATC>ACC	p.I239T		NM_198923	NP_944605	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	239	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(1)	1			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)															---	---	---	---
CCND1	595	broad.mit.edu	37	11	69465973	69465973	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69465973G>A	uc001opa.2	+	5	1020	c.811G>A	c.(811-813)GCC>ACC	p.A271T		NM_053056	NP_444284	P24385	CCND1_HUMAN	cyclin D1	271					cell division|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|mitotic cell cycle G1/S transition DNA damage checkpoint|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation|response to drug|response to UV-A|S phase of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol|membrane|nucleoplasm	protein kinase binding			ovary(1)|lung(1)	2	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)			T	IGH@|FSTL3	CLL|B-ALL|breast					Multiple Myeloma(6;0.086)			---	---	---	---
CHRDL2	25884	broad.mit.edu	37	11	74421903	74421903	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74421903G>A	uc001ovi.2	-	4	676	c.423C>T	c.(421-423)TGC>TGT	p.C141C	CHRDL2_uc001ovg.2_Silent_p.C25C|CHRDL2_uc001ovh.2_Silent_p.C141C|CHRDL2_uc001ovk.1_Silent_p.C141C			Q6WN34	CRDL2_HUMAN	RecName: Full=Chordin-like protein 2; AltName: Full=Chordin-related protein 2; AltName: Full=Breast tumor novel factor 1;          Short=BNF-1; Flags: Precursor;	141	VWFC 2.				cartilage development|cell differentiation|ossification	extracellular region|mitochondrion					0	Hepatocellular(1;0.098)																	---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75694509	75694509	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75694509C>T	uc001oxc.2	+	8	1019	c.778C>T	c.(778-780)CGG>TGG	p.R260W	UVRAG_uc010rrw.1_Missense_Mutation_p.R159W|UVRAG_uc001oxd.2_Translation_Start_Site|UVRAG_uc010rrx.1_Translation_Start_Site|UVRAG_uc009yuh.1_RNA	NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	260	Potential.				DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
WNT11	7481	broad.mit.edu	37	11	75907667	75907667	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75907667C>T	uc001oxe.2	-	2	302	c.179G>A	c.(178-180)CGC>CAC	p.R60H	WNT11_uc001oxf.1_Missense_Mutation_p.R60H	NM_004626	NP_004617	O96014	WNT11_HUMAN	wingless-type MMTV integration site family,	60					adrenal gland development|anterior/posterior pattern formation|artery morphogenesis|axis specification|bone mineralization|cellular response to retinoic acid|cloacal septation|embryonic skeletal system development|endoderm development|lung-associated mesenchyme development|mesonephric duct development|negative regulation of apoptosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell migration|negative regulation of transcription, DNA-dependent|neuroendocrine cell differentiation|neuron differentiation|osteoblast differentiation|outflow tract morphogenesis|palate development|positive regulation of cell migration|positive regulation of protein kinase C signaling cascade|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor-beta2 production|protein localization at cell surface|protein phosphorylation|tight junction assembly|ureteric bud morphogenesis|ventricular septum morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|protein kinase activator activity|Ras GTPase activator activity|transcription regulatory region DNA binding			lung(1)|skin(1)	2																		---	---	---	---
PCF11	51585	broad.mit.edu	37	11	82877632	82877632	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82877632C>T	uc001ozx.3	+	5	2038	c.1693C>T	c.(1693-1695)CGA>TGA	p.R565*	PCF11_uc010rsu.1_Nonsense_Mutation_p.R565*	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	565					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1																		---	---	---	---
C11orf73	51501	broad.mit.edu	37	11	86017511	86017511	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86017511A>G	uc001pbu.2	+	2	493	c.255A>G	c.(253-255)TCA>TCG	p.S85S	C11orf73_uc001pbt.2_Silent_p.S85S|C11orf73_uc010rto.1_Intron|C11orf73_uc010rtp.1_Intron|C11orf73_uc001pbv.2_RNA	NM_016401	NP_057485	Q53FT3	CK073_HUMAN	lethal, Chr 7, Rinchik 6	85						cytoplasm					0		Acute lymphoblastic leukemia(157;1.17e-07)|all_hematologic(158;0.000556)																---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92616283	92616283	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92616283G>A	uc001pdj.3	+	23	12678	c.12661G>A	c.(12661-12663)GTC>ATC	p.V4221I	FAT3_uc001pdi.3_Missense_Mutation_p.V661I	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	4221	Cytoplasmic (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)			---	---	---	---
MTNR1B	4544	broad.mit.edu	37	11	92702954	92702954	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92702954C>T	uc001pdk.1	+	1	166	c.63C>T	c.(61-63)GGC>GGT	p.G21G		NM_005959	NP_005950	P49286	MTR1B_HUMAN	melatonin receptor 1B	21	Extracellular (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|glucose homeostasis|regulation of insulin secretion|synaptic transmission	integral to plasma membrane	melatonin receptor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Ramelteon(DB00980)													---	---	---	---
C11orf54	28970	broad.mit.edu	37	11	93494832	93494832	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93494832C>T	uc009ywi.2	+	10	1257	c.926C>T	c.(925-927)ACG>ATG	p.T309M	C11orf54_uc001pef.2_Missense_Mutation_p.T259M|C11orf54_uc001peg.2_Missense_Mutation_p.T309M|C11orf54_uc001peh.2_Missense_Mutation_p.T309M|C11orf54_uc001pei.2_Missense_Mutation_p.T290M|C11orf54_uc001pej.2_Missense_Mutation_p.T290M|C11orf54_uc001pek.2_Missense_Mutation_p.T198M	NM_014039	NP_054758	Q9H0W9	CK054_HUMAN	hypothetical protein LOC28970	309						nucleus	hydrolase activity, acting on ester bonds|protein binding|zinc ion binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
SESN3	143686	broad.mit.edu	37	11	94922973	94922973	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94922973T>C	uc001pfk.1	-	4	717	c.495A>G	c.(493-495)CGA>CGG	p.R165R	SESN3_uc010rug.1_Intron|SESN3_uc001pfl.2_Silent_p.R165R	NM_144665	NP_653266	P58005	SESN3_HUMAN	sestrin 3	165					cell cycle arrest	nucleus					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)														---	---	---	---
PGR	5241	broad.mit.edu	37	11	100999546	100999546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100999546C>T	uc001pgh.2	-	1	999	c.256G>A	c.(256-258)GCA>ACA	p.A86T	PGR_uc001pgi.2_Missense_Mutation_p.A86T|PGR_uc009yww.1_RNA|PGR_uc001pgj.2_RNA|PGR_uc009ywx.1_RNA|uc010rum.1_5'Flank	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	86	Modulating, Pro-Rich.				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)													---	---	---	---
ALG9	79796	broad.mit.edu	37	11	111707021	111707021	+	Intron	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111707021T>A	uc001pmb.2	-						ALG9_uc001ply.2_Intron|ALG9_uc001plz.2_Intron|ALG9_uc010rwm.1_Intron|ALG9_uc010rwn.1_Intron|ALG9_uc010rwo.1_Intron	NM_001077690	NP_001071158			asparagine-linked glycosylation 9 protein						dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			large_intestine(1)|ovary(1)	2		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)														---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113629418	113629418	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113629418A>C	uc001poe.2	-	6	628	c.591T>G	c.(589-591)AGT>AGG	p.S197R	ZW10_uc009yyv.2_RNA	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10	197	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)														---	---	---	---
C11orf71	54494	broad.mit.edu	37	11	114270731	114270731	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114270731T>G	uc001pou.3	-	1	525	c.323A>C	c.(322-324)CAG>CCG	p.Q108P	C11orf71_uc001pot.1_Missense_Mutation_p.Q108P|RBM7_uc001pov.2_5'Flank|RBM7_uc001pow.2_5'Flank|RBM7_uc001pox.2_5'Flank	NM_019021	NP_061894	Q6IPW1	CK071_HUMAN	hypothetical protein LOC54494	108											0		all_cancers(61;1.15e-11)|all_epithelial(67;5.3e-06)|all_hematologic(158;0.000303)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.6e-06)|Epithelial(105;4.31e-05)|all cancers(92;0.00036)														---	---	---	---
ROBO4	54538	broad.mit.edu	37	11	124767016	124767016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124767016G>A	uc001qbg.2	-	2	352	c.212C>T	c.(211-213)CCC>CTC	p.P71L	ROBO4_uc010sas.1_Intron|ROBO4_uc001qbh.2_Intron|ROBO4_uc010sat.1_5'Flank	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	71	Ig-like C2-type 1.				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)														---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	661272	661272	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:661272G>T	uc001qii.1	+	12	1151	c.1151G>T	c.(1150-1152)AGC>ATC	p.S384I	B4GALNT3_uc001qij.1_Missense_Mutation_p.S286I|B4GALNT3_uc001qik.1_5'Flank	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	384	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
TEAD4	7004	broad.mit.edu	37	12	3104142	3104142	+	Silent	SNP	C	T	T	rs148965461	byFrequency;by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3104142C>T	uc010sej.1	+	3	484	c.207C>T	c.(205-207)GAC>GAT	p.D69D	TEAD4_uc010sek.1_Silent_p.D69D|TEAD4_uc001qln.2_Intron	NM_003213	NP_003204	Q15561	TEAD4_HUMAN	TEA domain family member 4 isoform 1	70	TEA.				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	4778941	4778941	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4778941T>C	uc001qnc.2	+	8	768	c.758T>C	c.(757-759)GTT>GCT	p.V253A	NDUFA9_uc010ses.1_Missense_Mutation_p.V34A	NM_005002	NP_004993	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	253					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)													---	---	---	---
KCNA6	3742	broad.mit.edu	37	12	4919240	4919240	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4919240G>A	uc001qng.2	+	1	899	c.33G>A	c.(31-33)GCG>GCA	p.A11A		NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related	11						voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(2)|ovary(1)	3															HNSCC(72;0.22)			---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6701626	6701626	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6701626C>T	uc001qpo.2	-	19	3045	c.2881G>A	c.(2881-2883)GAT>AAT	p.D961N	CHD4_uc001qpn.2_Missense_Mutation_p.D954N|CHD4_uc001qpp.2_Missense_Mutation_p.D958N	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	961					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																		---	---	---	---
PZP	5858	broad.mit.edu	37	12	9301589	9301589	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9301589A>G	uc001qvl.2	-	36	4457	c.4428T>C	c.(4426-4428)GAT>GAC	p.D1476D	PZP_uc009zgl.2_Silent_p.D1262D	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
PRB2	653247	broad.mit.edu	37	12	11548471	11548471	+	5'UTR	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11548471G>A	uc010shk.1	-	1						NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)															---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19522658	19522658	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19522658G>T	uc001reb.2	+	25	3374	c.3288G>T	c.(3286-3288)TCG>TCT	p.S1096S	PLEKHA5_uc001rea.2_Silent_p.S1154S|PLEKHA5_uc009zin.2_Silent_p.S854S|PLEKHA5_uc010sif.1_Silent_p.S1085S|PLEKHA5_uc010sig.1_Silent_p.S1078S|PLEKHA5_uc009zio.2_Silent_p.S362S	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	1096							1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23689454	23689454	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23689454G>A	uc001rfw.2	-	14	2023	c.1921C>T	c.(1921-1923)CGC>TGC	p.R641C	SOX5_uc001rfx.2_Missense_Mutation_p.R628C|SOX5_uc001rfy.2_Missense_Mutation_p.R520C|SOX5_uc001rfv.2_Missense_Mutation_p.R255C|SOX5_uc010siv.1_Missense_Mutation_p.R628C|SOX5_uc010siw.1_RNA	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	641					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
FAR2	55711	broad.mit.edu	37	12	29469849	29469849	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29469849G>A	uc001ris.3	+	9	1178	c.1031G>A	c.(1030-1032)AGC>AAC	p.S344N	FAR2_uc001rit.2_Missense_Mutation_p.S344N|FAR2_uc009zjm.2_Missense_Mutation_p.S247N|uc001riu.1_Intron	NM_018099	NP_060569	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	344					ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0																		---	---	---	---
PUS7L	83448	broad.mit.edu	37	12	44148200	44148200	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44148200T>C	uc001rnq.3	-	2	1338	c.849A>G	c.(847-849)AAA>AAG	p.K283K	PUS7L_uc001rnr.3_Silent_p.K283K|PUS7L_uc001rns.3_Silent_p.K283K|PUS7L_uc009zkb.2_Intron	NM_001098615	NP_001092085	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S.	283					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			pancreas(1)	1	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)														---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46285639	46285639	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46285639T>C	uc001ros.1	+	17	4999	c.4999T>C	c.(4999-5001)TGT>CGT	p.C1667R	ARID2_uc001ror.2_Missense_Mutation_p.C1667R|ARID2_uc009zkg.1_Missense_Mutation_p.C1123R|ARID2_uc009zkh.1_Missense_Mutation_p.C1294R|ARID2_uc001rou.1_Missense_Mutation_p.C1001R	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1667					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)														---	---	---	---
HDAC7	51564	broad.mit.edu	37	12	48185439	48185439	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48185439A>G	uc010slo.1	-	15	2058	c.1863T>C	c.(1861-1863)TCT>TCC	p.S621S	HDAC7_uc009zku.2_RNA|HDAC7_uc001rqe.2_Silent_p.S55S|HDAC7_uc001rqj.3_Silent_p.S584S|HDAC7_uc001rqk.3_Silent_p.S604S	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a	582	Histone deacetylase.				negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)														---	---	---	---
TROAP	10024	broad.mit.edu	37	12	49724166	49724166	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49724166A>G	uc001rtx.3	+	13	1705	c.1538A>G	c.(1537-1539)CAG>CGG	p.Q513R	TROAP_uc009zlh.2_Missense_Mutation_p.Q513R|TROAP_uc001rty.2_Missense_Mutation_p.Q221R	NM_005480	NP_005471	Q12815	TROAP_HUMAN	tastin isoform 1	513	Cys-rich.				cell adhesion	cytoplasm				ovary(1)	1																		---	---	---	---
C1QL4	338761	broad.mit.edu	37	12	49729777	49729777	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49729777T>C	uc001rtz.1	-	1	1195	c.484A>G	c.(484-486)ATG>GTG	p.M162V		NM_001008223	NP_001008224	Q86Z23	C1QL4_HUMAN	complement component 1, q subcomponent-like 4	162	C1q.					collagen					0																		---	---	---	---
FAM186B	84070	broad.mit.edu	37	12	49993929	49993929	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49993929C>A	uc001ruo.2	-	4	1667	c.1494G>T	c.(1492-1494)GAG>GAT	p.E498D	FAM186B_uc010smk.1_Missense_Mutation_p.E408D	NM_032130	NP_115506	Q8IYM0	F186B_HUMAN	hypothetical protein LOC84070	498						protein complex				ovary(1)	1																		---	---	---	---
HOXC9	3225	broad.mit.edu	37	12	54394139	54394139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54394139C>T	uc001sep.2	+	2	265	c.167C>T	c.(166-168)GCG>GTG	p.A56V	HOXC9_uc001seq.2_Missense_Mutation_p.A56V	NM_006897	NP_008828	P31274	HXC9_HUMAN	homeobox C9	56					multicellular organismal development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)|skin(1)	3																		---	---	---	---
DGKA	1606	broad.mit.edu	37	12	56332996	56332996	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56332996T>C	uc001sij.2	+	8	765	c.501T>C	c.(499-501)ATT>ATC	p.I167I	DGKA_uc009zoc.1_Silent_p.I167I|DGKA_uc001sih.1_Silent_p.I55I|DGKA_uc001sii.1_Silent_p.I25I|DGKA_uc009zod.1_Silent_p.I86I|DGKA_uc009zoe.1_Silent_p.I167I|DGKA_uc001sik.2_Silent_p.I167I|DGKA_uc001sil.2_Silent_p.I167I|DGKA_uc001sim.2_Silent_p.I167I|DGKA_uc001sin.2_Silent_p.I167I|DGKA_uc009zof.2_5'UTR|DGKA_uc001sio.2_5'UTR	NM_001345	NP_001336	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	167	EF-hand 2.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			ovary(3)|pancreas(1)	4					Vitamin E(DB00163)													---	---	---	---
ESYT1	23344	broad.mit.edu	37	12	56525096	56525096	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56525096T>C	uc001sjq.2	+	5	760	c.710T>C	c.(709-711)ATG>ACG	p.M237T	ESYT1_uc001sjr.2_Missense_Mutation_p.M237T	NM_015292	NP_056107	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	237						integral to membrane				ovary(4)|skin(1)	5																		---	---	---	---
NACA	4666	broad.mit.edu	37	12	57114329	57114329	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57114329T>C	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Missense_Mutation_p.S329G|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Missense_Mutation_p.S329G|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672			nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1								T	BCL6	NHL								---	---	---	---
NACA	4666	broad.mit.edu	37	12	57114975	57114975	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57114975T>C	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Silent_p.P113P|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Silent_p.P113P|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672			nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1								T	BCL6	NHL								---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57648686	57648686	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57648686G>A	uc009zpm.1	-	22	2836	c.2801C>T	c.(2800-2802)GCT>GTT	p.A934V	R3HDM2_uc010srn.1_Intron|R3HDM2_uc001snu.2_Missense_Mutation_p.A629V|R3HDM2_uc001snr.2_Missense_Mutation_p.A661V|R3HDM2_uc001sns.2_Missense_Mutation_p.A934V|R3HDM2_uc001snt.2_Missense_Mutation_p.A948V|R3HDM2_uc009zpn.1_Intron	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	934						nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
CTDSP2	10106	broad.mit.edu	37	12	58221331	58221331	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58221331G>A	uc001sqm.2	-						CTDSP2_uc009zqf.2_Intron|CTDSP2_uc009zqg.2_Intron|uc001sqn.2_5'Flank|MIR26A2_hsa-mir-26a-2|MI0000750_5'Flank	NM_005730	NP_005721			nuclear LIM interactor-interacting factor 2						protein dephosphorylation	nucleus|soluble fraction	CTD phosphatase activity|metal ion binding			central_nervous_system(1)	1	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)																	---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63113972	63113972	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63113972C>A	uc001srk.3	-	6	1201	c.1052G>T	c.(1051-1053)AGG>ATG	p.R351M		NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)	351	PP2C-like.						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)														---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66531853	66531853	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66531853T>A	uc001stc.2	-	7	680	c.604A>T	c.(604-606)ATG>TTG	p.M202L	LLPH_uc010ssx.1_RNA|TMBIM4_uc001std.2_Missense_Mutation_p.M171L|TMBIM4_uc009zqr.2_Missense_Mutation_p.M249L|TMBIM4_uc001ste.2_RNA|TMBIM4_uc001stf.2_3'UTR|TMBIM4_uc009zqs.2_3'UTR	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4	202						integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67696213	67696213	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67696213T>A	uc001stn.2	+	8	1548	c.1111T>A	c.(1111-1113)TTC>ATC	p.F371I	CAND1_uc001sto.2_Missense_Mutation_p.F49I	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	371	HEAT 9.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)														---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72013085	72013085	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72013085T>C	uc001swo.2	-							NM_144982	NP_659419			proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78583914	78583914	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78583914T>G	uc001syp.2	+	34	6379	c.6206T>G	c.(6205-6207)CTT>CGT	p.L2069R	NAV3_uc001syo.2_Missense_Mutation_p.L2047R|NAV3_uc010sub.1_Missense_Mutation_p.L1526R|NAV3_uc009zsf.2_Missense_Mutation_p.L878R	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2069						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)			---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104156095	104156095	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104156095T>C	uc001tjw.2	+	67	7589	c.7403T>C	c.(7402-7404)ATC>ACC	p.I2468T	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	2468	Helical; (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																		---	---	---	---
NUAK1	9891	broad.mit.edu	37	12	106460931	106460931	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106460931C>T	uc001tlj.1	-	7	3015	c.1635G>A	c.(1633-1635)ATG>ATA	p.M545I		NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5	545							ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
UBE3B	89910	broad.mit.edu	37	12	109967832	109967832	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109967832G>A	uc001top.2	+	25	3368	c.2765G>A	c.(2764-2766)CGT>CAT	p.R922H	UBE3B_uc001toq.2_Missense_Mutation_p.R922H|UBE3B_uc001tos.2_Missense_Mutation_p.R349H|UBE3B_uc001tot.2_Missense_Mutation_p.R40H|UBE3B_uc010sxp.1_Missense_Mutation_p.R40H	NM_130466	NP_569733	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	922	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4																		---	---	---	---
GIT2	9815	broad.mit.edu	37	12	110370843	110370843	+	Silent	SNP	G	A	A	rs150244358		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110370843G>A	uc001tps.2	-	20	2385	c.2220C>T	c.(2218-2220)TAC>TAT	p.Y740Y	TCHP_uc001tpo.1_RNA|GIT2_uc001tpr.2_3'UTR|GIT2_uc001tpq.2_Silent_p.Y710Y|GIT2_uc001tpv.2_Silent_p.Y662Y|GIT2_uc001tpu.2_Silent_p.Y660Y|GIT2_uc001tpt.2_Silent_p.Y612Y|GIT2_uc010sxu.1_Silent_p.Y648Y	NM_057169	NP_476510	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting	740					regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110643263	110643263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110643263C>T	uc001tqi.2	+	16	1790	c.1660C>T	c.(1660-1662)CGT>TGT	p.R554C	IFT81_uc001tqh.2_Missense_Mutation_p.R554C|IFT81_uc001tqj.2_RNA	NM_001143779	NP_001137251	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81-like isoform 1	554	Potential.				cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
OAS1	4938	broad.mit.edu	37	12	113348996	113348996	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113348996A>G	uc001tud.2	+	3	716	c.610A>G	c.(610-612)AAG>GAG	p.K204E	OAS1_uc010syn.1_Missense_Mutation_p.K203E|OAS1_uc010syo.1_Missense_Mutation_p.Q187R|OAS1_uc001tub.2_Missense_Mutation_p.K204E|OAS1_uc001tuc.2_Missense_Mutation_p.K204E|OAS1_uc009zwf.2_Missense_Mutation_p.K203E	NM_016816	NP_058132	P00973	OAS1_HUMAN	2',5'-oligoadenylate synthetase 1 isoform 1	204					interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(2)	2																		---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123270349	123270349	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123270349G>A	uc001udc.2	+	4	625	c.480G>A	c.(478-480)ACG>ACA	p.T160T	CCDC62_uc010tah.1_RNA|CCDC62_uc001udf.2_Silent_p.T160T|CCDC62_uc001ude.2_Intron	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b	160	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)														---	---	---	---
EIF2B1	1967	broad.mit.edu	37	12	124106442	124106442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124106442G>A	uc001ufm.2	-	9	922	c.779C>T	c.(778-780)GCG>GTG	p.A260V	EIF2B1_uc001ufn.2_Missense_Mutation_p.A258V	NM_001414	NP_001405	Q14232	EI2BA_HUMAN	eukaryotic translation initiation factor 2B,	260					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)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133359063	133359063	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133359063C>T	uc001ukz.1	-	17	3843	c.3284G>A	c.(3283-3285)GGC>GAC	p.G1095D	GOLGA3_uc001ula.1_Missense_Mutation_p.G1095D	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1095	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
LNX2	222484	broad.mit.edu	37	13	28136741	28136741	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28136741G>A	uc001url.3	-	5	1342	c.1033C>T	c.(1033-1035)CGG>TGG	p.R345W	LNX2_uc001urm.1_Missense_Mutation_p.R345W	NM_153371	NP_699202	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	345	PDZ 2.						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)														---	---	---	---
DNAJC15	29103	broad.mit.edu	37	13	43643080	43643080	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43643080C>T	uc001uyy.2	+	3	576	c.175C>T	c.(175-177)CGG>TGG	p.R59W		NM_013238	NP_037370	Q9Y5T4	DJC15_HUMAN	DNAJ domain-containing	59						integral to membrane	heat shock protein binding				0		Lung NSC(96;4.3e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0737)														---	---	---	---
COG3	83548	broad.mit.edu	37	13	46083903	46083903	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46083903G>A	uc001vak.2	+	15	1772	c.1671G>A	c.(1669-1671)ACG>ACA	p.T557T	COG3_uc001vaj.1_Silent_p.T557T|COG3_uc010tfv.1_Silent_p.T394T|COG3_uc010aci.2_Silent_p.T333T	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3	557					ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)														---	---	---	---
DHRS12	79758	broad.mit.edu	37	13	52351200	52351200	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52351200C>T	uc001vfq.2	-	6	554	c.506G>A	c.(505-507)CGA>CAA	p.R169Q	DHRS12_uc001vfr.1_Missense_Mutation_p.R120Q|DHRS12_uc001vfs.1_Missense_Mutation_p.R120Q			A0PJE2	DHR12_HUMAN	RecName: Full=Dehydrogenase/reductase SDR family member 12;          EC=1.1.-.-;	169							binding|oxidoreductase activity				0		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)														---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99481946	99481946	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99481946T>C	uc001vnt.2	-	42	4689	c.4634A>G	c.(4633-4635)CAG>CGG	p.Q1545R	DOCK9_uc001vnw.2_Missense_Mutation_p.Q1544R|DOCK9_uc001vnv.1_RNA|DOCK9_uc010tir.1_Missense_Mutation_p.Q1545R|DOCK9_uc001vnq.2_Missense_Mutation_p.Q117R|DOCK9_uc001vnr.2_Missense_Mutation_p.Q188R|DOCK9_uc010tin.1_Missense_Mutation_p.Q188R|DOCK9_uc001vns.2_Missense_Mutation_p.Q117R|DOCK9_uc010tio.1_Missense_Mutation_p.Q237R|DOCK9_uc010tip.1_Missense_Mutation_p.Q255R|DOCK9_uc001vnu.1_Missense_Mutation_p.Q117R|DOCK9_uc010tiq.1_Missense_Mutation_p.Q523R	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1545	DHR-2.				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)																	---	---	---	---
ARGLU1	55082	broad.mit.edu	37	13	107219984	107219984	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107219984A>G	uc001vqk.3	-	1	531	c.284T>C	c.(283-285)CTG>CCG	p.L95P		NM_018011	NP_060481	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1	95											0	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	109475609	109475609	+	Silent	SNP	C	T	T	rs141132835	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109475609C>T	uc001vqt.1	+	9	1140	c.1014C>T	c.(1012-1014)CCC>CCT	p.P338P	MYO16_uc010agk.1_Silent_p.P360P|MYO16_uc001vqu.1_Silent_p.P138P	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	338					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	p.P338T(1)		ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110838771	110838771	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110838771C>T	uc001vqw.3	-	26	1980	c.1858G>A	c.(1858-1860)GCA>ACA	p.A620T	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	620	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)															---	---	---	---
F10	2159	broad.mit.edu	37	13	113783899	113783899	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113783899C>T	uc001vsx.2	+	2	261	c.204C>T	c.(202-204)CGC>CGT	p.R68R	F10_uc010agq.1_RNA|F10_uc001vsy.2_Silent_p.R68R|F10_uc001vsz.2_Silent_p.R68R	NM_000504	NP_000495	P00742	FA10_HUMAN	coagulation factor X preproprotein	68	Gla.				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of cell migration|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen	calcium ion binding|phospholipid binding|protein binding|serine-type endopeptidase activity			pancreas(1)	1	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;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Heparin(DB01109)|Menadione(DB00170)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
TMCO3	55002	broad.mit.edu	37	13	114188557	114188557	+	Splice_Site	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114188557T>C	uc001vtu.3	+	9	1900	c.1539_splice	c.e9+2	p.T513_splice	TMCO3_uc001vtt.3_Missense_Mutation_p.V514A	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)															---	---	---	---
EDDM3A	10876	broad.mit.edu	37	14	21216035	21216035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21216035C>T	uc001vyb.2	+	2	363	c.296C>T	c.(295-297)GCC>GTC	p.A99V	EDDM3A_uc001vyc.2_Missense_Mutation_p.A99V	NM_006683	NP_006674	Q14507	EP3A_HUMAN	human epididymis-specific 3 alpha precursor	99					sperm displacement	extracellular space					0																		---	---	---	---
NYNRIN	57523	broad.mit.edu	37	14	24882517	24882517	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24882517C>T	uc001wpf.3	+							NM_025081	NP_079357			hypothetical protein LOC57523						DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37641501	37641501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37641501C>T	uc001wtz.1	-	1	365	c.55G>A	c.(55-57)GCC>ACC	p.A19T	uc001wua.2_5'UTR	NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial	19	Helical; Name=1; (Potential).|Solcar 1.				lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)														---	---	---	---
PPIL5	122769	broad.mit.edu	37	14	50074337	50074337	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50074337C>T	uc001wwn.2	+	3	826	c.502C>T	c.(502-504)CGA>TGA	p.R168*	SDCCAG1_uc010anj.1_Intron|PPIL5_uc001wwo.2_Intron|PPIL5_uc010ank.2_Nonsense_Mutation_p.R109*|PPIL5_uc001wwp.2_RNA	NM_152329	NP_689542	Q96L50	LLR1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 5	168	LRR 1.										0	all_epithelial(31;0.0021)|Breast(41;0.0124)																	---	---	---	---
L2HGDH	79944	broad.mit.edu	37	14	50769617	50769617	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50769617T>C	uc001wxu.2	-						L2HGDH_uc010tqn.1_Intron|L2HGDH_uc010tqo.1_Intron	NM_024884	NP_079160			L-2-hydroxyglutarate dehydrogenase precursor						2-oxoglutarate metabolic process|cellular protein metabolic process	integral to mitochondrial inner membrane	2-hydroxyglutarate dehydrogenase activity			ovary(2)	2	all_epithelial(31;0.000599)|Breast(41;0.0102)																	---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51467459	51467459	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51467459G>A	uc001wyx.3	-	6	2171	c.1406C>T	c.(1405-1407)ACG>ATG	p.T469M	TRIM9_uc001wyy.2_Missense_Mutation_p.T465M|TRIM9_uc001wyz.3_Missense_Mutation_p.T469M	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	469	Fibronectin type-III.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)																	---	---	---	---
NID2	22795	broad.mit.edu	37	14	52478375	52478375	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52478375G>A	uc001wzo.2	-	17	3681	c.3447C>T	c.(3445-3447)TAC>TAT	p.Y1149Y	NID2_uc010tqs.1_Silent_p.Y1101Y|NID2_uc010tqt.1_Silent_p.Y1149Y	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	1149						basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)																	---	---	---	---
DAAM1	23002	broad.mit.edu	37	14	59834294	59834294	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59834294C>T	uc001xdz.1	+	25	3129	c.3004C>T	c.(3004-3006)CGT>TGT	p.R1002C	DAAM1_uc001xea.1_Missense_Mutation_p.R992C|DAAM1_uc001xec.1_RNA	NM_014992	NP_055807	Q9Y4D1	DAAM1_HUMAN	dishevelled-associated activator of	1002	FH2.				actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64514742	64514742	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64514742T>C	uc001xgm.2	+	46	7476	c.7246T>C	c.(7246-7248)TCA>CCA	p.S2416P	SYNE2_uc001xgl.2_Missense_Mutation_p.S2416P	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2416	Cytoplasmic (Potential).				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)														---	---	---	---
SPTB	6710	broad.mit.edu	37	14	65253382	65253382	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65253382G>A	uc001xht.2	-	15	3355	c.3301C>T	c.(3301-3303)CAG>TAG	p.Q1101*	SPTB_uc001xhr.2_Nonsense_Mutation_p.Q1101*|SPTB_uc001xhs.2_Nonsense_Mutation_p.Q1101*|SPTB_uc001xhu.2_Nonsense_Mutation_p.Q1101*	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b	1101	Spectrin 8.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)														---	---	---	---
ZFYVE26	23503	broad.mit.edu	37	14	68234521	68234521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68234521G>A	uc001xka.2	-	31	5829	c.5690C>T	c.(5689-5691)TCG>TTG	p.S1897L	ZFYVE26_uc010tsz.1_RNA|ZFYVE26_uc001xkc.3_Missense_Mutation_p.S1897L	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1897					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)														---	---	---	---
SLC8A3	6547	broad.mit.edu	37	14	70527359	70527359	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70527359G>A	uc001xly.2	-						SLC8A3_uc001xlu.2_Intron|SLC8A3_uc001xlv.2_Intron|SLC8A3_uc001xlw.2_Intron|SLC8A3_uc001xlx.2_Intron|SLC8A3_uc001xlz.2_Intron|SLC8A3_uc010ara.2_Intron|SLC8A3_uc001xma.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	73079270	73079270	+	RNA	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73079270A>G	uc010arh.1	-	1		c.534T>C								Homo sapiens cDNA FLJ14079 fis, clone HEMBB1002134, weakly similar to ZINC-FINGER PROTEIN NEURO-D4.																														---	---	---	---
C14orf43	91748	broad.mit.edu	37	14	74193673	74193673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74193673C>T	uc001xot.2	-	6	2948	c.2165G>A	c.(2164-2166)CGG>CAG	p.R722Q	C14orf43_uc001xos.2_5'UTR|C14orf43_uc001xou.2_Missense_Mutation_p.R722Q|C14orf43_uc010tud.1_Missense_Mutation_p.R722Q|C14orf43_uc010arw.2_RNA	NM_194278	NP_919254	Q6PJG2	CN043_HUMAN	hypothetical protein LOC91748	722	ELM2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115)														---	---	---	---
C14orf118	55668	broad.mit.edu	37	14	76633039	76633039	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76633039T>C	uc001xsh.2	+	3	782	c.696T>C	c.(694-696)ACT>ACC	p.T232T	C14orf118_uc001xsi.2_Silent_p.T232T|C14orf118_uc001xsj.1_Silent_p.T232T|C14orf118_uc001xsk.1_Silent_p.T232T|C14orf118_uc001xsl.2_RNA	NM_017926	NP_060396	Q9NWQ4	CN118_HUMAN	hypothetical protein LOC55668 isoform 1	232										ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.0172)														---	---	---	---
C14orf4	64207	broad.mit.edu	37	14	77492310	77492310	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77492310C>T	uc001xsy.2	-	1	2725	c.1826G>A	c.(1825-1827)CGG>CAG	p.R609Q		NM_024496	NP_078772	Q9H1B7	I2BPL_HUMAN	chromosome 14 open reading frame 4	609	Pro-rich.					nucleus					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)														---	---	---	---
C14orf148	122945	broad.mit.edu	37	14	77889102	77889102	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77889102A>G	uc001xtr.2	-	1	278	c.131T>C	c.(130-132)TTC>TCC	p.F44S	C14orf148_uc010tvi.1_Missense_Mutation_p.F44S	NM_001113475	NP_001106946	Q6NXP6	CN148_HUMAN	hypothetical protein LOC122945 isoform 1	44					proline biosynthetic process		binding|pyrroline-5-carboxylate reductase activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)														---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	78018519	78018519	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78018519G>A	uc001xub.2	-	9	1411	c.1223C>T	c.(1222-1224)GCC>GTC	p.A408V		NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base	408						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)													---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88938739	88938739	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88938739C>T	uc001xwv.3	-	15	3051	c.2720G>A	c.(2719-2721)CGG>CAG	p.R907Q	PTPN21_uc010twc.1_Missense_Mutation_p.R703Q	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	907	Tyrosine-protein phosphatase.					cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91211166	91211166	+	Silent	SNP	G	A	A	rs141007402	byFrequency;by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91211166G>A	uc001xyp.2	-	4	668	c.546C>T	c.(544-546)ATC>ATT	p.I182I		NM_001010854	NP_001010854	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	182							binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
BCL11B	64919	broad.mit.edu	37	14	99641482	99641482	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99641482C>T	uc001yga.2	-	4	1958	c.1691G>A	c.(1690-1692)CGC>CAC	p.R564H	BCL11B_uc001ygb.2_Missense_Mutation_p.R493H	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1	564						nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)				T	TLX3	T-ALL								---	---	---	---
SNORD114-16	767594	broad.mit.edu	37	14	101439032	101439032	+	5'Flank	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101439032G>A	uc001yjg.2	+						SNORD114-15_uc001yjf.1_RNA|SNORD114-17_uc001yjh.2_5'Flank	NR_003209				Homo sapiens small nucleolar RNA, C/D box 114-16 (SNORD114-16), non-coding RNA.												0																		---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104121009	104121009	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104121009A>G	uc001yno.2	+	2	416	c.108A>G	c.(106-108)GAA>GAG	p.E36E	KLC1_uc010tyd.1_Silent_p.E195E|KLC1_uc010tye.1_Silent_p.E32E|KLC1_uc001ynm.1_Silent_p.E36E|KLC1_uc001ynn.1_Silent_p.E32E|KLC1_uc010tyf.1_Silent_p.E36E	NM_182923	NP_891553	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 2	36					blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
PAR4	347745	broad.mit.edu	37	15	25453235	25453235	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25453235G>A	uc001yzk.1	+						PAR4_uc010ayo.1_Intron|SNORD115-20_uc001yzq.1_Intron|SNORD115-22_uc001yzr.1_5'Flank					Homo sapiens clone Rt-13I SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42139856	42139856	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42139856G>A	uc010bco.2	+	20	2245	c.2144G>A	c.(2143-2145)CGG>CAG	p.R715Q	JMJD7-PLA2G4B_uc001zoo.3_Missense_Mutation_p.R946Q|JMJD7-PLA2G4B_uc010bcn.2_Missense_Mutation_p.G884R|JMJD7-PLA2G4B_uc001zoq.3_Missense_Mutation_p.R416Q	NM_001114633	NP_001108105	P0C869	PA24B_HUMAN	phospholipase A2, group IVB	715	PLA2c.				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	42170721	42170721	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42170721G>A	uc001zos.2	-	17	3517	c.3184C>T	c.(3184-3186)CGC>TGC	p.R1062C		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1097					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)														---	---	---	---
PLA2G4F	255189	broad.mit.edu	37	15	42442797	42442797	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42442797C>T	uc001zoz.2	-						PLA2G4F_uc001zoy.2_5'Flank|PLA2G4F_uc010bcr.2_Intron|PLA2G4F_uc001zpa.2_Intron|PLA2G4F_uc010bcs.2_Intron	NM_213600	NP_998765			phospholipase A2, group IVF						phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity			ovary(4)	4		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)														---	---	---	---
DUOX1	53905	broad.mit.edu	37	15	45433228	45433228	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45433228C>T	uc001zus.1	+	14	1871	c.1525C>T	c.(1525-1527)CGG>TGG	p.R509W	DUOX1_uc001zut.1_Missense_Mutation_p.R509W|DUOX1_uc010bee.1_Translation_Start_Site	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	509	Peroxidase-like; mediates peroxidase activity.|Extracellular (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)														---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58256130	58256130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58256130G>A	uc002aex.2	-	9	1097	c.1039C>T	c.(1039-1041)CGC>TGC	p.R347C	ALDH1A2_uc002aey.2_Missense_Mutation_p.R309C|ALDH1A2_uc010ugv.1_Missense_Mutation_p.R326C|ALDH1A2_uc010ugw.1_Missense_Mutation_p.R318C|ALDH1A2_uc002aew.2_Missense_Mutation_p.R251C	NM_003888	NP_003879	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	347					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)													---	---	---	---
CSNK1G1	53944	broad.mit.edu	37	15	64496717	64496717	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64496717G>A	uc002anf.2	-	9	1402	c.922C>T	c.(922-924)CGG>TGG	p.R308W	CSNK1G1_uc002ane.2_RNA|CSNK1G1_uc002ang.1_Missense_Mutation_p.R308W|CSNK1G1_uc002anh.1_Missense_Mutation_p.R308W|CSNK1G1_uc002anj.2_Missense_Mutation_p.R290W	NM_022048	NP_071331	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	308	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
NPTN	27020	broad.mit.edu	37	15	73879916	73879916	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73879916C>T	uc002avs.2	-	4	852	c.655G>A	c.(655-657)GTA>ATA	p.V219I	NPTN_uc010bjc.2_Missense_Mutation_p.V219I|NPTN_uc002avt.2_Missense_Mutation_p.V103I|NPTN_uc002avr.2_Missense_Mutation_p.V103I|NPTN_uc010ula.1_Intron	NM_012428	NP_036560	Q9Y639	NPTN_HUMAN	neuroplastin isoform b precursor	219	Ig-like 2.|Extracellular (Potential).				elevation of cytosolic calcium ion concentration|homophilic cell adhesion|long-term synaptic potentiation|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of long-term neuronal synaptic plasticity|positive regulation of neuron projection development|positive regulation of protein phosphorylation	integral to membrane|plasma membrane|presynaptic membrane	cell adhesion molecule binding|type 1 fibroblast growth factor receptor binding				0																		---	---	---	---
C15orf59	388135	broad.mit.edu	37	15	74043456	74043456	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74043456C>T	uc002avy.2	-	1	361	c.16G>A	c.(16-18)GCC>ACC	p.A6T		NM_001039614	NP_001034703	Q2T9L4	CO059_HUMAN	hypothetical protein LOC388135	6										pancreas(1)	1																		---	---	---	---
LMAN1L	79748	broad.mit.edu	37	15	75112400	75112400	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75112400T>C	uc002ayt.1	+	7	736	c.734T>C	c.(733-735)CTG>CCG	p.L245P	LMAN1L_uc010bkd.2_3'UTR|LMAN1L_uc010ulo.1_3'UTR|LMAN1L_uc010bke.1_Intron	NM_021819	NP_068591	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like precursor	245	Lumenal (Potential).|L-type lectin-like.					ER-Golgi intermediate compartment membrane|integral to membrane	sugar binding				0																		---	---	---	---
SCAMP5	192683	broad.mit.edu	37	15	75309055	75309055	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75309055C>T	uc002azk.1	+	4	420	c.258C>T	c.(256-258)TAC>TAT	p.Y86Y	SCAMP5_uc002azl.1_Silent_p.Y86Y|SCAMP5_uc002azm.1_Silent_p.Y86Y|SCAMP5_uc002azn.1_Silent_p.Y86Y|SCAMP5_uc010uly.1_Intron	NM_138967	NP_620417	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	86	Helical; (Potential).				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																		---	---	---	---
SH2D7	646892	broad.mit.edu	37	15	78393576	78393576	+	Silent	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78393576C>A	uc010blb.1	+	5	981	c.981C>A	c.(979-981)ACC>ACA	p.T327T		NM_001101404	NP_001094874	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	327											0																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81176682	81176682	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81176682C>T	uc002bfw.1	+	6	1044	c.784C>T	c.(784-786)CAC>TAC	p.H262Y	KIAA1199_uc010unn.1_Missense_Mutation_p.H262Y	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	262										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83331474	83331474	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83331474G>A	uc010uoh.1	-	22	2925	c.2748C>T	c.(2746-2748)GGC>GGT	p.G916G	AP3B2_uc010uoi.1_Silent_p.G935G|AP3B2_uc010uoj.1_Silent_p.G884G|AP3B2_uc010bmp.2_5'Flank|AP3B2_uc010uog.1_Silent_p.G552G	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	916					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85400935	85400935	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85400935G>A	uc002ble.2	+	6	3739	c.3572G>A	c.(3571-3573)GGA>GAA	p.G1191E		NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1191					heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
C15orf42	90381	broad.mit.edu	37	15	90168613	90168613	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90168613C>T	uc002boe.2	+	20	5072	c.5072C>T	c.(5071-5073)GCG>GTG	p.A1691V	C15orf42_uc010upv.1_RNA	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1	1691					cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
ANPEP	290	broad.mit.edu	37	15	90342507	90342507	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90342507C>T	uc002bop.3	-	14	2285	c.1993G>A	c.(1993-1995)GCC>ACC	p.A665T		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	665	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)													---	---	---	---
RHBDF1	64285	broad.mit.edu	37	16	115006	115006	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:115006T>C	uc002cfl.3	-	5	156	c.8A>G	c.(7-9)GAG>GGG	p.E3G	RHBDF1_uc010uty.1_Missense_Mutation_p.E3G|RHBDF1_uc010utz.1_Missense_Mutation_p.E3G|RHBDF1_uc010bqo.1_RNA	NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	3	Cytoplasmic (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|protein transport|proteolysis|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)																---	---	---	---
METRN	79006	broad.mit.edu	37	16	767234	767234	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:767234C>T	uc002cjd.2	+	4	846	c.729C>T	c.(727-729)GGC>GGT	p.G243G	uc010bra.1_5'Flank	NM_024042	NP_076947	Q9UJH8	METRN_HUMAN	meteorin, glial cell differentiation regulator	243											0		Hepatocellular(780;0.00335)																---	---	---	---
PTX4	390667	broad.mit.edu	37	16	1536245	1536245	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1536245C>T	uc010uvf.1	-	3	1117	c.1117G>A	c.(1117-1119)GTG>ATG	p.V373M		NM_001013658	NP_001013680	Q96A99	PTX4_HUMAN	neuronal pentraxin II-like	378	Pentaxin.					extracellular region	metal ion binding				0																		---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1818554	1818554	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1818554G>A	uc002cmk.2	+	31	3936	c.3816G>A	c.(3814-3816)TCG>TCA	p.S1272S	MAPK8IP3_uc002cml.2_Silent_p.S1266S|MAPK8IP3_uc010uvl.1_Silent_p.S1273S	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	1272					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
CLDN9	9080	broad.mit.edu	37	16	3063873	3063873	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3063873G>T	uc010uwo.1	+	1	1417	c.510G>T	c.(508-510)GCG>GCT	p.A170A		NM_020982	NP_066192	O95484	CLD9_HUMAN	claudin 9	170	Helical; (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity				0																		---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4016487	4016487	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4016487C>T	uc002cvx.2	-	11	3890	c.3351G>A	c.(3349-3351)GCG>GCA	p.A1117A		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	1117	Guanylate cyclase 2.|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 plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27692862	27692862	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27692862C>T	uc002dow.2	+						KIAA0556_uc002dox.1_Intron	NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
CLN3	1201	broad.mit.edu	37	16	28488902	28488902	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28488902G>T	uc002dpo.2	-	15	1575	c.1252C>A	c.(1252-1254)CTG>ATG	p.L418M	uc010vct.1_Intron|CLN3_uc002dpl.2_Missense_Mutation_p.L340M|CLN3_uc010vcu.1_Missense_Mutation_p.L318M|CLN3_uc002dpn.2_Missense_Mutation_p.L319M|CLN3_uc002dpm.2_Missense_Mutation_p.L364M|CLN3_uc010vcv.1_Missense_Mutation_p.L394M|CLN3_uc010byd.2_Missense_Mutation_p.L321M|CLN3_uc002dpp.2_Missense_Mutation_p.L418M|CLN3_uc002dpt.1_Missense_Mutation_p.L318M|CLN3_uc002dpq.1_Missense_Mutation_p.L370M|CLN3_uc010bye.1_Missense_Mutation_p.L401M|CLN3_uc002dpr.1_RNA|CLN3_uc010byf.1_RNA|CLN3_uc002dps.1_Missense_Mutation_p.L291M|CLN3_uc002dpu.1_Missense_Mutation_p.L316M	NM_000086	NP_000077	Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3	418	Helical; (Potential).				amyloid precursor protein catabolic process|arginine transport|associative learning|autophagic vacuole fusion|cell death|cellular amino acid metabolic process|cytosolic calcium ion homeostasis|galactosylceramide metabolic process|globoside metabolic process|glucosylceramide metabolic process|ionotropic glutamate receptor signaling pathway|lysosomal lumen acidification|lysosomal lumen pH elevation|negative regulation of catalytic activity|negative regulation of macroautophagy|negative regulation of neuron apoptosis|negative regulation of proteolysis|neuromuscular process controlling balance|neurotransmitter metabolic process|protein catabolic process|protein folding|protein processing|receptor-mediated endocytosis|regulation of action potential|sphingomyelin metabolic process|vacuolar transport	autophagic vacuole|caveola|cytosol|early endosome|Golgi membrane|Golgi stack|integral to endoplasmic reticulum membrane|late endosome|lysosomal membrane|membrane fraction|mitochondrion|neuron projection|nucleus|synaptic vesicle|trans-Golgi network	unfolded protein binding				0																		---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28917352	28917352	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28917352G>A	uc002drq.2	-	9	1459	c.1411C>T	c.(1411-1413)CGG>TGG	p.R471W	uc010vct.1_Intron|RABEP2_uc010vdf.1_Missense_Mutation_p.R400W|RABEP2_uc010byn.2_Missense_Mutation_p.R439W	NM_024816	NP_079092	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	471	Potential.				endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
SEZ6L2	26470	broad.mit.edu	37	16	29888645	29888645	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29888645G>A	uc002duq.3	-	11	2096	c.1856C>T	c.(1855-1857)CCG>CTG	p.P619L	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Missense_Mutation_p.P549L|SEZ6L2_uc002dur.3_Missense_Mutation_p.P549L|SEZ6L2_uc002dus.3_Missense_Mutation_p.P505L|SEZ6L2_uc010vec.1_Missense_Mutation_p.P619L|SEZ6L2_uc010ved.1_Missense_Mutation_p.P575L	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	619	CUB 3.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30723591	30723591	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30723591G>A	uc002dze.1	+	13	2209	c.1824G>A	c.(1822-1824)ACG>ACA	p.T608T	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.T465T|SRCAP_uc010bzz.1_Silent_p.T178T	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	608					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	30982823	30982823	+	Silent	SNP	C	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30982823C>G	uc002ead.1	+	13	3827	c.3141C>G	c.(3139-3141)TCC>TCG	p.S1047S		NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	1047	Ser-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																		---	---	---	---
ABCC11	85320	broad.mit.edu	37	16	48234332	48234332	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48234332C>T	uc002eff.1	-	14	2287	c.1937G>A	c.(1936-1938)CGC>CAC	p.R646H	ABCC11_uc002efg.1_Missense_Mutation_p.R646H|ABCC11_uc002efh.1_Missense_Mutation_p.R646H|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	646	ABC transporter 1.|Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												Cerumen_Type				---	---	---	---
N4BP1	9683	broad.mit.edu	37	16	48577044	48577044	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48577044C>T	uc002efp.2	-	7	2699	c.2462G>A	c.(2461-2463)AGC>AAC	p.S821N		NM_153029	NP_694574	O75113	N4BP1_HUMAN	Nedd4 binding protein 1	821					negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)																---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53488589	53488589	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53488589T>C	uc002ehi.3	+	8	1132	c.1014T>C	c.(1012-1014)TAT>TAC	p.Y338Y	RBL2_uc010vgv.1_Silent_p.Y264Y|RBL2_uc002ehj.2_Silent_p.Y48Y|RBL2_uc010vgw.1_Silent_p.Y122Y	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	338					cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65006929	65006929	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65006929C>T	uc002eoi.2	-	9	1702	c.1268G>A	c.(1267-1269)CGT>CAT	p.R423H	CDH11_uc010cdn.2_Intron|CDH11_uc002eoj.2_Missense_Mutation_p.R423H|CDH11_uc010vin.1_Missense_Mutation_p.R297H	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	423	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
RLTPR	146206	broad.mit.edu	37	16	67682227	67682227	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67682227A>G	uc002etn.2	+						RLTPR_uc010cel.1_Intron|RLTPR_uc010vjr.1_Intron	NM_001013838	NP_001013860			RGD motif, leucine rich repeats, tropomodulin											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)														---	---	---	---
RANBP10	57610	broad.mit.edu	37	16	67762413	67762413	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67762413C>T	uc002eud.2	-	11	1470	c.1354G>A	c.(1354-1356)GAC>AAC	p.D452N	RANBP10_uc010ceo.2_Missense_Mutation_p.D223N|RANBP10_uc010vju.1_Missense_Mutation_p.D426N|RANBP10_uc010vjv.1_Missense_Mutation_p.D365N|RANBP10_uc010vjw.1_Missense_Mutation_p.D143N	NM_020850	NP_065901	Q6VN20	RBP10_HUMAN	RAN binding protein 10	452	Ser-rich.									ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)														---	---	---	---
TERF2	7014	broad.mit.edu	37	16	69390851	69390851	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69390851C>T	uc002exd.2	-	10	1578	c.1453G>A	c.(1453-1455)GTG>ATG	p.V485M		NM_005652	NP_005643	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	485	HTH myb-type.|H-T-H motif.				age-dependent telomere shortening|cell cycle|cellular senescence|negative regulation of telomere maintenance via semi-conservative replication|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of transcription, DNA-dependent|telomeric loop formation	Golgi apparatus|nuclear telomere cap complex|nucleoplasm	double-stranded telomeric DNA binding|protein C-terminus binding|protein homodimerization activity			lung(1)	1		Ovarian(137;0.101)																---	---	---	---
NOB1	28987	broad.mit.edu	37	16	69778767	69778767	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69778767G>A	uc002exs.2	-							NM_014062	NP_054781			nin one binding protein							nucleus	metal ion binding|protein binding				0																		---	---	---	---
MTSS1L	92154	broad.mit.edu	37	16	70708346	70708346	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70708346G>A	uc002ezj.2	-	11	1176	c.916C>T	c.(916-918)CGC>TGC	p.R306C		NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	306	Ser-rich.				filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1																		---	---	---	---
PSMD7	5713	broad.mit.edu	37	16	74339301	74339301	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74339301C>T	uc002fcq.2	+	7	777	c.645C>T	c.(643-645)GTC>GTT	p.V215V	PSMD7_uc010vmr.1_Silent_p.V138V	NM_002811	NP_002802	P51665	PSD7_HUMAN	proteasome 26S non-ATPase subunit 7	215					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 regulatory particle	protein binding				0																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77353831	77353831	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77353831C>A	uc002ffc.3	-	16	2866	c.2447G>T	c.(2446-2448)GGG>GTG	p.G816V	ADAMTS18_uc010chc.1_Missense_Mutation_p.G404V|ADAMTS18_uc002ffe.1_Missense_Mutation_p.G512V	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	816	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
CDH15	1013	broad.mit.edu	37	16	89258129	89258129	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89258129C>A	uc002fmt.2	+	10	1519	c.1442C>A	c.(1441-1443)CCT>CAT	p.P481H		NM_004933	NP_004924	P55291	CAD15_HUMAN	cadherin 15 preproprotein	481	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	calcium ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0261)														---	---	---	---
SPG7	6687	broad.mit.edu	37	16	89592837	89592837	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89592837G>T	uc002fnj.2	+	5	740	c.719G>T	c.(718-720)AGG>ATG	p.R240M	SPG7_uc002fni.2_Missense_Mutation_p.R240M	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	240	Mitochondrial intermembrane (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)														---	---	---	---
DBNDD1	79007	broad.mit.edu	37	16	90075763	90075763	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90075763G>A	uc002fqf.1	-	2	295	c.107C>T	c.(106-108)ACG>ATG	p.T36M	DBNDD1_uc002fqe.1_Missense_Mutation_p.T56M|DBNDD1_uc002fqg.1_RNA	NM_001042610	NP_001036075	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1)	36						cytoplasm					0		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)														---	---	---	---
SMG6	23293	broad.mit.edu	37	17	1985258	1985258	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1985258T>C	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
OR3A2	4995	broad.mit.edu	37	17	3181654	3181654	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3181654C>A	uc002fvg.2	-	1	615	c.576G>T	c.(574-576)CAG>CAT	p.Q192H		NM_002551	NP_002542	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A,	192	Extracellular (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3920672	3920672	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3920672C>A	uc002fxe.2	-	48	8058	c.7994G>T	c.(7993-7995)TGG>TTG	p.W2665L	ZZEF1_uc002fxg.1_5'UTR	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	2665							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
MINK1	50488	broad.mit.edu	37	17	4796057	4796057	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4796057G>A	uc010vsl.1	+	19	2501	c.2305G>A	c.(2305-2307)GTG>ATG	p.V769M	MINK1_uc010vsk.1_Missense_Mutation_p.V732M|MINK1_uc010vsm.1_Missense_Mutation_p.V749M|MINK1_uc010vsn.1_Missense_Mutation_p.V732M|MINK1_uc010vso.1_Missense_Mutation_p.V677M|MINK1_uc010vsp.1_Missense_Mutation_p.V222M	NM_153827	NP_722549	Q8N4C8	MINK1_HUMAN	misshapen-like kinase 1 isoform 3	769					JNK cascade	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
PITPNM3	83394	broad.mit.edu	37	17	6367557	6367557	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6367557T>C	uc002gdd.3	-	16	2240	c.2089A>G	c.(2089-2091)ATC>GTC	p.I697V	PITPNM3_uc010cln.2_Missense_Mutation_p.I661V|PITPNM3_uc010clm.2_Missense_Mutation_p.I180V|PITPNM3_uc002gdc.3_Missense_Mutation_p.I288V	NM_031220	NP_112497	Q9BZ71	PITM3_HUMAN	PITPNM family member 3 isoform 1	697					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)														---	---	---	---
PITPNM3	83394	broad.mit.edu	37	17	6381912	6381912	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6381912G>T	uc002gdd.3	-	7	883	c.732C>A	c.(730-732)TAC>TAA	p.Y244*	PITPNM3_uc010cln.2_Nonsense_Mutation_p.Y208*|PITPNM3_uc002gdc.3_5'UTR	NM_031220	NP_112497	Q9BZ71	PITM3_HUMAN	PITPNM family member 3 isoform 1	244					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)														---	---	---	---
NLGN2	57555	broad.mit.edu	37	17	7320661	7320661	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7320661C>T	uc002ggt.1	+	7	2124	c.2051C>T	c.(2050-2052)GCC>GTC	p.A684V	FGF11_uc010vtw.1_5'Flank	NM_020795	NP_065846	Q8NFZ4	NLGN2_HUMAN	neuroligin 2 precursor	684	Helical; (Potential).				cell-cell junction maintenance|neuron cell-cell adhesion|positive regulation of synaptogenesis|regulation of inhibitory postsynaptic membrane potential|synapse assembly	cell surface|integral to plasma membrane|postsynaptic membrane	neurexin binding|receptor activity			central_nervous_system(1)	1		Prostate(122;0.157)																---	---	---	---
ZBTB4	57659	broad.mit.edu	37	17	7366997	7366997	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7366997G>A	uc002ghc.3	-	4	1554	c.1304C>T	c.(1303-1305)CCG>CTG	p.P435L	ZBTB4_uc002ghd.3_Missense_Mutation_p.P435L	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	435	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)														---	---	---	---
TP53	7157	broad.mit.edu	37	17	7578263	7578263	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578263G>A	uc002gim.2	-	6	780	c.586C>T	c.(586-588)CGA>TGA	p.R196*	TP53_uc002gig.1_Nonsense_Mutation_p.R196*|TP53_uc002gih.2_Nonsense_Mutation_p.R196*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.R64*|TP53_uc010cng.1_Nonsense_Mutation_p.R64*|TP53_uc002gii.1_Nonsense_Mutation_p.R64*|TP53_uc010cnh.1_Nonsense_Mutation_p.R196*|TP53_uc010cni.1_Nonsense_Mutation_p.R196*|TP53_uc002gij.2_Nonsense_Mutation_p.R196*|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Nonsense_Mutation_p.R103*|TP53_uc002gio.2_Nonsense_Mutation_p.R64*|TP53_uc010vug.1_Nonsense_Mutation_p.R157*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	196	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R196*(125)|p.R196P(12)|p.0?(7)|p.R196R(5)|p.R196fs*51(4)|p.A189_V197delAPPQHLIRV(4)|p.R196Q(3)|p.K164_P219del(1)|p.R196L(1)|p.I195fs*50(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.R64*(1)|p.I195fs*12(1)|p.R103*(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7674152	7674152	+	Silent	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7674152C>A	uc002giu.1	+	26	4277	c.4263C>A	c.(4261-4263)GCC>GCA	p.A1421A		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1421	TPR 1.|Stem (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)																---	---	---	---
LSMD1	84316	broad.mit.edu	37	17	7760123	7760123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7760123C>T	uc002giz.2	-	3	403	c.304G>A	c.(304-306)GCC>ACC	p.A102T	LSMD1_uc002gja.2_Missense_Mutation_p.A150T|CYB5D1_uc010cnn.1_5'Flank|CYB5D1_uc002gjb.3_5'Flank			Q9BRA0	LSMD1_HUMAN	RecName: Full=LSM domain-containing protein 1; AltName: Full=Phosphonoformate immuno-associated protein 2;	102						cytoplasm|nucleus				ovary(1)	1		all_cancers(10;0.11)|Prostate(122;0.219)														OREG0024146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8409738	8409738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8409738G>A	uc002gll.2	-	25	3287	c.3191C>T	c.(3190-3192)ACG>ATG	p.T1064M	MYH10_uc002glm.2_Missense_Mutation_p.T1095M|MYH10_uc010cnx.2_Missense_Mutation_p.T1073M	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1064	Potential.				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																		---	---	---	---
PIK3R6	146850	broad.mit.edu	37	17	8732080	8732080	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8732080T>C	uc002glq.1	-	11	1357	c.1117A>G	c.(1117-1119)AAG>GAG	p.K373E	PIK3R6_uc002glr.1_RNA|PIK3R6_uc002gls.1_RNA	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	373					platelet activation	cytosol					0																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11520904	11520904	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11520904C>T	uc002gne.2	+	5	1149	c.1081C>T	c.(1081-1083)CTG>TTG	p.L361L		NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	361	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			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)														---	---	---	---
PMP22	5376	broad.mit.edu	37	17	15134393	15134393	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15134393C>T	uc002goj.2	-	4	373	c.324G>A	c.(322-324)CTG>CTA	p.L108L	PMP22_uc002gok.2_Silent_p.L108L|PMP22_uc002gol.2_Silent_p.L108L	NM_153322	NP_696997	Q01453	PMP22_HUMAN	peripheral myelin protein 22	108	Helical; (By similarity).				peripheral nervous system development|synaptic transmission	integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0884)|BRCA - Breast invasive adenocarcinoma(8;4.92e-06)														---	---	---	---
TRPV2	51393	broad.mit.edu	37	17	16332204	16332204	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16332204C>T	uc002gpy.2	+	10	1862	c.1495C>T	c.(1495-1497)CTT>TTT	p.L499F	TRPV2_uc002gpz.2_Missense_Mutation_p.L69F	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,	499	Helical; (Potential).				sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)														---	---	---	---
MPRIP	23164	broad.mit.edu	37	17	17078646	17078646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17078646C>T	uc002gqu.1	+	19	2685	c.2629C>T	c.(2629-2631)CGG>TGG	p.R877W	MPRIP_uc002gqv.1_Missense_Mutation_p.R877W|MPRIP_uc002gqw.1_Missense_Mutation_p.R632W|MPRIP_uc002gqx.1_Missense_Mutation_p.R1106W|MPRIP_uc002gqy.1_Missense_Mutation_p.R1106W|MPRIP_uc010cpl.1_Intron|MPRIP_uc010cpm.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	877	Interaction with PPP1R12A.|Potential.					cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
ALKBH5	54890	broad.mit.edu	37	17	18088027	18088027	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18088027C>A	uc010cpw.2	+	1	1161	c.470C>A	c.(469-471)CCG>CAG	p.P157Q	uc002gsn.2_RNA|ALKBH5_uc010cpx.2_5'Flank	NM_017758	NP_060228	Q6P6C2	ALKB5_HUMAN	alkB, alkylation repair homolog 5	157						integral to membrane	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_neural(463;0.228)																	---	---	---	---
SLC5A10	125206	broad.mit.edu	37	17	18923663	18923663	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18923663C>T	uc002guu.1	+	15	1751	c.1710C>T	c.(1708-1710)CAC>CAT	p.H570H	SLC5A10_uc002gur.1_Silent_p.H540H|SLC5A10_uc002gut.1_Silent_p.H586H|SLC5A10_uc002guv.1_Silent_p.H543H|SLC5A10_uc010vyl.1_Silent_p.H534H	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose	570	Cytoplasmic (Potential).				sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1																		---	---	---	---
MAPK7	5598	broad.mit.edu	37	17	19285498	19285498	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19285498G>A	uc002gvn.2	+	5	2268	c.1882G>A	c.(1882-1884)GTA>ATA	p.V628I	MAPK7_uc002gvo.2_Missense_Mutation_p.V489I|MAPK7_uc002gvq.2_Missense_Mutation_p.V628I|MAPK7_uc002gvp.2_Missense_Mutation_p.V628I|uc010vyt.1_5'Flank	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	628	May not be required for kinase activity; required to stimulate MEF2C activity (By similarity).|Pro-rich.				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)																	---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21318889	21318889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21318889C>T	uc002gyv.1	+	3	940	c.235C>T	c.(235-237)CGC>TGC	p.R79C		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	79	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)			---	---	---	---
NLK	51701	broad.mit.edu	37	17	26449711	26449711	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26449711A>G	uc010crj.2	+	2	753	c.541A>G	c.(541-543)AGG>GGG	p.R181G	NLK_uc010cri.1_RNA	NM_016231	NP_057315	Q9UBE8	NLK_HUMAN	nemo like kinase	181	Protein 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)														---	---	---	---
FOXN1	8456	broad.mit.edu	37	17	26854350	26854350	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26854350T>C	uc010crm.2	+	4	868	c.670T>C	c.(670-672)TAC>CAC	p.Y224H	FOXN1_uc002hbj.2_Missense_Mutation_p.Y224H	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	224					defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|thymus 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			skin(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
GOSR1	9527	broad.mit.edu	37	17	28811743	28811743	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28811743T>C	uc002hfe.2	+	4	329	c.303T>C	c.(301-303)AAT>AAC	p.N101N	GOSR1_uc002hfd.2_Silent_p.N99N|GOSR1_uc002hff.2_Silent_p.N36N|GOSR1_uc002hfc.1_Silent_p.N101N	NM_004871	NP_004862	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1 isoform 1	101	Cytoplasmic (Potential).				intra-Golgi vesicle-mediated transport|protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|SNARE complex	SNAP receptor activity				0																		---	---	---	---
TMEM132E	124842	broad.mit.edu	37	17	32964419	32964419	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32964419G>A	uc002hif.2	+	10	2451	c.2123G>A	c.(2122-2124)CGC>CAC	p.R708H		NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E precursor	708	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)														---	---	---	---
PEX12	5193	broad.mit.edu	37	17	33904228	33904228	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33904228C>A	uc002hjp.2	-	2	1125	c.509G>T	c.(508-510)TGG>TTG	p.W170L		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	170	Helical; (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
FBXO47	494188	broad.mit.edu	37	17	37099048	37099048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37099048C>T	uc002hrc.2	-	9	1266	c.1066G>A	c.(1066-1068)GTA>ATA	p.V356I		NM_001008777	NP_001008777	Q5MNV8	FBX47_HUMAN	F-box protein 47	356											0																		---	---	---	---
WNK4	65266	broad.mit.edu	37	17	40940150	40940150	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40940150T>C	uc002ibj.2	+	9	1887	c.1866T>C	c.(1864-1866)GCT>GCC	p.A622A	WNK4_uc010wgx.1_Silent_p.A286A|WNK4_uc002ibk.1_Silent_p.A394A|WNK4_uc010wgy.1_5'UTR	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	622					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)														---	---	---	---
BECN1	8678	broad.mit.edu	37	17	40970864	40970864	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40970864T>G	uc002ibo.3	-	5	427	c.292A>C	c.(292-294)ACT>CCT	p.T98P	BECN1_uc010whb.1_Missense_Mutation_p.T11P|BECN1_uc010whc.1_Intron|BECN1_uc002ibn.2_Missense_Mutation_p.T98P	NM_003766	NP_003757	Q14457	BECN1_HUMAN	beclin 1	98					anti-apoptosis|cell cycle|cellular defense response|cytokinesis|response to virus	membrane	protein binding			ovary(1)	1		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)														---	---	---	---
AOC2	314	broad.mit.edu	37	17	40997723	40997723	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40997723G>T	uc002ibu.2	+	1	1115	c.1080G>T	c.(1078-1080)CAG>CAT	p.Q360H	AOC2_uc002ibt.2_Missense_Mutation_p.Q360H	NM_009590	NP_033720	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 isoform b	360					catecholamine metabolic process|visual perception	cytoplasm|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|electron carrier activity|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			ovary(2)	2		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)														---	---	---	---
ARL4D	379	broad.mit.edu	37	17	41477611	41477611	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41477611G>C	uc002idt.2	+	2	692	c.511G>C	c.(511-513)GTG>CTG	p.V171L		NM_001661	NP_001652	P49703	ARL4D_HUMAN	ADP-ribosylation factor-like 4D	171					protein secretion|small GTPase mediated signal transduction	cytoplasm|nucleolus|plasma membrane	GTP binding|GTPase activity|protein binding			ovary(1)	1		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.155)														---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41568548	41568548	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41568548C>A	uc002idu.1	+	4	396	c.323C>A	c.(322-324)CCT>CAT	p.P108H	DHX8_uc010wif.1_Missense_Mutation_p.P17H|DHX8_uc010wig.1_Missense_Mutation_p.P108H	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	108						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)														---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42475142	42475142	+	Missense_Mutation	SNP	C	T	T	rs148434401		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42475142C>T	uc002igw.1	-	8	4367	c.4303G>A	c.(4303-4305)GCT>ACT	p.A1435T	GPATCH8_uc002igv.1_Missense_Mutation_p.A1357T|GPATCH8_uc010wiz.1_Missense_Mutation_p.A1357T	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1435						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)														---	---	---	---
FMNL1	752	broad.mit.edu	37	17	43314678	43314678	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43314678G>A	uc002iin.2	+	8	954	c.754G>A	c.(754-756)GCC>ACC	p.A252T		NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1	252	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1																		---	---	---	---
FAM117A	81558	broad.mit.edu	37	17	47799955	47799955	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47799955G>A	uc002ipk.2	-	3	437	c.368C>T	c.(367-369)ACG>ATG	p.T123M	FAM117A_uc010wlz.1_Translation_Start_Site	NM_030802	NP_110429	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	123										ovary(1)	1																		---	---	---	---
ACSF2	80221	broad.mit.edu	37	17	48539865	48539865	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48539865C>T	uc002iqu.2	+	6	815	c.711C>T	c.(709-711)AGC>AGT	p.S237S	ACSF2_uc010wml.1_Silent_p.S194S|ACSF2_uc010wmm.1_Silent_p.S262S|ACSF2_uc010wmn.1_Silent_p.S224S|ACSF2_uc010wmo.1_Silent_p.S77S	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor	237					fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
VEZF1	7716	broad.mit.edu	37	17	56060478	56060478	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56060478G>T	uc002ivf.1	-	2	453	c.310C>A	c.(310-312)CGG>AGG	p.R104R	VEZF1_uc010dcn.1_5'UTR	NM_007146	NP_009077	Q14119	VEZF1_HUMAN	zinc finger protein 161	104					cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56389796	56389796	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56389796G>A	uc002ivx.3	-	17	3257	c.2386C>T	c.(2386-2388)CGT>TGT	p.R796C	BZRAP1_uc010dcs.2_Missense_Mutation_p.R736C|BZRAP1_uc010wnt.1_Missense_Mutation_p.R796C	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	796	Fibronectin type-III 1.					mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
USP32	84669	broad.mit.edu	37	17	58288792	58288792	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58288792T>C	uc002iyo.1	-	20	2549	c.2263A>G	c.(2263-2265)ACA>GCA	p.T755A	USP32_uc002iyn.1_Missense_Mutation_p.T425A	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	755					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)															---	---	---	---
MIR633	693218	broad.mit.edu	37	17	61021590	61021590	+	RNA	SNP	T	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61021590T>A	hsa-mir-633|MI0003648	+			c.15T>A																				0																		---	---	---	---
CASKIN2	57513	broad.mit.edu	37	17	73498994	73498994	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73498994C>T	uc002joc.2	-	18	2711	c.2161G>A	c.(2161-2163)GGT>AGT	p.G721S	CASKIN2_uc010wsc.1_Missense_Mutation_p.G639S	NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	721	Pro-rich.					cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73747202	73747202	+	Intron	SNP	A	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73747202A>T	uc002jpg.2	+						ITGB4_uc002jph.2_Intron|ITGB4_uc002jpi.3_Intron|ITGB4_uc002jpj.2_Intron	NM_000213	NP_000204			integrin beta 4 isoform 1 precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78286879	78286879	+	Missense_Mutation	SNP	C	T	T	rs148610110		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78286879C>T	uc002jyf.2	+	15	2866	c.2723C>T	c.(2722-2724)GCT>GTT	p.A908V	uc002jyg.1_Missense_Mutation_p.A639V	NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80714084	80714084	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80714084G>A	uc002kfz.2	+	2	358	c.228G>A	c.(226-228)CCG>CCA	p.P76P	TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Silent_p.P76P	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D	76					'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)															---	---	---	---
USP14	9097	broad.mit.edu	37	18	211160	211160	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:211160A>C	uc002kkf.1	+	16	1577	c.1361A>C	c.(1360-1362)AAA>ACA	p.K454T	USP14_uc002kkg.1_Missense_Mutation_p.K419T|USP14_uc010wyr.1_Missense_Mutation_p.K443T	NM_005151	NP_005142	P54578	UBP14_HUMAN	ubiquitin specific protease 14 isoform a	454					regulation of chemotaxis|regulation of proteasomal protein catabolic process|ubiquitin-dependent protein catabolic process	cell surface|cytoplasmic membrane-bounded vesicle|plasma membrane|proteasome complex	cysteine-type endopeptidase activity|endopeptidase inhibitor activity|proteasome binding|tRNA guanylyltransferase activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)	2		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18550402	18550402	+	Silent	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18550402C>A	uc002kte.2	-	23	3668	c.2727G>T	c.(2725-2727)CTG>CTT	p.L909L		NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein	909	Glu-rich.				actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)																	---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29867460	29867460	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867460T>C	uc002kxl.2	-	4	1156	c.1100A>G	c.(1099-1101)CAC>CGC	p.H367R	FAM59A_uc002kxk.1_Missense_Mutation_p.H367R	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	367										ovary(1)|skin(1)	2																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34340718	34340718	+	Missense_Mutation	SNP	G	A	A	rs149906669		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34340718G>A	uc002kzt.1	+	22	4094	c.3997G>A	c.(3997-3999)GTC>ATC	p.V1333I	FHOD3_uc002kzs.1_Missense_Mutation_p.V1350I|FHOD3_uc010dmz.1_Missense_Mutation_p.V1065I|FHOD3_uc010dnb.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1333					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)																---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42531918	42531918	+	Silent	SNP	T	C	C	rs36110095		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42531918T>C	uc010dni.2	+	4	2909	c.2613T>C	c.(2611-2613)ATT>ATC	p.I871I		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	871			I -> T (in SGMFS).			nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46385731	46385731	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46385731G>A	uc002ldc.2	+	12	1883	c.1598G>A	c.(1597-1599)CGG>CAG	p.R533Q	KIAA0427_uc002ldd.2_Missense_Mutation_p.R535Q|KIAA0427_uc002lde.3_Missense_Mutation_p.R162Q	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1	533	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
DCC	1630	broad.mit.edu	37	18	50278508	50278508	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50278508T>C	uc002lfe.1	+	2	763	c.176T>C	c.(175-177)CTC>CCC	p.L59P	DCC_uc010xdr.1_5'UTR	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	59	Extracellular (Potential).|Ig-like C2-type 1.				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72776341	72776341	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72776341G>A	uc002llw.2	+	8	6721	c.6664G>A	c.(6664-6666)GTG>ATG	p.V2222M		NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	2222					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74649233	74649233	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74649233G>A	uc002lmi.2	+	26	4908	c.4710G>A	c.(4708-4710)ACG>ACA	p.T1570T	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1570					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)														---	---	---	---
HCN2	610	broad.mit.edu	37	19	605189	605189	+	Silent	SNP	G	A	A	rs139997813	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:605189G>A	uc002lpe.2	+	3	1238	c.1185G>A	c.(1183-1185)CCG>CCA	p.P395P		NM_001194	NP_001185	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic	395	Extracellular (Potential).				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)														---	---	---	---
ELANE	1991	broad.mit.edu	37	19	852928	852928	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:852928G>A	uc002lqb.2	+	2	158	c.120G>A	c.(118-120)GCG>GCA	p.A40A		NM_001972	NP_001963	P08246	ELNE_HUMAN	neutrophil elastase preproprotein	40	Peptidase S1.				cellular calcium ion homeostasis|negative regulation of chemokine biosynthetic process|negative regulation of chemotaxis|negative regulation of inflammatory response|negative regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of MAP kinase activity|positive regulation of smooth muscle cell proliferation|protein catabolic process|proteolysis|response to UV	cell surface|extracellular region|stored secretory granule	bacterial cell surface binding|cytokine binding|heparin binding			pancreas(1)	1					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)									Kostmann_syndrome				---	---	---	---
LMNB2	84823	broad.mit.edu	37	19	2435142	2435142	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2435142C>T	uc002lvy.2	-	5	739	c.652G>A	c.(652-654)GAG>AAG	p.E218K	LMNB2_uc002lwa.1_Missense_Mutation_p.E238K	NM_032737	NP_116126	Q03252	LMNB2_HUMAN	lamin B2	218	Rod.|Linker 2.					nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		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)														---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4704312	4704312	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4704312G>A	uc002mba.2	-	6	689	c.431C>T	c.(430-432)ACG>ATG	p.T144M	DPP9_uc002mbb.2_Missense_Mutation_p.T144M|DPP9_uc002mbc.2_Missense_Mutation_p.T144M	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	115					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	4941597	4941597	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4941597G>A	uc002mbo.2	+	6	1011	c.843G>A	c.(841-843)GAG>GAA	p.E281E	UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Silent_p.E294E	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	281					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)														---	---	---	---
XAB2	56949	broad.mit.edu	37	19	7690872	7690872	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7690872T>C	uc002mgx.2	-	6	742	c.716A>G	c.(715-717)AAT>AGT	p.N239S		NM_020196	NP_064581	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	239	HAT 7.				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					---	---	---	---
PCP2	126006	broad.mit.edu	37	19	7697386	7697386	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7697386C>T	uc002mgz.2	-	3	411	c.184G>A	c.(184-186)GAG>AAG	p.E62K	XAB2_uc002mgx.2_5'Flank	NM_174895	NP_777555	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2	62					signal transduction		GTPase activator activity				0																		---	---	---	---
TIMM44	10469	broad.mit.edu	37	19	7998892	7998892	+	Intron	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7998892C>T	uc002miz.2	-						TIMM44_uc002mja.2_Intron|TIMM44_uc010dvx.1_Intron	NM_006351	NP_006342			translocase of inner mitochondrial membrane 44						protein targeting to mitochondrion	mitochondrial inner membrane presequence translocase complex|mitochondrial matrix	ATP binding|P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
OR7D4	125958	broad.mit.edu	37	19	9325158	9325158	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9325158G>A	uc002mla.1	-	1	356	c.356C>T	c.(355-357)GCC>GTC	p.A119V		NM_001005191	NP_001005191	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D,	119	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
ZNF763	284390	broad.mit.edu	37	19	12089240	12089240	+	Silent	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12089240C>A	uc002msw.2	+	4	656	c.501C>A	c.(499-501)ACC>ACA	p.T167T	ZNF763_uc010xmf.1_Silent_p.T187T|ZNF763_uc002msv.2_Silent_p.T170T|ZNF763_uc010xmg.1_Silent_p.T45T	NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763	167					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
TNPO2	30000	broad.mit.edu	37	19	12821569	12821569	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12821569G>A	uc002muo.2	-	12	1321	c.1136C>T	c.(1135-1137)GCA>GTA	p.A379V	TNPO2_uc002mup.2_Missense_Mutation_p.A471V|TNPO2_uc002muq.2_Missense_Mutation_p.A379V|TNPO2_uc002mur.2_Missense_Mutation_p.A379V	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	379					intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14736376	14736376	+	Silent	SNP	G	A	A	rs147270469	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14736376G>A	uc002mzi.3	-	15	1996	c.1848C>T	c.(1846-1848)ATC>ATT	p.I616I	EMR3_uc010dzp.2_Silent_p.I564I|EMR3_uc010xnv.1_Silent_p.I490I	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	616	Cytoplasmic (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6																		---	---	---	---
CYP4F2	8529	broad.mit.edu	37	19	15989624	15989624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15989624C>T	uc002nbs.1	-	13	1570	c.1520G>A	c.(1519-1521)CGC>CAC	p.R507H	CYP4F2_uc010xot.1_Missense_Mutation_p.R358H	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	507					leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17015120	17015120	+	Silent	SNP	C	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17015120C>G	uc002nfb.2	-	32	4340	c.4308G>C	c.(4306-4308)CTG>CTC	p.L1436L	CPAMD8_uc002nfd.1_5'Flank	NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1389						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17015121	17015121	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17015121A>C	uc002nfb.2	-	32	4339	c.4307T>G	c.(4306-4308)CTG>CGG	p.L1436R	CPAMD8_uc002nfd.1_5'Flank	NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1389						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
PIK3R2	5296	broad.mit.edu	37	19	18271854	18271854	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18271854G>A	uc002nia.1	+						PIK3R2_uc002nib.1_Intron|PIK3R2_uc010ebi.1_Intron	NM_005027	NP_005018			phosphoinositide-3-kinase, regulatory subunit 2						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding			lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
SSBP4	170463	broad.mit.edu	37	19	18538151	18538151	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18538151G>A	uc002niy.2	+						SSBP4_uc010ebp.2_Intron|SSBP4_uc002niz.2_Intron	NM_032627	NP_116016			single stranded DNA binding protein 4 isoform a							nucleus	single-stranded DNA binding				0																		---	---	---	---
NCAN	1463	broad.mit.edu	37	19	19338902	19338902	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19338902A>G	uc002nlz.2	+	8	2572	c.2473A>G	c.(2473-2475)ACT>GCT	p.T825A	NCAN_uc010ecc.1_Missense_Mutation_p.T389A	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	825					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)															---	---	---	---
WTIP	126374	broad.mit.edu	37	19	34991049	34991049	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34991049C>T	uc002nvm.2	+	8	1168	c.1168C>T	c.(1168-1170)CTG>TTG	p.L390L		NM_001080436	NP_001073905			Wilms tumor 1 interacting protein												0	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)															---	---	---	---
MAG	4099	broad.mit.edu	37	19	35793406	35793406	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35793406G>A	uc002nyy.1	+	7	1175	c.1026G>A	c.(1024-1026)ACG>ACA	p.T342T	MAG_uc002nyx.1_Silent_p.T342T|MAG_uc010eds.1_Silent_p.T317T|MAG_uc002nyz.1_Silent_p.T342T	NM_002361	NP_002352	P20916	MAG_HUMAN	myelin associated glycoprotein isoform a	342	Ig-like C2-type 3.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane	sugar binding			breast(3)|lung(2)|central_nervous_system(1)|skin(1)	7	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)															---	---	---	---
TMEM147	10430	broad.mit.edu	37	19	36038232	36038232	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36038232C>T	uc002oaj.1	+	7	655	c.558C>T	c.(556-558)TTC>TTT	p.F186F	uc010eec.1_5'Flank|uc002oag.2_5'Flank|TMEM147_uc002oai.1_Silent_p.F137F|TMEM147_uc002oak.1_Silent_p.F141F	NM_032635	NP_116024	Q9BVK8	TM147_HUMAN	transmembrane protein 147	186	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	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)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36558338	36558338	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36558338A>G	uc002odc.2	+	6	783	c.692A>G	c.(691-693)GAG>GGG	p.E231G	WDR62_uc002odd.2_Missense_Mutation_p.E231G|WDR62_uc002odb.2_Missense_Mutation_p.E231G	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	231	WD 3.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36595830	36595830	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36595830C>T	uc002odc.2	+	32	4548	c.4457C>T	c.(4456-4458)CCG>CTG	p.P1486L	WDR62_uc002odd.2_Missense_Mutation_p.P1491L	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	1486					cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF571	51276	broad.mit.edu	37	19	38055639	38055639	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38055639C>A	uc002ogt.2	-	4	1792	c.1691G>T	c.(1690-1692)GGG>GTG	p.G564V	uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF540_uc002ogq.2_Intron|ZNF571_uc002ogr.1_Intron|uc002ogs.1_5'Flank|ZNF571_uc010efp.2_Missense_Mutation_p.G564V	NM_016536	NP_057620	Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	564	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38990408	38990408	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38990408C>T	uc002oit.2	+	44	7291	c.7161C>T	c.(7159-7161)TCC>TCT	p.S2387S	RYR1_uc002oiu.2_Silent_p.S2387S|RYR1_uc002oiv.1_5'UTR	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	2387	Cytoplasmic.|6 X approximate repeats.				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)													---	---	---	---
SARS2	54938	broad.mit.edu	37	19	39410406	39410406	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39410406C>T	uc002oka.2	-	7	915	c.755G>A	c.(754-756)CGC>CAC	p.R252H	SARS2_uc002ojz.2_Missense_Mutation_p.R62H|SARS2_uc010xup.1_Missense_Mutation_p.R254H|SARS2_uc002okb.2_Missense_Mutation_p.R252H|SARS2_uc010xuq.1_Missense_Mutation_p.R252H|SARS2_uc010xur.1_RNA	NM_017827	NP_060297	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2 isoform b precursor	252					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)															---	---	---	---
NCCRP1	342897	broad.mit.edu	37	19	39691287	39691287	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39691287G>A	uc002okq.1	+	6	738	c.719G>A	c.(718-720)GGT>GAT	p.G240D		NM_001001414	NP_001001414	Q6ZVX7	NCRP1_HUMAN	non-specific cytotoxic cell receptor protein 1	240	FBA.				protein catabolic process					ovary(1)	1																		---	---	---	---
IL28B	282617	broad.mit.edu	37	19	39734754	39734754	+	Missense_Mutation	SNP	G	A	A	rs145428712	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39734754G>A	uc010xut.1	-	3	306	c.302C>T	c.(301-303)ACG>ATG	p.T101M	IL28B_uc010xuu.1_Missense_Mutation_p.T101M	NM_172139	NP_742151	Q8IZI9	IL28B_HUMAN	interleukin 28B	101					response to virus	extracellular space	cytokine activity				0	all_cancers(60;2.81e-07)|all_lung(34;7.81e-08)|Lung NSC(34;9.29e-08)|all_epithelial(25;3.9e-07)|Ovarian(47;0.0315)		Epithelial(26;1.55e-27)|all cancers(26;1.41e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)															---	---	---	---
C19orf47	126526	broad.mit.edu	37	19	40842077	40842077	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40842077G>A	uc002oni.3	-	4	274	c.273C>T	c.(271-273)GGC>GGT	p.G91G	C19orf47_uc002ong.2_5'UTR|C19orf47_uc002onh.2_Silent_p.G24G	NM_178830	NP_849152	Q8N9M1	CS047_HUMAN	hypothetical protein LOC126526	91										ovary(1)|skin(1)	2			Lung(22;0.000636)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	40996063	40996063	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40996063G>A	uc002ony.2	+	4	489	c.403G>A	c.(403-405)GTG>ATG	p.V135M	SPTBN4_uc002onx.2_Missense_Mutation_p.V135M|SPTBN4_uc002onz.2_Missense_Mutation_p.V135M	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	135	CH 1.|Actin-binding.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SNRPA	6626	broad.mit.edu	37	19	41265330	41265330	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41265330T>C	uc002ooz.2	+						SNRPA_uc002opa.2_Intron	NM_004596	NP_004587			small nuclear ribonucleoprotein polypeptide A							nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding			skin(2)|ovary(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
CIC	23152	broad.mit.edu	37	19	42795129	42795129	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42795129G>A	uc002otf.1	+	10	2249	c.2209G>A	c.(2209-2211)GCC>ACC	p.A737T		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	737	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	p.A737A(1)		ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
ZNF285	26974	broad.mit.edu	37	19	44892073	44892073	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44892073C>T	uc002ozd.3	-	4	421	c.334G>A	c.(334-336)GCA>ACA	p.A112T	ZFP112_uc010xwz.1_Intron|ZNF285_uc010xxa.1_Missense_Mutation_p.A119T	NM_152354	NP_689567	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	112					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(2)	4																		---	---	---	---
IGFL3	388555	broad.mit.edu	37	19	46627291	46627291	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46627291G>A	uc002pea.1	-	3	227	c.202C>T	c.(202-204)CGC>TGC	p.R68C		NM_207393	NP_997276	Q6UXB1	IGFL3_HUMAN	IGF-like family member 3 precursor	68						extracellular region	protein binding				0		Ovarian(192;0.0175)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00473)|GBM - Glioblastoma multiforme(486;0.0149)|Epithelial(262;0.239)														---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47570582	47570582	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47570582G>A	uc002pga.3	-	15	2981	c.2943C>T	c.(2941-2943)CCC>CCT	p.P981P	ZC3H4_uc002pgb.1_Intron	NM_015168	NP_055983	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	981							nucleic acid binding|zinc ion binding			skin(4)|ovary(2)	6		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)														---	---	---	---
GLTSCR2	29997	broad.mit.edu	37	19	48254334	48254334	+	Missense_Mutation	SNP	C	T	T	rs34462252	byFrequency;by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48254334C>T	uc002phm.2	+	4	592	c.568C>T	c.(568-570)CGG>TGG	p.R190W	GLTSCR2_uc002phk.2_Missense_Mutation_p.R190W|GLTSCR2_uc002phl.2_Missense_Mutation_p.R190W|GLTSCR2_uc010elj.2_Missense_Mutation_p.R190W|GLTSCR2_uc010elk.1_5'Flank	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	190				RRKEQLWEKLAKQGELPREVRRAQARLLNPSATRAKPGPQD TVERP -> SGRSSYGRSWPSRASSPGGAQGPSPVAQPFCN KGPNPAPGHRIAA (in Ref. 3; AAG30413).		nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)														---	---	---	---
LMTK3	114783	broad.mit.edu	37	19	49005730	49005730	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49005730G>T	uc002pjk.2	-	8	841	c.841C>A	c.(841-843)CGC>AGC	p.R281S		NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49685882	49685882	+	Silent	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49685882G>T	uc002pmw.2	+	11	1383	c.1311G>T	c.(1309-1311)CGG>CGT	p.R437R	TRPM4_uc010emu.2_Silent_p.R437R|TRPM4_uc010yak.1_5'UTR|TRPM4_uc002pmx.2_Silent_p.R263R|TRPM4_uc010emv.2_Silent_p.R322R|TRPM4_uc010yal.1_Silent_p.R83R|TRPM4_uc002pmy.2_5'UTR	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	437	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)														---	---	---	---
SLC6A16	28968	broad.mit.edu	37	19	49794007	49794007	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49794007G>A	uc002pmz.2	-	11	2030	c.1796C>T	c.(1795-1797)ACG>ATG	p.T599M	SLC6A16_uc002pna.2_Missense_Mutation_p.T599M	NM_014037	NP_054756	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	599						integral to membrane|intracellular	neurotransmitter:sodium symporter activity			skin(2)|ovary(1)|kidney(1)	4		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)														---	---	---	---
SCAF1	58506	broad.mit.edu	37	19	50156263	50156263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50156263C>T	uc002poq.2	+	7	2741	c.2617C>T	c.(2617-2619)CGC>TGC	p.R873C		NM_021228	NP_067051	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	873					mRNA processing|RNA splicing	nucleus	RNA binding				0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)														---	---	---	---
IL4I1	259307	broad.mit.edu	37	19	50393802	50393802	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50393802G>A	uc002pqt.1	-	8	907	c.829C>T	c.(829-831)CTG>TTG	p.L277L	IL4I1_uc002pqv.1_Silent_p.L286L|IL4I1_uc010eno.1_Silent_p.L285L|IL4I1_uc002pqw.1_Silent_p.L285L|IL4I1_uc002pqu.1_Silent_p.L299L	NM_152899	NP_690863	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 1 precursor	277						lysosome	L-amino-acid oxidase activity			lung(1)|ovary(1)|prostate(1)	3		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)														---	---	---	---
SPIB	6689	broad.mit.edu	37	19	50925723	50925723	+	Intron	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50925723G>A	uc002psd.2	+						SPIB_uc002pse.2_Intron|SPIB_uc010ycc.1_Intron	NM_003121	NP_003112			Spi-B transcription factor (Spi-1/PU.1 related)						regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	sequence-specific DNA binding			lung(1)|kidney(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
LRRC4B	94030	broad.mit.edu	37	19	51021562	51021562	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51021562C>T	uc002pss.2	-	3	1545	c.1408G>A	c.(1408-1410)GGC>AGC	p.G470S		NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor	470	Gly-rich.|Extracellular (Potential).					cell junction|integral to membrane|presynaptic membrane				central_nervous_system(1)|skin(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51219975	51219975	+	Missense_Mutation	SNP	C	T	T	rs150390491		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51219975C>T	uc002psx.1	-	1	221	c.202G>A	c.(202-204)GCC>ACC	p.A68T		NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	68					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)														---	---	---	---
KLK14	43847	broad.mit.edu	37	19	51582715	51582715	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51582715T>G	uc002pvs.1	-	5	724	c.505A>C	c.(505-507)AGC>CGC	p.S169R		NM_022046	NP_071329	Q9P0G3	KLK14_HUMAN	kallikrein 14 preproprotein	169	Peptidase S1.				epidermis morphogenesis|fertilization|negative regulation of G-protein coupled receptor protein signaling pathway|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis|seminal clot liquefaction	extracellular space	serine-type endopeptidase activity			skin(1)	1		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)														---	---	---	---
MIR525	574470	broad.mit.edu	37	19	54200863	54200863	+	RNA	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54200863C>T	hsa-mir-525|MI0003152	+			c.77C>T			MIR523_hsa-mir-523|MI0003153_5'Flank|MIR518F_hsa-mir-518f|MI0003154_5'Flank																	0																		---	---	---	---
LILRB5	10990	broad.mit.edu	37	19	54760565	54760565	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54760565A>C	uc002qex.2	-	3	253	c.142T>G	c.(142-144)TGG>GGG	p.W48G	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.W48G|LILRB5_uc002qey.2_Missense_Mutation_p.W48G|LILRB5_uc002qez.2_Missense_Mutation_p.W48G|LILRB5_uc002qfa.1_Missense_Mutation_p.W38G|LILRB5_uc010yes.1_RNA	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	48	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)														---	---	---	---
NLRP4	147945	broad.mit.edu	37	19	56382340	56382340	+	Silent	SNP	G	T	T	rs142568700	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56382340G>T	uc002qmd.3	+	7	2924	c.2502G>T	c.(2500-2502)CCG>CCT	p.P834P	NLRP4_uc002qmf.2_Silent_p.P759P|NLRP4_uc010etf.2_Silent_p.P609P	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	834							ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)														---	---	---	---
ZNF582	147948	broad.mit.edu	37	19	56896019	56896019	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56896019T>G	uc002qmz.1	-	5	926	c.767A>C	c.(766-768)GAA>GCA	p.E256A	ZNF582_uc002qmy.2_Missense_Mutation_p.E287A	NM_144690	NP_653291	Q96NG8	ZN582_HUMAN	zinc finger protein 582	256	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|large_intestine(1)	4		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)														---	---	---	---
ZBTB45	84878	broad.mit.edu	37	19	59028872	59028872	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59028872A>T	uc002qtd.2	-	2	461	c.169T>A	c.(169-171)TTC>ATC	p.F57I	ZBTB45_uc002qte.2_Missense_Mutation_p.F57I|ZBTB45_uc002qtf.2_Missense_Mutation_p.F57I	NM_032792	NP_116181	Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	57	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		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;0.0165)|Lung(386;0.18)												OREG0025700	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PSMF1	9491	broad.mit.edu	37	20	1145696	1145696	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1145696C>A	uc002wel.3	+	8	956	c.788C>A	c.(787-789)CCG>CAG	p.P263Q	PSMF1_uc010zpo.1_Intron|PSMF1_uc002wem.3_Intron|PSMF1_uc010zpp.1_Intron|PSMF1_uc002wen.3_Missense_Mutation_p.P263Q|PSMF1_uc002wep.3_Missense_Mutation_p.P214Q	NM_178578	NP_848693	Q92530	PSMF1_HUMAN	proteasome inhibitor subunit 1	263	Pro-rich.				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 core complex	endopeptidase inhibitor activity|protein binding				0																		---	---	---	---
CDS2	8760	broad.mit.edu	37	20	5165505	5165505	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5165505T>C	uc002wls.2	+	8	930	c.673T>C	c.(673-675)TTC>CTC	p.F225L	CDS2_uc002wlr.1_Missense_Mutation_p.F147L|CDS2_uc010zqt.1_RNA|CDS2_uc002wlu.2_Missense_Mutation_p.F170L|CDS2_uc010zqu.1_Missense_Mutation_p.F105L|CDS2_uc002wlv.2_Missense_Mutation_p.F127L|CDS2_uc010zqv.1_Missense_Mutation_p.F46L	NM_003818	NP_003809	O95674	CDS2_HUMAN	phosphatidate cytidylyltransferase 2	225	Helical; (Potential).				phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphatidate cytidylyltransferase activity				0																		---	---	---	---
ANKRD5	63926	broad.mit.edu	37	20	10033880	10033880	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10033880C>A	uc002wno.2	+	9	2384	c.1991C>A	c.(1990-1992)CCT>CAT	p.P664H	uc002wnn.1_Intron|ANKRD5_uc002wnp.2_Missense_Mutation_p.P664H|ANKRD5_uc010gbz.2_Missense_Mutation_p.P475H	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	664							calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
ANKRD5	63926	broad.mit.edu	37	20	10036224	10036224	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10036224G>T	uc002wno.2	+	11	2640	c.2247G>T	c.(2245-2247)GAG>GAT	p.E749D	uc002wnn.1_Intron|ANKRD5_uc002wnp.2_Missense_Mutation_p.E749D|ANKRD5_uc010gbz.2_Missense_Mutation_p.E560D	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	749							calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31381410	31381410	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31381410T>C	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_Intron|DNMT3B_uc002wyg.2_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																		---	---	---	---
C20orf134	170487	broad.mit.edu	37	20	32255583	32255583	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32255583G>A	uc002wzt.2	+	1	1280	c.280G>A	c.(280-282)GAC>AAC	p.D94N	NECAB3_uc002wzm.3_Intron|NECAB3_uc002wzn.3_Intron|NECAB3_uc002wzo.3_Intron|NECAB3_uc002wzp.3_Intron|NECAB3_uc002wzq.3_Intron|NECAB3_uc002wzr.3_Intron|NECAB3_uc010geo.2_Intron	NM_001024675	NP_001019846	Q5JWF8	CT134_HUMAN	hypothetical protein LOC170487	94										pancreas(1)	1																		---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35060141	35060141	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35060141C>T	uc002xff.2	+	3	456	c.21C>T	c.(19-21)AGC>AGT	p.S7S	DLGAP4_uc010zvp.1_Silent_p.S7S	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a	7					cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
ZNF334	55713	broad.mit.edu	37	20	45130805	45130805	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45130805G>A	uc002xsc.2	-	5	1357	c.1173C>T	c.(1171-1173)GCC>GCT	p.A391A	ZNF334_uc002xsa.2_Silent_p.A414A|ZNF334_uc002xsb.2_Silent_p.A353A|ZNF334_uc002xsd.2_Silent_p.A353A|ZNF334_uc010ghl.2_Silent_p.A390A	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a	391	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47865975	47865975	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47865975G>T	uc002xui.2	-	14	3833	c.3586C>A	c.(3586-3588)CTC>ATC	p.L1196I		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1196							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48129730	48129730	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48129730G>T	uc002xut.2	-	8	1147	c.1093C>A	c.(1093-1095)CTG>ATG	p.L365M	PTGIS_uc010zyi.1_Missense_Mutation_p.L226M	NM_000961	NP_000952	Q16647	PTGIS_HUMAN	prostaglandin I2 synthase	365					hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|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|prostaglandin-I synthase activity			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)													---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50139969	50139969	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50139969G>A	uc002xwd.2	-	2	1031	c.811C>T	c.(811-813)CGC>TGC	p.R271C	NFATC2_uc002xwc.2_Missense_Mutation_p.R271C|NFATC2_uc010zyv.1_Missense_Mutation_p.R52C|NFATC2_uc010zyw.1_Missense_Mutation_p.R52C|NFATC2_uc010zyx.1_Missense_Mutation_p.R251C|NFATC2_uc010zyy.1_Missense_Mutation_p.R52C|NFATC2_uc010zyz.1_Missense_Mutation_p.R52C|NFATC2_uc002xwe.2_Missense_Mutation_p.R251C	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	271	3 X approximate SP repeats.				B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
C20orf177	63939	broad.mit.edu	37	20	58519082	58519082	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58519082C>T	uc002yba.2	+	5	499	c.84C>T	c.(82-84)CAC>CAT	p.H28H	C20orf177_uc010zzx.1_Intron|C20orf177_uc002ybc.2_Silent_p.H28H	NM_022106	NP_071389	Q9NTX9	CT177_HUMAN	hypothetical protein LOC63939	28										ovary(2)|breast(1)	3	all_lung(29;0.00693)		BRCA - Breast invasive adenocarcinoma(7;1.22e-08)															---	---	---	---
SLCO4A1	28231	broad.mit.edu	37	20	61288207	61288207	+	Missense_Mutation	SNP	G	A	A	rs79135275		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61288207G>A	uc002ydb.1	+	2	606	c.401G>A	c.(400-402)CGC>CAC	p.R134H	SLCO4A1_uc002ydc.1_RNA	NM_016354	NP_057438	Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family	134	Extracellular (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)															---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61541269	61541269	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61541269T>C	uc002ydr.1	-	4	1207	c.943A>G	c.(943-945)ATC>GTC	p.I315V	DIDO1_uc002yds.1_Missense_Mutation_p.I315V|DIDO1_uc002ydt.1_Missense_Mutation_p.I315V|DIDO1_uc002ydu.1_Missense_Mutation_p.I315V|DIDO1_uc002ydv.1_Missense_Mutation_p.I315V|DIDO1_uc002ydw.1_Missense_Mutation_p.I315V|DIDO1_uc002ydx.1_Missense_Mutation_p.I315V|DIDO1_uc011aao.1_Missense_Mutation_p.I315V	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	315	PHD-type.				apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62839241	62839241	+	Missense_Mutation	SNP	G	A	A	rs139069988		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62839241G>A	uc002yii.2	+	7	1056	c.692G>A	c.(691-693)CGC>CAC	p.R231H	MYT1_uc002yih.2_Intron|MYT1_uc002yij.2_5'UTR	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	231	Glu-rich.				cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)																	---	---	---	---
KRTAP26-1	388818	broad.mit.edu	37	21	31691822	31691822	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31691822C>T	uc002ynw.2	-	1	786	c.532G>A	c.(532-534)GTT>ATT	p.V178I		NM_203405	NP_981950	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	178						intermediate filament				ovary(1)	1																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32617973	32617973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32617973C>T	uc002yow.1	-	7	1887	c.1415G>A	c.(1414-1416)TGC>TAC	p.C472Y	TIAM1_uc011adk.1_Missense_Mutation_p.C472Y|TIAM1_uc011adl.1_Missense_Mutation_p.C472Y|TIAM1_uc002yox.1_Missense_Mutation_p.C80Y	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	472	PH 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43162041	43162041	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43162041C>T	uc002yzn.1	-	8	1360	c.1312G>A	c.(1312-1314)GGT>AGT	p.G438S		NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3	438						cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
PKNOX1	5316	broad.mit.edu	37	21	44437072	44437072	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44437072G>A	uc002zcq.1	+	6	765	c.577G>A	c.(577-579)GCG>ACG	p.A193T	PKNOX1_uc002zcp.1_Missense_Mutation_p.A193T|PKNOX1_uc011aex.1_Missense_Mutation_p.A76T|PKNOX1_uc002zcr.2_Missense_Mutation_p.A193T	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	193							sequence-specific DNA binding			large_intestine(2)	2																		---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17983977	17983977	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17983977C>T	uc010gqw.1	+	6	799	c.673C>T	c.(673-675)CGA>TGA	p.R225*	CECR2_uc010gqv.1_Nonsense_Mutation_p.R104*|CECR2_uc002zml.2_Nonsense_Mutation_p.R104*|CECR2_uc002zmm.1_Nonsense_Mutation_p.R104*	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	267					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)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	18021539	18021539	+	Silent	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18021539A>G	uc010gqw.1	+	14	1956	c.1830A>G	c.(1828-1830)GTA>GTG	p.V610V	CECR2_uc010gqv.1_Silent_p.V469V|CECR2_uc002zml.2_Silent_p.V469V	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	652					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)														---	---	---	---
SLC25A18	83733	broad.mit.edu	37	22	18070848	18070848	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18070848A>G	uc002zmp.1	+						SLC25A18_uc010gqx.2_Missense_Mutation_p.K245E|SLC25A18_uc002zmq.1_Intron	NM_031481	NP_113669			solute carrier							integral to membrane|mitochondrial inner membrane	binding|symporter activity				0				Lung(27;0.124)	L-Glutamic Acid(DB00142)													---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18355566	18355566	+	Intron	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18355566T>C	uc002zng.3	-						MICAL3_uc011agl.1_Intron|MICAL3_uc002znh.2_Intron|MICAL3_uc002znj.1_Intron|MICAL3_uc002znk.1_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc002znm.2_Intron|MICAL3_uc010grf.2_Missense_Mutation_p.N854D	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)														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23055685	23055685	+	RNA	SNP	C	A	A	rs112258197		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23055685C>A	uc011aim.1	+	153		c.9400C>A								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24717989	24717989	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24717989T>C	uc002zzw.2	+	5	1348	c.1041T>C	c.(1039-1041)AGT>AGC	p.S347S	CYTSA_uc002zzv.3_Silent_p.S347S|CYTSA_uc011ajq.1_Silent_p.S347S	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A	347					cell cycle|cell division						0																		---	---	---	---
RNF215	200312	broad.mit.edu	37	22	30782597	30782597	+	Intron	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30782597C>A	uc003ahp.2	-						RNF215_uc011akw.1_Intron	NM_001017981	NP_001017981			ring finger protein 215							integral to membrane	zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
PIK3IP1	113791	broad.mit.edu	37	22	31679239	31679239	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31679239A>G	uc003akm.2	-	6	813	c.623T>C	c.(622-624)GTA>GCA	p.V208A	PIK3IP1_uc003akl.2_RNA|PIK3IP1_uc011alo.1_3'UTR|PIK3IP1_uc003akn.2_Missense_Mutation_p.V188A	NM_052880	NP_443112	Q96FE7	P3IP1_HUMAN	HGFL protein isoform 1	208	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
L3MBTL2	83746	broad.mit.edu	37	22	41620769	41620769	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41620769G>T	uc003azo.2	+	10	1269	c.1215G>T	c.(1213-1215)AAG>AAT	p.K405N	L3MBTL2_uc010gyi.1_Missense_Mutation_p.K314N|L3MBTL2_uc003azn.2_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	405	MBT 3.				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																		---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43227589	43227589	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43227589T>C	uc003bdd.2	-	6	751	c.531A>G	c.(529-531)TCA>TCG	p.S177S	ARFGAP3_uc010gzf.2_Silent_p.S133S|ARFGAP3_uc011apu.1_Silent_p.S105S	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating	177					intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1																		---	---	---	---
RIBC2	26150	broad.mit.edu	37	22	45818216	45818216	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45818216G>A	uc011aqs.1	+	5	797	c.588G>A	c.(586-588)AAG>AAA	p.K196K		NM_015653	NP_056468	Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2	128											0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46774624	46774624	+	Intron	SNP	G	T	T	rs143614301	by1000genomes	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46774624G>T	uc003bhw.1	-						CELSR1_uc011arc.1_Intron	NM_014246	NP_055061			cadherin EGF LAG seven-pass G-type receptor 1						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)														---	---	---	---
SBF1	6305	broad.mit.edu	37	22	50906280	50906280	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50906280C>T	uc003blh.2	-	3	409	c.214G>A	c.(214-216)GAC>AAC	p.D72N	SBF1_uc011arx.1_5'Flank|SBF1_uc003bli.2_Missense_Mutation_p.D72N	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	72	UDENN.				protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				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;0.206)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TLR8	51311	broad.mit.edu	37	X	12940244	12940244	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12940244C>T	uc004cve.2	+	2	3153	c.3085C>T	c.(3085-3087)CGG>TGG	p.R1029W	TLR8_uc004cvd.2_Missense_Mutation_p.R1047W	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	1029	Cytoplasmic (Potential).				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|lung(2)|large_intestine(1)	7																		---	---	---	---
PHKA2	5256	broad.mit.edu	37	X	18969298	18969298	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18969298G>A	uc004cyv.3	-	4	808	c.378C>T	c.(376-378)GGC>GGT	p.G126G	PHKA2_uc010nfh.1_Intron|PHKA2_uc010nfi.1_Silent_p.G68G	NM_000292	NP_000283	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	126					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	19031842	19031842	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19031842G>A	uc004cyx.2	-	16	1225	c.1061C>T	c.(1060-1062)GCG>GTG	p.A354V	GPR64_uc004cyy.2_Missense_Mutation_p.A351V|GPR64_uc004cyz.2_Missense_Mutation_p.A340V|GPR64_uc004czb.2_Missense_Mutation_p.A354V|GPR64_uc004czc.2_Missense_Mutation_p.A338V|GPR64_uc004czd.2_Missense_Mutation_p.A330V|GPR64_uc004cze.2_Missense_Mutation_p.A324V|GPR64_uc004czf.2_Missense_Mutation_p.A316V|GPR64_uc004cza.2_Missense_Mutation_p.A332V|GPR64_uc004cyw.2_Missense_Mutation_p.A338V|GPR64_uc010nfj.2_Missense_Mutation_p.A324V	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	354	Extracellular (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
SAT1	6303	broad.mit.edu	37	X	23801523	23801523	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23801523C>T	uc004dau.2	+	1	249	c.55C>T	c.(55-57)CGG>TGG	p.R19W	SAT1_uc010nfv.2_Missense_Mutation_p.R19W|SAT1_uc004dav.2_RNA	NM_002970	NP_002961	P21673	SAT1_HUMAN	diamine N-acetyltransferase 1	19	N-acetyltransferase.				angiogenesis|polyamine biosynthetic process	cytosol	diamine N-acetyltransferase activity|protein binding				0					Spermine(DB00127)											OREG0019712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM48B1	100130302	broad.mit.edu	37	X	24382737	24382737	+	Silent	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24382737C>A	uc011mjx.1	+	1	1860	c.1860C>A	c.(1858-1860)GCC>GCA	p.A620A		NM_001136234	NP_001129706			hypothetical protein LOC100130302											kidney(1)	1																		---	---	---	---
FAM47A	158724	broad.mit.edu	37	X	34150134	34150134	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34150134C>G	uc004ddg.2	-	1	295	c.262G>C	c.(262-264)GCT>CCT	p.A88P		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	88										ovary(4)|central_nervous_system(1)	5																		---	---	---	---
FAM47C	442444	broad.mit.edu	37	X	37028447	37028447	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37028447G>A	uc004ddl.1	+	1	1978	c.1964G>A	c.(1963-1965)TGC>TAC	p.C655Y		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	655										ovary(3)	3																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46508232	46508232	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46508232C>T	uc004dgu.1	-	11	1356	c.1348G>A	c.(1348-1350)GTT>ATT	p.V450I		NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	450	Helical; (Potential).				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																		---	---	---	---
KCND1	3750	broad.mit.edu	37	X	48826129	48826129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48826129C>T	uc004dlx.1	-	1	2123	c.550G>A	c.(550-552)GCA>ACA	p.A184T	KCND1_uc004dlw.1_5'Flank	NM_004979	NP_004970	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related	184	Cytoplasmic (Potential).					voltage-gated potassium channel complex	metal ion binding|voltage-gated potassium channel activity			ovary(2)|lung(1)	3																		---	---	---	---
CCNB3	85417	broad.mit.edu	37	X	50085219	50085219	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50085219C>T	uc004dox.3	+	9	3833	c.3535C>T	c.(3535-3537)CAT>TAT	p.H1179Y	CCNB3_uc004doy.2_Missense_Mutation_p.H1179Y|CCNB3_uc004doz.2_Missense_Mutation_p.H75Y|CCNB3_uc010njq.2_Missense_Mutation_p.H71Y|CCNB3_uc004dpa.2_Missense_Mutation_p.H18Y	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	1179					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)																	---	---	---	---
DGKK	139189	broad.mit.edu	37	X	50213578	50213578	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50213578G>A	uc010njr.1	-	1	160	c.100C>T	c.(100-102)CCA>TCA	p.P34S		NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa	34					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)																	---	---	---	---
SMC1A	8243	broad.mit.edu	37	X	53438754	53438754	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53438754T>C	uc004dsg.2	-	7	1280	c.1211A>G	c.(1210-1212)CAG>CGG	p.Q404R	SMC1A_uc011moe.1_Missense_Mutation_p.Q382R|SMC1A_uc011mof.1_Missense_Mutation_p.Q170R	NM_006306	NP_006297	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	404	Potential.				cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)|central_nervous_system(1)	6																		---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53600835	53600835	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53600835T>C	uc004dsp.2	-	47	6589	c.6187A>G	c.(6187-6189)AAA>GAA	p.K2063E	HUWE1_uc004dsn.2_Missense_Mutation_p.K887E	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	2063					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17																		---	---	---	---
TRO	7216	broad.mit.edu	37	X	54956889	54956889	+	Silent	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54956889T>C	uc004dtq.2	+	12	3839	c.3732T>C	c.(3730-3732)GGT>GGC	p.G1244G	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.G775G|TRO_uc004dtw.2_Silent_p.G847G|TRO_uc004dtx.2_Silent_p.G627G	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	1244	44.|62 X 10 AA approximate tandem repeats.				embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1																		---	---	---	---
EDA	1896	broad.mit.edu	37	X	69253319	69253319	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69253319C>A	uc004dxs.2	+	7	1107	c.865C>A	c.(865-867)CGC>AGC	p.R289S	EDA_uc004dxr.2_Missense_Mutation_p.R289S|EDA_uc011mpj.1_Missense_Mutation_p.R286S	NM_001399	NP_001390	Q92838	EDA_HUMAN	ectodysplasin A isoform EDA-A1	289	Extracellular (Potential).				cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3																OREG0019847	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
OTUD6A	139562	broad.mit.edu	37	X	69283028	69283028	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69283028C>T	uc004dxu.1	+	1	688	c.654C>T	c.(652-654)GGC>GGT	p.G218G		NM_207320	NP_997203	Q7L8S5	OTU6A_HUMAN	OTU domain containing 6A	218	OTU.									lung(1)|skin(1)	2																		---	---	---	---
PDZD11	51248	broad.mit.edu	37	X	69509183	69509183	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69509183G>A	uc004dyd.1	-	2	111	c.9C>T	c.(7-9)AGC>AGT	p.S3S	KIF4A_uc004dyg.2_5'Flank|KIF4A_uc010nkw.2_5'Flank|PDZD11_uc004dye.1_Silent_p.S35S|KIF4A_uc004dyf.1_5'Flank	NM_016484	NP_057568	Q5EBL8	PDZ11_HUMAN	PDZ domain containing 11	3						basolateral plasma membrane|cytosol|extracellular region	protein C-terminus binding				0																		---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70602920	70602920	+	Missense_Mutation	SNP	G	A	A	rs143439292		TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70602920G>A	uc004dzu.3	+	12	1901	c.1850G>A	c.(1849-1851)CGC>CAC	p.R617H	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.R638H	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	617					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
HDX	139324	broad.mit.edu	37	X	83724526	83724526	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83724526C>G	uc004eek.1	-	3	314	c.205G>C	c.(205-207)GCA>CCA	p.A69P	HDX_uc011mqv.1_Missense_Mutation_p.A69P|HDX_uc004eel.1_Missense_Mutation_p.A11P	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	69						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
KLHL4	56062	broad.mit.edu	37	X	86887291	86887291	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86887291T>G	uc004efb.2	+	7	1588	c.1406T>G	c.(1405-1407)TTT>TGT	p.F469C	KLHL4_uc004efa.2_Missense_Mutation_p.F469C	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	469	Kelch 1.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
NOX1	27035	broad.mit.edu	37	X	100099016	100099016	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100099016C>T	uc004egj.2	-	13	1826	c.1620G>A	c.(1618-1620)CTG>CTA	p.L540L	NOX1_uc004egl.3_Silent_p.L491L|NOX1_uc010nne.2_Silent_p.L503L	NM_007052	NP_008983	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1 isoform long	540	Cytoplasmic (Potential).				angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106846277	106846277	+	IGR	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106846277A>G								CXorf41 (358805 upstream) : PRPS1 (25377 downstream)																																			---	---	---	---
CAPN6	827	broad.mit.edu	37	X	110489890	110489890	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110489890C>T	uc004epc.1	-	13	2009	c.1841G>A	c.(1840-1842)CGT>CAT	p.R614H	CAPN6_uc011msu.1_Missense_Mutation_p.R359H	NM_014289	NP_055104	Q9Y6Q1	CAN6_HUMAN	calpain 6	614	C2.				microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
LRCH2	57631	broad.mit.edu	37	X	114357090	114357090	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114357090C>A	uc010nqe.2	-	20	2209	c.2178G>T	c.(2176-2178)CAG>CAT	p.Q726H	LRCH2_uc004epz.2_Missense_Mutation_p.Q709H	NM_020871	NP_065922	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH)	726	CH.									ovary(1)	1																		---	---	---	---
KIAA1210	57481	broad.mit.edu	37	X	118222233	118222233	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118222233C>T	uc004era.3	-	11	2960	c.2960G>A	c.(2959-2961)TGC>TAC	p.C987Y		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	987										ovary(4)|skin(1)	5																		---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122319737	122319737	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122319737G>A	uc004etq.3	+	3	456	c.163G>A	c.(163-165)GTG>ATG	p.V55M	GRIA3_uc004etr.3_Missense_Mutation_p.V55M|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_Missense_Mutation_p.V39M|GRIA3_uc010nqs.1_Missense_Mutation_p.V55M	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	55	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122537342	122537342	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122537342A>G	uc004etq.3	+	10	1558	c.1265A>G	c.(1264-1266)AAT>AGT	p.N422S	GRIA3_uc004etr.3_Missense_Mutation_p.N422S|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_Missense_Mutation_p.N406S	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	422	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129147951	129147951	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129147951G>A	uc004evb.1	+	4	1317	c.1203G>A	c.(1201-1203)ACG>ACA	p.T401T	BCORL1_uc010nrd.1_Silent_p.T303T	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	401	Pro-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7																		---	---	---	---
ZNF280C	55609	broad.mit.edu	37	X	129370483	129370483	+	Silent	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129370483G>A	uc004evm.2	-	7	778	c.624C>T	c.(622-624)GGC>GGT	p.G208G	ZNF280C_uc010nrf.1_Silent_p.G208G	NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	208	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3																		---	---	---	---
FHL1	2273	broad.mit.edu	37	X	135292049	135292049	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135292049T>C	uc004ezo.2	+	7	1008	c.908T>C	c.(907-909)GTG>GCG	p.V303A	FHL1_uc010nrz.2_Silent_p.S236S|FHL1_uc004ezm.2_RNA|FHL1_uc004ezl.2_Silent_p.S236S|FHL1_uc004ezq.2_Missense_Mutation_p.V174A|FHL1_uc011mvy.1_Silent_p.S236S|FHL1_uc011mvz.1_Silent_p.S236S|FHL1_uc004ezn.2_Silent_p.S236S|FHL1_uc011mwa.1_Silent_p.S265S|FHL1_uc011mwb.1_RNA|FHL1_uc004ezp.2_Silent_p.S252S|FHL1_uc004ezr.2_Missense_Mutation_p.V55A	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN	four and a half LIM domains 1 isoform 1	303					cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)															OREG0019943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135789067	135789067	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135789067C>A	uc004fab.2	-	9	1508	c.1046G>T	c.(1045-1047)AGT>ATT	p.S349I	ARHGEF6_uc011mwd.1_Missense_Mutation_p.S222I|ARHGEF6_uc011mwe.1_Missense_Mutation_p.S195I	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	349	DH.				apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135795536	135795536	+	Intron	SNP	A	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135795536A>G	uc004fab.2	-						ARHGEF6_uc011mwd.1_Intron|ARHGEF6_uc011mwe.1_Intron	NM_004840	NP_004831			Rac/Cdc42 guanine nucleotide exchange factor 6						apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAGEA10	4109	broad.mit.edu	37	X	151303089	151303089	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151303089T>C	uc004ffk.2	-	5	1412	c.1004A>G	c.(1003-1005)AAA>AGA	p.K335R	MAGEA10_uc004ffl.2_Missense_Mutation_p.K335R	NM_001011543	NP_001011543	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	335											0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HAUS7	55559	broad.mit.edu	37	X	152721808	152721808	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152721808G>A	uc004fho.1	-	7	1208	c.650C>T	c.(649-651)GCC>GTC	p.A217V	HAUS7_uc004fhl.2_RNA|HAUS7_uc004fhm.2_RNA|HAUS7_uc004fhn.1_Missense_Mutation_p.A217V|HAUS7_uc004fhp.1_RNA|HAUS7_uc011myq.1_RNA	NM_017518	NP_059988	Q99871	HAUS7_HUMAN	HAUS augmin-like complex subunit 7	217	Potential.				cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0																		---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152813345	152813345	+	Silent	SNP	G	A	A	rs142541769	byFrequency	TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152813345G>A	uc004fht.1	+	7	1137	c.1011G>A	c.(1009-1011)GCG>GCA	p.A337A	ATP2B3_uc004fhs.1_Silent_p.A337A	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	337	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PLXNB3	5365	broad.mit.edu	37	X	153036432	153036432	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153036432T>G	uc004fii.2	+	12	2323	c.2149T>G	c.(2149-2151)TCC>GCC	p.S717A	PLXNB3_uc011mzb.1_Silent_p.P172P|PLXNB3_uc011mzc.1_Missense_Mutation_p.S399A|PLXNB3_uc010nuk.2_Missense_Mutation_p.S740A|PLXNB3_uc011mzd.1_Missense_Mutation_p.S356A	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3 isoform 1	717	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ARHGAP4	393	broad.mit.edu	37	X	153175711	153175711	+	Silent	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153175711C>T	uc004fjk.1	-	17	2112	c.2070G>A	c.(2068-2070)CAG>CAA	p.Q690Q	ARHGAP4_uc004fjj.1_Silent_p.Q41Q|ARHGAP4_uc011mzf.1_Silent_p.Q667Q|ARHGAP4_uc004fjl.1_Silent_p.Q730Q|ARHGAP4_uc010nup.1_Intron	NM_001666	NP_001657	P98171	RHG04_HUMAN	Rho GTPase activating protein 4 isoform 2	690	Rho-GAP.				apoptosis|cytoskeleton organization|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|Rho protein signal transduction	cytosol|focal adhesion|nucleus	Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			central_nervous_system(1)	1	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153218271	153218271	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153218271C>A	uc004fjp.2	-	19	5164	c.4636G>T	c.(4636-4638)GCC>TCC	p.A1546S		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	1546					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)															OREG0003630	type=REGULATORY REGION|Gene=BC010606|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
FLNA	2316	broad.mit.edu	37	X	153585838	153585838	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4363-01A-01D-1158-08	TCGA-BR-4363-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153585838C>T	uc004fkk.2	-	29	5158	c.4909G>A	c.(4909-4911)GTG>ATG	p.V1637M	FLNA_uc011mzn.1_Translation_Start_Site|FLNA_uc010nuu.1_Missense_Mutation_p.V1637M	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1637			Missing (in otopalatodigital spectrum disorder).		actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)																	---	---	---	---
