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	ref_context	gc_content	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	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
GABRD	2563	broad.mit.edu	37	1	1961110	1961110	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1961110C>T	uc001aip.2	+	8	1063	c.968C>T	c.(967-969)GCC>GTC	p.A323V		NM_000815	NP_000806	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	323	Helical; (Probable).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		TTCGTGTTTGCCGCCCTGGTG	0.592													4	106	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22920016	22920016	+	Splice_Site	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22920016G>C	uc001bfx.1	+	7	1566	c.1441_splice	c.e7-1	p.D481_splice		NM_020526	NP_065387	P29322	EPHA8_HUMAN	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)		TCCCGTGGCAGGACAAGGAGA	0.652													8	17	---	---	---	---	PASS
MED18	54797	broad.mit.edu	37	1	28661113	28661113	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28661113T>A	uc001bpt.3	+	3	504	c.259T>A	c.(259-261)TAC>AAC	p.Y87N	MED18_uc009vtg.2_Missense_Mutation_p.Y87N	NM_017638	NP_060108	Q9BUE0	MED18_HUMAN	mediator complex subunit 18	87					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	identical protein binding				0		Colorectal(325;0.000147)|Lung NSC(340;0.000818)|all_lung(284;0.000996)|Renal(390;0.00357)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0557)|Ovarian(437;0.113)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0141)|READ - Rectum adenocarcinoma(331;0.0649)		GCATCTGCGCTACCTGGGACA	0.577													111	115	---	---	---	---	PASS
RNF19B	127544	broad.mit.edu	37	1	33415334	33415334	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33415334A>G	uc010oho.1	-	2	677	c.677T>C	c.(676-678)CTA>CCA	p.L226P	RNF19B_uc001bwm.3_Missense_Mutation_p.L226P|RNF19B_uc010ohp.1_Missense_Mutation_p.L226P	NM_153341	NP_699172	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B isoform a	226	IBR-type.					integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTCACAAGTTAGCTTCGGGCA	0.478													7	48	---	---	---	---	PASS
PGM1	5236	broad.mit.edu	37	1	64059088	64059088	+	5'UTR	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64059088G>C	uc001dbh.2	+	1					PGM1_uc010ooy.1_5'Flank	NM_002633	NP_002624	P36871	PGM1_HUMAN	phosphoglucomutase 1						cellular calcium ion homeostasis|galactose catabolic process|glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity			ovary(2)|kidney(1)	3						CCCCAGAGCAGCTGCAGCCTC	0.692													5	17	---	---	---	---	PASS
ATXN7L2	127002	broad.mit.edu	37	1	110031529	110031529	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110031529G>C	uc001dxr.2	+	7	859	c.844G>C	c.(844-846)GTG>CTG	p.V282L	ATXN7L2_uc001dxs.2_5'UTR|ATXN7L2_uc001dxt.2_5'Flank	NM_153340	NP_699171	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	282	SCA7.									ovary(2)	2		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		TGACGTGCTGGTGGCAGAGCT	0.617													20	75	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	145039629	145039629	+	5'UTR	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145039629G>A	uc001elx.3	-	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_5'UTR|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCTTTCCTTAGTCTCAGGACG	0.597			T	PDGFRB	MPD								5	67	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145302714	145302714	+	Silent	SNP	A	G	G	rs9424867		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145302714A>G	uc001end.3	+	8	1187	c.1152A>G	c.(1150-1152)TTA>TTG	p.L384L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_5'UTR|NBPF10_uc001emq.1_Silent_p.L113L	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGGAGAAGTTACGGGAAGGGA	0.527													4	62	---	---	---	---	PASS
ZNF687	57592	broad.mit.edu	37	1	151259347	151259347	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151259347C>G	uc001exq.2	+	2	678	c.580C>G	c.(580-582)CCT>GCT	p.P194A	ZNF687_uc001exp.1_Missense_Mutation_p.P203A|ZNF687_uc009wmo.2_Missense_Mutation_p.P194A|ZNF687_uc009wmp.2_Missense_Mutation_p.P194A	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	194	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GACCCCGCCTCCTTTCCCCTC	0.632													37	96	---	---	---	---	PASS
UBAP2L	9898	broad.mit.edu	37	1	154229659	154229659	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154229659A>C	uc001fep.3	+	19	2445	c.2278A>C	c.(2278-2280)AGT>CGT	p.S760R	UBAP2L_uc009wot.2_Missense_Mutation_p.S760R|UBAP2L_uc010pek.1_Missense_Mutation_p.S752R|UBAP2L_uc010pel.1_Missense_Mutation_p.S770R|UBAP2L_uc010pen.1_Missense_Mutation_p.S674R|UBAP2L_uc001feq.2_5'UTR|UBAP2L_uc001fer.2_5'UTR	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	760					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CAATAGTGGCAGTAGCCTGGG	0.552													23	64	---	---	---	---	PASS
UBQLN4	56893	broad.mit.edu	37	1	156006880	156006880	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156006880C>A	uc001fna.2	-	11	1719	c.1695G>T	c.(1693-1695)CAG>CAT	p.Q565H	UBQLN4_uc010pgx.1_Missense_Mutation_p.Q545H	NM_020131	NP_064516	Q9NRR5	UBQL4_HUMAN	ataxin-1 ubiquitin-like interacting protein	565	UBA.					cytosol|endoplasmic reticulum membrane|nucleus	identical protein binding			pancreas(1)|skin(1)	2	Hepatocellular(266;0.133)|all_neural(408;0.195)					TGGAGTTGAGCTGCTCCAGCT	0.577													4	109	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175375877	175375877	+	5'UTR	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175375877G>A	uc001gkp.1	-	1					TNR_uc009wwu.1_5'UTR|TNR_uc010pmz.1_5'UTR	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					CTGGGTTCAGGACCAGCCTGC	0.537													24	81	---	---	---	---	PASS
CHI3L1	1116	broad.mit.edu	37	1	203148901	203148901	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203148901G>C	uc001gzi.2	-	9	1170	c.999C>G	c.(997-999)AGC>AGG	p.S333R	FMOD_uc010pqi.1_Intron|CHI3L1_uc001gzk.1_Missense_Mutation_p.S69R|CHI3L1_uc001gzj.2_Missense_Mutation_p.S272R|CHI3L1_uc001gzl.3_5'Flank	NM_001276	NP_001267	P36222	CH3L1_HUMAN	chitinase 3-like 1 precursor	333					chitin catabolic process	extracellular space|proteinaceous extracellular matrix	cation binding|chitinase activity|extracellular matrix structural constituent|sugar binding			pancreas(1)	1						TGCTTTTGACGCTTTCCTGGT	0.587													98	105	---	---	---	---	PASS
LIN9	286826	broad.mit.edu	37	1	226420810	226420810	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226420810C>T	uc001hqa.2	-	14	1868	c.1558G>A	c.(1558-1560)GCT>ACT	p.A520T	LIN9_uc001hqb.2_Missense_Mutation_p.A485T|LIN9_uc001hqc.2_Missense_Mutation_p.A452T|LIN9_uc009xel.1_Missense_Mutation_p.A485T	NM_173083	NP_775106	Q5TKA1	LIN9_HUMAN	lin-9 homolog	504					cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		ATATTAGAAGCGTCTATTGTA	0.313													5	143	---	---	---	---	PASS
MYCN	4613	broad.mit.edu	37	2	16085629	16085629	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16085629G>A	uc002rci.2	+	3	1105	c.805G>A	c.(805-807)GAA>AAA	p.E269K	MYCN_uc010yjr.1_Missense_Mutation_p.E261K	NM_005378	NP_005369	P04198	MYCN_HUMAN	v-myc myelocytomatosis viral related oncogene,	269	Asp/Glu-rich (acidic).				regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			tgaagatgatgaagaggaaga	0.348			A		neuroblastoma								15	23	---	---	---	---	PASS
PPM1B	5495	broad.mit.edu	37	2	44428909	44428909	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44428909C>A	uc002rtt.2	+	2	999	c.571C>A	c.(571-573)CGT>AGT	p.R191S	PPM1B_uc002rts.2_Missense_Mutation_p.R191S|PPM1B_uc002rtu.2_Missense_Mutation_p.R191S|PPM1B_uc002rtv.2_Intron|PPM1B_uc002rtw.2_Missense_Mutation_p.R191S|PPM1B_uc002rtx.2_Missense_Mutation_p.R191S	NM_002706	NP_002697	O75688	PPM1B_HUMAN	protein phosphatase 1B isoform 1	191					protein dephosphorylation	protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			kidney(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GATGATACAACGTGTTAATGG	0.468													56	90	---	---	---	---	PASS
POTEF	728378	broad.mit.edu	37	2	130831636	130831636	+	3'UTR	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130831636C>T	uc010fmh.2	-	17						NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						TTGGAGGAAGCTTCCTCCAAC	0.368													5	16	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141643767	141643767	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141643767G>A	uc002tvj.1	-	24	4876	c.3904C>T	c.(3904-3906)CTT>TTT	p.L1302F	LRP1B_uc010fnl.1_Missense_Mutation_p.L484F	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1302	Extracellular (Potential).|LDL-receptor class B 9.				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)		GTCCAATAAAGTAAACTTTGA	0.323										TSP Lung(27;0.18)			62	115	---	---	---	---	PASS
PKP4	8502	broad.mit.edu	37	2	159499107	159499107	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159499107C>G	uc002tzv.2	+	11	2065	c.1805C>G	c.(1804-1806)TCT>TGT	p.S602C	PKP4_uc002tzt.1_Missense_Mutation_p.S454C|PKP4_uc002tzu.2_Missense_Mutation_p.S602C|PKP4_uc002tzw.2_Missense_Mutation_p.S602C|PKP4_uc002tzx.2_Missense_Mutation_p.S259C|PKP4_uc002tzy.1_Missense_Mutation_p.S260C|PKP4_uc002tzz.1_Missense_Mutation_p.S600C|PKP4_uc002uaa.2_Missense_Mutation_p.S454C	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	602					cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						TTTGGCAAGTCTACAGATGAA	0.428										HNSCC(62;0.18)			60	146	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179428026	179428026	+	Silent	SNP	T	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179428026T>C	uc010zfg.1	-	275	75353	c.75129A>G	c.(75127-75129)GAA>GAG	p.E25043E	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.E18738E|TTN_uc010zfi.1_Silent_p.E18671E|TTN_uc010zfj.1_Silent_p.E18546E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	25970							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)			CCGCAGCAGCTTCTTTGACCT	0.458													54	89	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179441832	179441832	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179441832A>T	uc010zfg.1	-	273	61750	c.61526T>A	c.(61525-61527)CTT>CAT	p.L20509H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.L14204H|TTN_uc010zfi.1_Missense_Mutation_p.L14137H|TTN_uc010zfj.1_Missense_Mutation_p.L14012H|uc002umv.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	21436							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)			TCTCTTTTCAAGTATATAGGA	0.433													64	102	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179616303	179616303	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179616303T>G	uc002unb.2	-	46	11048	c.10824A>C	c.(10822-10824)GAA>GAC	p.E3608D	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	3603							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)			TTTTCAGAAATTCTAAATATT	0.398													54	347	---	---	---	---	PASS
ZNF804A	91752	broad.mit.edu	37	2	185801058	185801058	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185801058G>C	uc002uph.2	+	4	1529	c.935G>C	c.(934-936)TGC>TCC	p.C312S		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	312						intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11						CCTTCATTTTGCAAGTTTCAA	0.348													17	90	---	---	---	---	PASS
AAMP	14	broad.mit.edu	37	2	219134719	219134719	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219134719C>A	uc002vhk.2	-	1	175	c.91G>T	c.(91-93)GTA>TTA	p.V31L	PNKD_uc002vhn.2_5'Flank|AAMP_uc002vhj.2_5'Flank|AAMP_uc010fvo.2_Missense_Mutation_p.V31L|AAMP_uc002vhl.2_Missense_Mutation_p.V31L|PNKD_uc002vhm.1_5'Flank	NM_001087	NP_001078	Q13685	AAMP_HUMAN	angio-associated, migratory cell protein	31					angiogenesis|cell differentiation|positive regulation of endothelial cell migration|smooth muscle cell migration	cell surface|cytoplasm|plasma membrane	heparin binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCAAGTTCTACCACCTCGATA	0.612													10	365	---	---	---	---	PASS
USP40	55230	broad.mit.edu	37	2	234431973	234431973	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234431973C>T	uc010zmr.1	-	15	2077	c.2077G>A	c.(2077-2079)GCA>ACA	p.A693T	USP40_uc010zmt.1_Missense_Mutation_p.A337T	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40	681					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GCTGGGATTGCTAAGGCTGTG	0.512													110	173	---	---	---	---	PASS
AGAP1	116987	broad.mit.edu	37	2	236706509	236706509	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236706509G>A	uc002vvs.2	+	7	1375	c.780G>A	c.(778-780)GTG>GTA	p.V260V	AGAP1_uc002vvt.2_Silent_p.V260V	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	260	Small GTPase-like.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						CCGCGCAGGTGTCTGCCGTGC	0.502													138	234	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188207	10188207	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188207G>A	uc003bvc.2	+	2	563	c.350G>A	c.(349-351)TGG>TAG	p.W117*	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	117	Involved in binding to CCT complex.		W -> C (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.W117*(5)|p.W117R(5)|p.W117fs*42(3)|p.W117C(2)|p.W117L(1)|p.?(1)|p.L118fs*14(1)|p.W117G(1)|p.W117fs*14(1)|p.W117fs*40(1)|p.H115fs*41(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GGTCACCTTTGGCTCTTCAGA	0.348		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				97	68	---	---	---	---	PASS
LTF	4057	broad.mit.edu	37	3	46497830	46497830	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46497830G>A	uc003cpq.2	-	3	304	c.266C>T	c.(265-267)GCC>GTC	p.A89V	LTF_uc003fzr.2_Missense_Mutation_p.A45V|LTF_uc010hjh.2_Missense_Mutation_p.A89V|LTF_uc003cpr.2_Missense_Mutation_p.A76V	NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor	89	Transferrin-like 1.				cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)	TTTGTAGGGGGCCAGGCCTGC	0.587													4	110	---	---	---	---	PASS
MGLL	11343	broad.mit.edu	37	3	127410961	127410961	+	3'UTR	SNP	C	A	A	rs73859251		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127410961C>A	uc003ejx.2	-	8					MGLL_uc003ejw.2_3'UTR|MGLL_uc011bko.1_3'UTR|MGLL_uc003ejv.2_3'UTR	NM_001003794	NP_001003794	Q99685	MGLL_HUMAN	monoglyceride lipase isoform 2						arachidonic acid metabolic process|fatty acid biosynthetic process|inflammatory response|platelet activation|regulation of endocannabinoid signaling pathway|regulation of inflammatory response|regulation of sensory perception of pain|triglyceride catabolic process	plasma membrane	acylglycerol lipase activity|carboxylesterase activity|lysophospholipase activity|protein homodimerization activity				0						ttttttttGGCAAGCCATATC	0.428													4	21	---	---	---	---	PASS
NPHP3	27031	broad.mit.edu	37	3	132419270	132419270	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132419270A>G	uc003epe.1	-	11	1728	c.1651T>C	c.(1651-1653)TCC>CCC	p.S551P	NPHP3_uc003epd.1_5'UTR|NPHP3_uc003epf.1_Missense_Mutation_p.S306P	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3	551					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						GTGTTGGGGGAATTCTTCTGT	0.363													55	31	---	---	---	---	PASS
ZBTB38	253461	broad.mit.edu	37	3	141162598	141162598	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141162598G>A	uc003etw.2	+	8	2350	c.1368G>A	c.(1366-1368)GGG>GGA	p.G456G	ZBTB38_uc010hun.2_Silent_p.G453G|ZBTB38_uc010huo.2_Silent_p.G456G|ZBTB38_uc003ety.2_Silent_p.G456G|ZBTB38_uc010hup.2_Silent_p.G457G	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	456					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TTGTTAATGGGCAAATGCTCT	0.418													4	67	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142184019	142184019	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142184019A>T	uc003eux.3	-	41	7083	c.6961T>A	c.(6961-6963)TTC>ATC	p.F2321I	ATR_uc003euy.1_Missense_Mutation_p.F207I	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2321					cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						ATGATGTAGAACTTTCCATCT	0.343								Other_conserved_DNA_damage_response_genes					41	29	---	---	---	---	PASS
MCF2L2	23101	broad.mit.edu	37	3	183029534	183029534	+	Silent	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183029534C>T	uc003fli.1	-	8	870	c.780G>A	c.(778-780)CAG>CAA	p.Q260Q	MCF2L2_uc003flj.1_Silent_p.Q260Q|MCF2L2_uc003flp.1_Silent_p.Q295Q|MCF2L2_uc011bqs.1_5'Flank	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	260					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			ATGTGGTCCCCTGCTTTCCAA	0.388													4	82	---	---	---	---	PASS
SDHAP2	727956	broad.mit.edu	37	3	195400728	195400728	+	Silent	SNP	A	G	G	rs12107841	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195400728A>G	uc003fuw.2	+	9	1218	c.24A>G	c.(22-24)CCA>CCG	p.P8P	SDHAP2_uc011btb.1_Missense_Mutation_p.S156G|SDHAP2_uc011btc.1_RNA|SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						GATTGTGCCCAGCCTGTACGC	0.587													3	10	---	---	---	---	PASS
SCD5	79966	broad.mit.edu	37	4	83719576	83719576	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83719576G>A	uc003hna.2	-	1	435	c.115C>T	c.(115-117)CGC>TGC	p.R39C	SCD5_uc003hnb.3_Missense_Mutation_p.R39C|SCD5_uc003hnc.2_Missense_Mutation_p.R39C	NM_001037582	NP_001032671	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5 isoform a	39					fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CGCTGCCCGCGCGCGCCTGGC	0.662													18	15	---	---	---	---	PASS
NAF1	92345	broad.mit.edu	37	4	164050071	164050071	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164050071G>T	uc003iqj.2	-	8	1657	c.1463C>A	c.(1462-1464)TCT>TAT	p.S488Y	NAF1_uc010iqw.1_Intron	NM_138386	NP_612395	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 homolog isoform a	488					rRNA processing|snRNA pseudouridine synthesis	cytoplasm|nucleus|small nucleolar ribonucleoprotein complex	protein binding|snoRNA binding			ovary(2)	2	all_hematologic(180;0.166)	Prostate(90;0.109)				TCCAAAATGAGAATTACTATC	0.259													36	35	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70841097	70841097	+	Intron	SNP	T	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70841097T>A	uc003kbp.1	+						BDP1_uc003kbo.2_3'UTR|BDP1_uc003kbq.1_Intron|BDP1_uc003kbr.1_Intron	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TTCCTCCATTTAAAAAAAAAA	0.199													16	35	---	---	---	---	PASS
FEM1C	56929	broad.mit.edu	37	5	114878826	114878826	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114878826G>A	uc003krb.1	-	2	927	c.365C>T	c.(364-366)GCT>GTT	p.A122V		NM_020177	NP_064562	Q96JP0	FEM1C_HUMAN	feminization 1 homolog a	122	ANK 4.					cytoplasm				breast(2)|ovary(1)	3		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		GAAACACGCAGCTCGAAGAGG	0.458													69	97	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115298600	115298600	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115298600C>G	uc003kro.2	+	1	450	c.286C>G	c.(286-288)CTA>GTA	p.L96V	AQPEP_uc003krp.2_RNA|uc003krn.1_5'UTR	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	96	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						CTGGGACCAGCTACGCCTGCC	0.701													35	36	---	---	---	---	PASS
DTWD2	285605	broad.mit.edu	37	5	118183854	118183854	+	Silent	SNP	T	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118183854T>C	uc003ksa.2	-	5	691	c.657A>G	c.(655-657)AGA>AGG	p.R219R		NM_173666	NP_775937	Q8NBA8	DTWD2_HUMAN	DTW domain containing 2	219											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)		TAGAAAGGCATCTATTAGTCG	0.323													5	150	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140346845	140346845	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140346845C>A	uc003lii.2	+	1	734	c.494C>A	c.(493-495)GCG>GAG	p.A165E	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Missense_Mutation_p.A165E	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	165	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCCTGGAGCGCGCTTTCAC	0.597													21	35	---	---	---	---	PASS
PCDHGB7	56099	broad.mit.edu	37	5	140798869	140798869	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140798869C>G	uc003lkn.1	+	1	1588	c.1443C>G	c.(1441-1443)TTC>TTG	p.F481L	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkm.2_Missense_Mutation_p.F481L|PCDHGA11_uc003lko.1_5'Flank|PCDHGA11_uc003lkp.1_5'Flank|PCDHGA11_uc003lkq.1_5'Flank	NM_018927	NP_061750	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7 isoform 1	481	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCCAGACTTCGGGCTCAACG	0.622													58	104	---	---	---	---	PASS
PCDHGC5	56097	broad.mit.edu	37	5	140870296	140870296	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140870296C>T	uc003lla.1	+	1	1489	c.1489C>T	c.(1489-1491)CAG>TAG	p.Q497*	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc003lky.1_Intron|PCDHGC5_uc011dbc.1_Nonsense_Mutation_p.Q497*	NM_018929	NP_061752	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5 isoform 1	497	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTAGGAAATCAGGTTCAGGG	0.547													101	157	---	---	---	---	PASS
MAML1	9794	broad.mit.edu	37	5	179193074	179193074	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179193074C>G	uc003mkm.2	+	2	1326	c.1063C>G	c.(1063-1065)CGG>GGG	p.R355G	MAML1_uc003mkn.1_Missense_Mutation_p.R355G	NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1	355					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)			TGGTCAGCCCCGGGCGGACAA	0.622													56	79	---	---	---	---	PASS
CDYL	9425	broad.mit.edu	37	6	4892566	4892566	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4892566G>A	uc003mwi.2	+	4	937	c.806G>A	c.(805-807)GGC>GAC	p.G269D	CDYL_uc003mwj.2_Missense_Mutation_p.G215D|CDYL_uc003mwk.2_Intron|CDYL_uc011dhx.1_Missense_Mutation_p.G83D|CDYL_uc011dhy.1_Missense_Mutation_p.G83D	NM_001143971	NP_001137443	Q9Y232	CDYL1_HUMAN	chromodomain protein, Y chromosome-like isoform	269					regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		CAGGTGCCCGGCCCTGTGACT	0.642													30	36	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12164030	12164030	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12164030T>C	uc003nac.2	+	9	7672	c.7493T>C	c.(7492-7494)ATT>ACT	p.I2498T	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	2498					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)				ACCGTCAATATTGTAGGCCTA	0.522													12	59	---	---	---	---	PASS
HLA-F	3134	broad.mit.edu	37	6	29691207	29691207	+	5'UTR	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29691207A>G	uc010jrl.2	+	1					HLA-F_uc003nnm.3_5'UTR|HLA-F_uc003nno.3_5'UTR|HLA-F_uc011dlx.1_5'UTR|HLA-F_uc011dly.1_5'Flank	NM_018950	NP_061823	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0						ACCCCGCGGGACTCATATTTT	0.632													24	57	---	---	---	---	PASS
PPARD	5467	broad.mit.edu	37	6	35393878	35393878	+	3'UTR	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35393878G>C	uc003okm.2	+	8					PPARD_uc003okn.2_3'UTR|PPARD_uc011dtb.1_3'UTR|PPARD_uc011dtc.1_3'UTR	NM_006238	NP_006229	Q03181	PPARD_HUMAN	peroxisome proliferative activated receptor,						apoptosis|axon ensheathment|cholesterol metabolic process|decidualization|embryo implantation|fatty acid beta-oxidation|fatty acid transport|generation of precursor metabolites and energy|glucose metabolic process|glucose transport|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fat cell differentiation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|linoleic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1					Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	AGGCCTCCCTGCAGACTCCAA	0.612													3	25	---	---	---	---	PASS
LRP11	84918	broad.mit.edu	37	6	150164137	150164137	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150164137C>T	uc003qng.2	-	3	1219	c.895G>A	c.(895-897)GCA>ACA	p.A299T	LRP11_uc003qnh.1_Missense_Mutation_p.A299T	NM_032832	NP_116221	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein	299	PKD.|Extracellular (Potential).					integral to membrane	receptor activity				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		GAGTAGGCTGCGCGAAGCACT	0.592													10	59	---	---	---	---	PASS
LRP11	84918	broad.mit.edu	37	6	150164138	150164138	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150164138G>A	uc003qng.2	-	3	1218	c.894C>T	c.(892-894)CGC>CGT	p.R298R	LRP11_uc003qnh.1_Silent_p.R298R	NM_032832	NP_116221	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein	298	PKD.|Extracellular (Potential).					integral to membrane	receptor activity				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		AGTAGGCTGCGCGAAGCACTG	0.592													10	61	---	---	---	---	PASS
C6orf97	80129	broad.mit.edu	37	6	151939400	151939400	+	3'UTR	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151939400A>G	uc003qol.2	+	11						NM_025059	NP_079335	Q8IYT3	CF097_HUMAN	hypothetical protein LOC80129												0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)		TTGATGATATAGTGAGAATGC	0.348													10	6	---	---	---	---	PASS
TULP4	56995	broad.mit.edu	37	6	158923758	158923758	+	Silent	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158923758G>C	uc003qrf.2	+	13	4420	c.3063G>C	c.(3061-3063)GGG>GGC	p.G1021G	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	1021					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GGCCCGGGGGGGTGGTGACAC	0.726													3	7	---	---	---	---	PASS
FSCN1	6624	broad.mit.edu	37	7	5632742	5632742	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5632742G>C	uc003sou.2	+	1	289	c.175G>C	c.(175-177)GCC>CCC	p.A59P		NM_003088	NP_003079	Q16658	FSCN1_HUMAN	fascin 1	59					actin filament bundle assembly|cell migration|cell proliferation	cell junction|cytoplasm|filopodium|invadopodium|stress fiber	actin filament binding|drug binding|protein binding, bridging			ovary(1)	1		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		GGGCAGCGCGGCCGTGTGCCT	0.701													5	11	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82544733	82544733	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82544733T>C	uc003uhx.2	-	7	12858	c.12569A>G	c.(12568-12570)AAG>AGG	p.K4190R	PCLO_uc003uhv.2_Missense_Mutation_p.K4190R|PCLO_uc010lec.2_Missense_Mutation_p.K1155R	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4121					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TTTCTTATGCTTTGACTGCTT	0.353													37	43	---	---	---	---	PASS
CALU	813	broad.mit.edu	37	7	128407619	128407619	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128407619G>T	uc003vns.2	+	6	905	c.753G>T	c.(751-753)AAG>AAT	p.K251N	CALU_uc003vnq.2_Missense_Mutation_p.K251N|CALU_uc003vnr.2_Missense_Mutation_p.K251N	NM_001130674	NP_001124146	O43852	CALU_HUMAN	calumenin isoform b precursor	251	EF-hand 5.|5 (Potential).				platelet activation|platelet degranulation	extracellular region|Golgi apparatus|melanosome|sarcoplasmic reticulum lumen	calcium ion binding|protein binding				0						AGATGGACAAGGAAGAGACCA	0.483													41	55	---	---	---	---	PASS
CPA4	51200	broad.mit.edu	37	7	129938646	129938646	+	Silent	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129938646A>T	uc003vpr.2	+	2	176	c.129A>T	c.(127-129)CTA>CTT	p.L43L	CPA4_uc011kpd.1_Silent_p.L43L|CPA4_uc011kpe.1_Intron	NM_016352	NP_057436	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4 preproprotein	43					histone acetylation|proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)					TGAGTCAACTAGTGAATTCAA	0.388													34	87	---	---	---	---	PASS
ZC3HAV1	56829	broad.mit.edu	37	7	138794026	138794026	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138794026C>T	uc003vun.2	-	1	440	c.52G>A	c.(52-54)GGG>AGG	p.G18R	ZC3HAV1_uc003vup.2_Missense_Mutation_p.G18R	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1	18					response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						ATGCGGCCCCCGTGGGCGCAC	0.706													11	15	---	---	---	---	PASS
LOXL2	4017	broad.mit.edu	37	8	23155588	23155588	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23155588C>A	uc003xdh.1	-	14	2632	c.2293G>T	c.(2293-2295)GGG>TGG	p.G765W	LOXL2_uc010lty.1_Silent_p.A266A	NM_002318	NP_002309	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2 precursor	765					aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|ovary(1)	3		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		TTTAAGAGCCCGCTGAAGTGC	0.527													3	64	---	---	---	---	PASS
POTEA	340441	broad.mit.edu	37	8	43218201	43218201	+	3'UTR	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43218201C>T	uc003xpz.1	+	14					POTEA_uc003xqa.1_3'UTR	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2											ovary(1)	1						AACATCAGAACCAGCTAAGGG	0.333													8	10	---	---	---	---	PASS
INSL6	11172	broad.mit.edu	37	9	5185530	5185530	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5185530C>T	uc003zix.2	-	1	89	c.73G>A	c.(73-75)GAC>AAC	p.D25N		NM_007179	NP_009110	Q9Y581	INSL6_HUMAN	insulin-like 6 precursor	25						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)		CTGCTGATGTCGCTCAGTTCA	0.587													16	44	---	---	---	---	PASS
DDX58	23586	broad.mit.edu	37	9	32488009	32488009	+	Silent	SNP	C	T	T	rs151092988		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32488009C>T	uc003zra.2	-	8	1304	c.1146G>A	c.(1144-1146)CCG>CCA	p.P382P	DDX58_uc010mjj.2_RNA|DDX58_uc010mjk.1_Silent_p.P337P|DDX58_uc011lnr.1_Silent_p.P179P|DDX58_uc010mji.2_Silent_p.P311P	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	382	Helicase ATP-binding.				detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TCATATTGTACGGGTGTTGTT	0.393													80	88	---	---	---	---	PASS
KIF27	55582	broad.mit.edu	37	9	86518083	86518083	+	Silent	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86518083C>T	uc004ana.2	-	4	1494	c.1350G>A	c.(1348-1350)AGG>AGA	p.R450R	KIF27_uc010mpw.2_Silent_p.R450R|KIF27_uc010mpx.2_Silent_p.R450R	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27	450					cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						GGACAGCCTTCCTGACCTCTT	0.468													5	121	---	---	---	---	PASS
QSOX2	169714	broad.mit.edu	37	9	139118696	139118696	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139118696G>A	uc010nbi.2	-	2	391	c.353C>T	c.(352-354)GCA>GTA	p.A118V		NM_181701	NP_859052	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2 precursor	118	Thioredoxin.				cell redox homeostasis	extracellular region|integral to membrane|nuclear membrane|plasma membrane	thiol oxidase activity			ovary(1)	1		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GTCCAGAGCTGCGACGCGAAT	0.597											OREG0019616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	76	107	---	---	---	---	PASS
ARMC4	55130	broad.mit.edu	37	10	28270411	28270411	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28270411T>G	uc009xky.2	-	7	1018	c.920A>C	c.(919-921)GAA>GCA	p.E307A	ARMC4_uc010qds.1_5'UTR|ARMC4_uc010qdt.1_5'UTR|ARMC4_uc001itz.2_Missense_Mutation_p.E307A|ARMC4_uc010qdu.1_5'UTR	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	307							binding			ovary(4)|skin(2)	6						AGACATATTTTCTGAAAATTT	0.284													90	83	---	---	---	---	PASS
DDX21	9188	broad.mit.edu	37	10	70733381	70733381	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70733381C>G	uc001jov.1	+	10	1719	c.1629C>G	c.(1627-1629)CAC>CAG	p.H543Q	DDX21_uc001jow.1_Missense_Mutation_p.H475Q	NM_004728	NP_004719	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	543	Helicase C-terminal.					nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3						TTTATCAGCACAAGGAAGAAT	0.418													6	124	---	---	---	---	PASS
GBF1	8729	broad.mit.edu	37	10	104111114	104111114	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104111114C>G	uc001kux.1	+	5	637	c.397C>G	c.(397-399)CTG>GTG	p.L133V	GBF1_uc001kuw.2_Missense_Mutation_p.L133V|GBF1_uc001kuy.1_Missense_Mutation_p.L133V|GBF1_uc001kuz.1_Missense_Mutation_p.L133V	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine	133					COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TGAAGTTGTCCTGATGAAAAT	0.537													13	52	---	---	---	---	PASS
OR51L1	119682	broad.mit.edu	37	11	5020376	5020376	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020376C>T	uc010qyu.1	+	1	164	c.164C>T	c.(163-165)TCC>TTC	p.S55F		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	55	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGATAGAATCCTCTCTCCAT	0.438													25	333	---	---	---	---	PASS
OR51Q1	390061	broad.mit.edu	37	11	5443672	5443672	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5443672C>G	uc010qzd.1	+	1	242	c.242C>G	c.(241-243)CCC>CGC	p.P81R	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004757	NP_001004757	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q,	81	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCACCCTACCCACAGTCATG	0.517													101	141	---	---	---	---	PASS
DNHD1	144132	broad.mit.edu	37	11	6519865	6519865	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6519865G>C	uc001mdw.3	+	3	984	c.420G>C	c.(418-420)TTG>TTC	p.L140F	DNHD1_uc001mdp.2_Missense_Mutation_p.L140F	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	140					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACAGCTCTTTGTTAGACAGTG	0.602													170	267	---	---	---	---	PASS
USH1C	10083	broad.mit.edu	37	11	17531374	17531374	+	Intron	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17531374C>T	uc001mnf.2	-						USH1C_uc001mne.2_Silent_p.G514G|USH1C_uc009yhb.2_Intron|USH1C_uc001mng.2_Intron|USH1C_uc001mnd.2_Intron	NM_005709	NP_005700	Q9Y6N9	USH1C_HUMAN	harmonin isoform a						equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1						GAGGCGGGGGCCCTGTGGTCA	0.577													21	39	---	---	---	---	PASS
RAB3IL1	5866	broad.mit.edu	37	11	61665702	61665702	+	3'UTR	SNP	T	G	G	rs36099026		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61665702T>G	uc001nso.2	-	10					RAB3IL1_uc001nsp.2_3'UTR	NM_013401	NP_037533	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1								protein binding			skin(2)|central_nervous_system(1)	3						TGTTCTGGGGTGGGTGTTTGC	0.642											OREG0021017	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	141	---	---	---	---	PASS
MYO7A	4647	broad.mit.edu	37	11	76893001	76893001	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76893001T>G	uc001oyb.2	+	24	3181	c.2909T>G	c.(2908-2910)CTG>CGG	p.L970R	MYO7A_uc010rsl.1_Missense_Mutation_p.L970R|MYO7A_uc010rsm.1_Missense_Mutation_p.L959R|MYO7A_uc001oyc.2_Missense_Mutation_p.L970R|MYO7A_uc001oyd.2_Missense_Mutation_p.L310R|MYO7A_uc009yus.1_RNA|MYO7A_uc009yut.1_Missense_Mutation_p.L181R	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1	970					actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						CTTCAGGACCTGGAGCGAGGG	0.373													35	56	---	---	---	---	PASS
ARHGAP20	57569	broad.mit.edu	37	11	110451607	110451607	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110451607G>T	uc001pkz.1	-	16	2348	c.2063C>A	c.(2062-2064)ACA>AAA	p.T688K	ARHGAP20_uc001pky.1_Missense_Mutation_p.T665K|ARHGAP20_uc009yyb.1_Missense_Mutation_p.T652K|ARHGAP20_uc001pla.1_Missense_Mutation_p.T652K|ARHGAP20_uc001plb.2_Missense_Mutation_p.T231K	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	688					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		TGCTGCAGCTGTGGACAGGTA	0.537													46	108	---	---	---	---	PASS
BACE1	23621	broad.mit.edu	37	11	117162408	117162408	+	Intron	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117162408C>A	uc001pqz.2	-						BACE1_uc001pqw.2_Intron|BACE1_uc001pqx.2_Intron|BACE1_uc001pqy.2_Intron|BACE1_uc010rxg.1_Intron|BACE1_uc010rxh.1_Intron|BACE1_uc009yzo.1_Intron|uc010rxi.1_RNA	NM_012104	NP_036236	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1 isoform A						beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		CTCTTTTACCCCCATCCTTAG	0.512													4	90	---	---	---	---	PASS
FOXR1	283150	broad.mit.edu	37	11	118849549	118849549	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118849549C>T	uc001pui.2	+	2	344	c.119C>T	c.(118-120)CCC>CTC	p.P40L	FOXR1_uc001puj.2_RNA|FOXR1_uc001puk.2_5'UTR	NM_181721	NP_859072	Q6PIV2	FOXR1_HUMAN	forkhead box R1	40					embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|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	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		GAGAAAAAACCCAACCCTGAT	0.473													83	148	---	---	---	---	PASS
FOXR1	283150	broad.mit.edu	37	11	118849551	118849551	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118849551A>T	uc001pui.2	+	2	346	c.121A>T	c.(121-123)AAC>TAC	p.N41Y	FOXR1_uc001puj.2_RNA|FOXR1_uc001puk.2_5'UTR	NM_181721	NP_859072	Q6PIV2	FOXR1_HUMAN	forkhead box R1	41					embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|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	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		GAAAAAACCCAACCCTGATAA	0.478													84	154	---	---	---	---	PASS
DPAGT1	1798	broad.mit.edu	37	11	118972074	118972074	+	Intron	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118972074C>A	uc001pvi.2	-						DPAGT1_uc001pvj.2_Intron|DPAGT1_uc009zaq.2_Intron|DPAGT1_uc001pvk.2_5'UTR|DPAGT1_uc010ryz.1_Intron|DPAGT1_uc001pvm.1_5'Flank|DPAGT1_uc010rza.1_Intron	NM_001382	NP_001373	Q9H3H5	GPT_HUMAN	UDP-N-acetylglucosamine-dolichyl-phosphate						dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity			breast(2)|ovary(1)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		CTCATCACCTCTCCGAGTTCC	0.602											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	43	56	---	---	---	---	PASS
TNFRSF1A	7132	broad.mit.edu	37	12	6440021	6440021	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6440021G>A	uc001qnu.2	-	6	904	c.623C>T	c.(622-624)TCA>TTA	p.S208L	TNFRSF1A_uc001qnt.2_Missense_Mutation_p.S100L|TNFRSF1A_uc010sey.1_5'UTR|TNFRSF1A_uc010sez.1_Missense_Mutation_p.S100L|TNFRSF1A_uc009zek.2_Missense_Mutation_p.S165L	NM_001065	NP_001056	P19438	TNR1A_HUMAN	tumor necrosis factor receptor 1 precursor	208	Extracellular (Potential).				apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity			lung(2)|skin(1)	3						CTCCTCACCTGAGTCCTCAGT	0.458													34	54	---	---	---	---	PASS
KLRC2	3822	broad.mit.edu	37	12	10584769	10584769	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10584769C>G	uc001qyk.2	-	5	527	c.520G>C	c.(520-522)GGT>CGT	p.G174R	KLRC3_uc001qyh.2_Intron|KLRC2_uc010she.1_Missense_Mutation_p.G174R	NM_002260	NP_002251	P26717	NKG2C_HUMAN	killer cell lectin-like receptor subfamily C,	174	Extracellular (Potential).|C-type lectin.				cellular defense response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0						CGAAACACACCAATCCATGAG	0.289													30	55	---	---	---	---	PASS
MRPS35	60488	broad.mit.edu	37	12	27908200	27908200	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27908200G>A	uc001rih.2	+	8	837	c.789G>A	c.(787-789)CTG>CTA	p.L263L	MRPS35_uc001rii.2_3'UTR	NM_021821	NP_068593	P82673	RT35_HUMAN	mitochondrial ribosomal protein S35 precursor	263	Potential.				DNA damage response, detection of DNA damage	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)					GAAATATCCTGGAAACGCTTC	0.343													5	215	---	---	---	---	PASS
NR4A1	3164	broad.mit.edu	37	12	52432532	52432532	+	Intron	SNP	A	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52432532A>C	uc010sno.1	+							NM_173157	NP_775180	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ttctaattgaaggtaactggg	0.000													12	25	---	---	---	---	PASS
AVIL	10677	broad.mit.edu	37	12	58207208	58207208	+	Splice_Site	SNP	T	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58207208T>C	uc001sqj.1	-	3	171	c.142_splice	c.e3-1	p.T48_splice	AVIL_uc009zqe.1_Splice_Site_p.T41_splice|AVIL_uc001sql.3_Splice_Site_p.T25_splice	NM_006576	NP_006567	O75366	AVIL_HUMAN	advillin						actin filament capping|cilium morphogenesis|cytoskeleton organization|positive regulation of neuron projection development	actin cytoskeleton|axon|cytoplasm	actin binding			central_nervous_system(1)	1	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TCTCCGGGTCTGGGAGGTAGT	0.577													48	79	---	---	---	---	PASS
FAM71C	196472	broad.mit.edu	37	12	100042363	100042363	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100042363G>T	uc001tgn.2	+	1	833	c.411G>T	c.(409-411)CAG>CAT	p.Q137H	ANKS1B_uc001tge.1_Intron|ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_153364	NP_699195	Q8NEG0	FA71C_HUMAN	hypothetical protein LOC196472	137											0				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		TAAAAAAACAGCTCCACCTGA	0.463													66	96	---	---	---	---	PASS
DDX54	79039	broad.mit.edu	37	12	113618759	113618759	+	Silent	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113618759C>T	uc001tup.2	-	2	307	c.279G>A	c.(277-279)AAG>AAA	p.K93K	DDX54_uc001tuq.3_Silent_p.K93K	NM_024072	NP_076977	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	93					estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nucleolus	ATP binding|ATP-dependent RNA helicase activity|estrogen receptor binding|RNA binding|transcription corepressor activity			skin(2)|central_nervous_system(1)	3						CTCCAGACTTCTTCTTCTTCT	0.617													71	156	---	---	---	---	PASS
CDK8	1024	broad.mit.edu	37	13	26923220	26923220	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26923220G>A	uc001uqr.1	+	3	242	c.216G>A	c.(214-216)GAG>GAA	p.E72E	CDK8_uc001uqs.1_Silent_p.E72E|CDK8_uc001uqt.1_5'UTR	NM_001260	NP_001251	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	72	Protein kinase.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TACTTCGAGAGCTTAAGCATC	0.383													119	140	---	---	---	---	PASS
KBTBD6	89890	broad.mit.edu	37	13	41704758	41704758	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41704758G>A	uc001uxu.1	-	1	2179	c.1890C>T	c.(1888-1890)CTC>CTT	p.L630L	KBTBD6_uc010ace.1_Intron|KBTBD6_uc010tfe.1_Silent_p.L564L|uc001uxv.1_5'Flank	NM_152903	NP_690867	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain-containing 6	630							protein binding			ovary(1)|skin(1)	2		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CTTCTTCAGTGAGGAAACTCT	0.438													10	108	---	---	---	---	PASS
CKAP2	26586	broad.mit.edu	37	13	53035798	53035798	+	Silent	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53035798A>T	uc001vgv.2	+	4	1037	c.840A>T	c.(838-840)ACA>ACT	p.T280T	CKAP2_uc001vgt.2_Silent_p.T279T|CKAP2_uc001vgu.2_Silent_p.T279T|CKAP2_uc010tha.1_Silent_p.T231T	NM_001098525	NP_001091995	Q8WWK9	CKAP2_HUMAN	cytoskeleton associated protein 2 isoform 2	280					apoptosis|cell cycle	centrosome|microtubule|spindle pole				ovary(1)|skin(1)	2		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		CCAATGTTACAATCCGGAAAG	0.393													51	49	---	---	---	---	PASS
HS6ST3	266722	broad.mit.edu	37	13	97484944	97484944	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97484944A>G	uc001vmw.2	+	2	932	c.908A>G	c.(907-909)TAC>TGC	p.Y303C		NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	303	Lumenal (Potential).					integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					GATTGCACCTACAACCTGGCT	0.542													5	77	---	---	---	---	PASS
DAAM1	23002	broad.mit.edu	37	14	59834206	59834206	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59834206C>A	uc001xdz.1	+	25	3041	c.2916C>A	c.(2914-2916)TTC>TTA	p.F972L	DAAM1_uc001xea.1_Missense_Mutation_p.F962L|DAAM1_uc001xec.1_RNA	NM_014992	NP_055807	Q9Y4D1	DAAM1_HUMAN	dishevelled-associated activator of	972	FH2.				actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)		CAGATGAGTTCTTTGGCATTT	0.383													24	103	---	---	---	---	PASS
APBA2	321	broad.mit.edu	37	15	29400578	29400578	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29400578G>A	uc001zck.2	+	12	2230	c.2023G>A	c.(2023-2025)GTG>ATG	p.V675M	APBA2_uc010azj.2_Missense_Mutation_p.V663M|APBA2_uc010uat.1_Missense_Mutation_p.V663M|APBA2_uc001zcl.2_Missense_Mutation_p.V663M	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,	675	PDZ 2.				nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		GGGCTTCAGCGTGCAGAATGG	0.607													79	111	---	---	---	---	PASS
EIF2AK4	440275	broad.mit.edu	37	15	40266120	40266120	+	Intron	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40266120C>G	uc001zkm.1	+						EIF2AK4_uc001zkl.2_3'UTR|EIF2AK4_uc010bbj.1_Intron	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	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)		ATTTAAGTTACGCTGGACACA	0.413													5	10	---	---	---	---	PASS
RTF1	23168	broad.mit.edu	37	15	41762545	41762545	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41762545A>G	uc001zny.2	+	7	992	c.980A>G	c.(979-981)AAG>AGG	p.K327R		NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component	327	Glu-rich.				histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		TCCAGTGAAAAGTCAGACCGC	0.438													168	320	---	---	---	---	PASS
PGPEP1L	145814	broad.mit.edu	37	15	99511854	99511854	+	Silent	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99511854A>T	uc002bum.2	-	5	650	c.444T>A	c.(442-444)CCT>CCA	p.P148P	PGPEP1L_uc010bop.2_Missense_Mutation_p.L93H|PGPEP1L_uc002bun.2_RNA	NM_001102612	NP_001096082	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase 1-like protein	148					proteolysis		cysteine-type peptidase activity				0						GCGATAGTGGAGGGACATGGA	0.547													11	12	---	---	---	---	PASS
TRAP1	10131	broad.mit.edu	37	16	3713671	3713671	+	Intron	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3713671G>C	uc002cvt.3	-						TRAP1_uc002cvs.2_Intron|TRAP1_uc010uxf.1_Intron|uc002cvu.2_RNA	NM_016292	NP_057376	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1 precursor						cellular response to oxidative stress|protein folding	mitochondrion	ATP binding|tumor necrosis factor receptor binding|unfolded protein binding			central_nervous_system(1)	1		Ovarian(90;0.0261)				GGCCACACTGGGGAACACCGG	0.627													6	12	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15083531	15083531	+	Intron	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15083531C>A	uc010uzl.1	+						PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002dda.3_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron|uc010bvd.1_5'UTR	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	gccacggggccAGGACCTGGG	0.617													4	6	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51170989	51170989	+	3'UTR	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51170989A>G	uc010vgs.1	-	3					SALL1_uc010vgr.1_3'UTR|SALL1_uc010cbv.2_3'UTR	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a						adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			CATTCTGAACAGGAATGAATG	0.547													17	33	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58594198	58594198	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58594198T>G	uc002env.2	-	17	2341	c.2048A>C	c.(2047-2049)AAG>ACG	p.K683T	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.K683T|CNOT1_uc002enx.2_Missense_Mutation_p.K683T|CNOT1_uc002enz.1_Missense_Mutation_p.K112T|SNORA50_uc002eoa.1_5'Flank	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	683					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)		TTGTCTGGCCTTATTCATAAC	0.423													87	83	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70010650	70010650	+	3'UTR	SNP	A	G	G	rs144900726	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70010650A>G	uc010vlq.1	-	6					CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron					SubName: Full=Putative uncharacterized protein;												0						AGGGCCGAAGAAGGGAATGTT	0.468													5	73	---	---	---	---	PASS
SNAI3	333929	broad.mit.edu	37	16	88744902	88744902	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88744902G>A	uc002flj.2	-	3	901	c.833C>T	c.(832-834)TCC>TTC	p.S278F	MGC23284_uc002fli.3_Intron	NM_178310	NP_840101	Q3KNW1	SNAI3_HUMAN	snail homolog 3	278	C2H2-type 5; degenerate.				oxidation-reduction process		copper ion binding|DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.048)		CGCCAGGAGGGACATGCGGGA	0.677													9	30	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10436864	10436864	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10436864C>T	uc010coi.2	-	20	2394	c.2266G>A	c.(2266-2268)GAC>AAC	p.D756N	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.D756N|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	756	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						TGGTCAATGTCGATGGATGCA	0.403													16	266	---	---	---	---	PASS
SPAG5	10615	broad.mit.edu	37	17	26920003	26920003	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26920003A>G	uc002hbq.2	-	3	351	c.259T>C	c.(259-261)TCA>CCA	p.S87P	SGK494_uc010waq.1_Intron	NM_006461	NP_006452	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	87					cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)					AGCCACTTTGAGGAATGACTG	0.333													111	199	---	---	---	---	PASS
KRTAP4-12	83755	broad.mit.edu	37	17	39279933	39279933	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39279933A>T	uc002hwa.2	-	1	487	c.442T>A	c.(442-444)TCC>ACC	p.S148T		NM_031854	NP_114060	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	148	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].|27.					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			cagctgctggagatgcagcag	0.134													13	13	---	---	---	---	PASS
STAT5B	6777	broad.mit.edu	37	17	40370140	40370140	+	Intron	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40370140C>G	uc002hzh.2	-						STAT5B_uc002hzi.3_3'UTR	NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	AGACAAGTAGCAGGGAATGAG	0.522													10	23	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60038959	60038959	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60038959C>G	uc002izo.2	-	22	5323	c.5246G>C	c.(5245-5247)AGA>ACA	p.R1749T		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1749					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			large_intestine(1)|ovary(1)	2						ATCAGGACTTCTAAGGGCAGT	0.338													81	120	---	---	---	---	PASS
SOX9	6662	broad.mit.edu	37	17	70119068	70119068	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70119068T>C	uc002jiw.2	+	2	1012	c.640T>C	c.(640-642)TCC>CCC	p.S214P	uc002jiv.2_5'Flank	NM_000346	NP_000337	P48436	SOX9_HUMAN	transcription factor SOX9	214					cAMP-mediated signaling|negative regulation of transcription, DNA-dependent|positive regulation of branching involved in ureteric bud morphogenesis|protein complex assembly|renal vesicle induction	nucleus|protein complex	core promoter sequence-specific DNA binding|enhancer binding|protein kinase A catalytic subunit binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription				0		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			CTCGCCACACTCCTCCTCCGG	0.687													56	78	---	---	---	---	PASS
UNK	85451	broad.mit.edu	37	17	73814848	73814848	+	Silent	SNP	A	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73814848A>C	uc002jpm.2	+	12	1725	c.1725A>C	c.(1723-1725)GCA>GCC	p.A575A		NM_001080419	NP_001073888	Q9C0B0	UNK_HUMAN	zinc finger CCCH-type domain containing 5	499							nucleic acid binding|zinc ion binding				0			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCATGAATGCAAACGCTCTGC	0.592													21	37	---	---	---	---	PASS
EXOC7	23265	broad.mit.edu	37	17	74077512	74077512	+	3'UTR	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74077512A>G	uc002jqs.2	-	20					ZACN_uc002jqn.2_Intron|ZACN_uc002jqo.2_Intron|ZACN_uc010dgu.2_Intron|EXOC7_uc002jqp.1_3'UTR|EXOC7_uc010dgv.1_3'UTR|EXOC7_uc002jqq.2_3'UTR|EXOC7_uc010wsw.1_3'UTR|EXOC7_uc010wsx.1_3'UTR|EXOC7_uc002jqr.2_3'UTR|EXOC7_uc010wsv.1_3'UTR	NM_001145297	NP_001138769	Q9UPT5	EXOC7_HUMAN	exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)			AGGCCGACAGAGGGCTGCTGG	0.657													68	147	---	---	---	---	PASS
TCEB3C	162699	broad.mit.edu	37	18	44555134	44555134	+	Nonsense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44555134G>C	uc010xdb.1	-	1	1316	c.1080C>G	c.(1078-1080)TAC>TAG	p.Y360*	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	360	Activation domain (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0						CAAGAACCGAGTAGGGGACCC	0.627													24	674	---	---	---	---	PASS
KIAA1468	57614	broad.mit.edu	37	18	59949659	59949659	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59949659C>G	uc002lil.2	+	25	3450	c.3235C>G	c.(3235-3237)CCC>GCC	p.P1079A	KIAA1468_uc010xel.1_Missense_Mutation_p.P1079A|KIAA1468_uc002lim.2_Missense_Mutation_p.P757A	NM_020854	NP_065905	Q9P260	K1468_HUMAN	hypothetical protein LOC57614	1079							binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)				TAACGCAGAACCCAGGTTCCG	0.413													92	121	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8175825	8175825	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8175825G>A	uc002mjf.2	-	33	4258	c.4237C>T	c.(4237-4239)CTC>TTC	p.L1413F		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1413	EGF-like 22; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						AATGCACAGAGGTTCCCTTGC	0.622													68	103	---	---	---	---	PASS
ZNF765	91661	broad.mit.edu	37	19	53913053	53913053	+	3'UTR	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53913053G>A	uc010ydx.1	+	6					ZNF765_uc002qbm.2_3'UTR|ZNF765_uc002qbn.2_Intron	NM_001040185	NP_001035275	Q7L2R6	ZN765_HUMAN	zinc finger protein 765						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)		AGTGAGTGTGGCAAGACCTTT	0.408													4	139	---	---	---	---	PASS
NLRP12	91662	broad.mit.edu	37	19	54313706	54313706	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54313706C>A	uc002qch.3	-	3	1427	c.1207G>T	c.(1207-1209)GTC>TTC	p.V403F	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.V403F|NLRP12_uc002qcj.3_Missense_Mutation_p.V403F|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.V403F	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	403	NACHT.				negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		ACCAGGGGGACGAAGCACATG	0.557													107	206	---	---	---	---	PASS
NLRP12	91662	broad.mit.edu	37	19	54313711	54313711	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54313711C>T	uc002qch.3	-	3	1422	c.1202G>A	c.(1201-1203)TGC>TAC	p.C401Y	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.C401Y|NLRP12_uc002qcj.3_Missense_Mutation_p.C401Y|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.C401Y	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	401	NACHT.				negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		GGGGACGAAGCACATGGTGAA	0.567													101	215	---	---	---	---	PASS
CABIN1	23523	broad.mit.edu	37	22	24463082	24463082	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24463082G>C	uc002zzi.1	+	16	2309	c.2182G>C	c.(2182-2184)GAG>CAG	p.E728Q	CABIN1_uc002zzj.1_Missense_Mutation_p.E678Q|CABIN1_uc002zzl.1_Missense_Mutation_p.E728Q	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	728					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						CAAACACCTGGAGTTTATGAC	0.567													23	60	---	---	---	---	PASS
EIF4ENIF1	56478	broad.mit.edu	37	22	31850208	31850208	+	Silent	SNP	G	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31850208G>A	uc003akz.1	-	10	1598	c.1434C>T	c.(1432-1434)GAC>GAT	p.D478D	EIF4ENIF1_uc003akx.1_Silent_p.D157D|EIF4ENIF1_uc003aky.1_Silent_p.D157D|EIF4ENIF1_uc003ala.1_Silent_p.D478D|EIF4ENIF1_uc003alb.1_Silent_p.D315D|EIF4ENIF1_uc003akw.1_5'Flank	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E	478						nucleus	protein binding|protein transporter activity			ovary(1)	1						TCATGTCTCCGTCTTTCTTCA	0.478													50	89	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160816	77160816	+	3'UTR	SNP	A	G	G			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160816A>G	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TTGATGCCAAATTAAAGCACT	0.343													4	27	---	---	---	---	PASS
TAF7L	54457	broad.mit.edu	37	X	100541631	100541631	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100541631C>A	uc004ehb.2	-	3	347	c.335G>T	c.(334-336)TGT>TTT	p.C112F	TAF7L_uc004eha.2_Missense_Mutation_p.C26F|TAF7L_uc004ehc.1_Missense_Mutation_p.C26F	NM_024885	NP_079161	Q5H9L4	TAF7L_HUMAN	TATA box binding protein-associated factor, RNA	112					cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription initiation from RNA polymerase II promoter	cytoplasm|transcription factor TFIID complex	binding			breast(1)	1						CCTGACAGTACAAGCATGTTC	0.323													3	45	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152286259	152286260	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152286259_152286260delTG	uc001ezu.1	-	3	1138_1139	c.1102_1103delCA	c.(1102-1104)CAGfs	p.Q368fs	uc001ezv.2_RNA	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	368	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGATGCAGTCTGTCCACGAGAG	0.564									Ichthyosis				358	237	---	---	---	---	
C2orf43	60526	broad.mit.edu	37	2	21000848	21000849	+	Intron	DEL	AC	-	-	rs111544765		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21000848_21000849delAC	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTGacacaaacacacacacac	0.252													4	2	---	---	---	---	
THUMPD2	80745	broad.mit.edu	37	2	39988409	39988409	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39988409delA	uc002rru.2	-						THUMPD2_uc002rrv.2_Intron|THUMPD2_uc010ynt.1_Intron	NM_025264	NP_079540	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2								methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)				TCAATAAGAGACTGTATAAGT	0.333													76	51	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90475369	90475370	+	IGR	INS	-	TCCTTCT	TCCTTCT			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90475369_90475370insTCCTTCT								None (None upstream) : None (None downstream)																							tccttccttccttccttccttc	0.050													6	3	---	---	---	---	
RANBP2	5903	broad.mit.edu	37	2	109369249	109369249	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109369249delA	uc002tem.3	+							NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						actctgtctcaaaaaaaaaaa	0.144													4	4	---	---	---	---	
WDSUB1	151525	broad.mit.edu	37	2	160092388	160092388	+	3'UTR	DEL	T	-	-	rs34183718		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160092388delT	uc002uaj.3	-	11					WDSUB1_uc002uak.3_3'UTR|WDSUB1_uc002ual.3_3'UTR|WDSUB1_uc002uam.3_3'UTR|WDSUB1_uc010foo.2_3'UTR	NM_152528	NP_689741	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain							ubiquitin ligase complex	ubiquitin-protein ligase activity				0						AGTCCATGTGTTTTTTAAAGA	0.249													6	5	---	---	---	---	
MDH1B	130752	broad.mit.edu	37	2	207604137	207604137	+	Intron	DEL	A	-	-	rs141240854		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207604137delA	uc002vbs.2	-						MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Intron|MDH1B_uc010fuj.2_Intron|MDH1B_uc002vbt.2_Intron	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		accttgtcttaaaaaaaaaaa	0.249													5	3	---	---	---	---	
SNED1	25992	broad.mit.edu	37	2	242007466	242007466	+	Intron	DEL	C	-	-	rs67511252		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242007466delC	uc002wah.1	+						SNED1_uc002wai.1_Intron|SNED1_uc002waj.1_Intron|SNED1_uc002wak.2_Intron	NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor						cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GTGGACTGTACCACCTGCCGC	0.657													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	44742540	44742540	+	IGR	DEL	G	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44742540delG								ZNF35 (40258 upstream) : ZNF502 (11595 downstream)																							gagggaggaaggaaggaagga	0.025													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52584552	52584552	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52584552delA	uc003des.2	-	29	4794	c.4782delT	c.(4780-4782)TTTfs	p.F1594fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.F1487fs|PBRM1_uc003der.2_Frame_Shift_Del_p.F1507fs|PBRM1_uc003det.2_Frame_Shift_Del_p.F1502fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.F1557fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.F1539fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.F1514fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.F1487fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1594	Pro-rich.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GGGGAGCTACAAACATGGGTG	0.572			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								43	65	---	---	---	---	
ITIH4	3700	broad.mit.edu	37	3	52854657	52854657	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52854657delG	uc003dfz.2	-	13	1860	c.1824delC	c.(1822-1824)CCCfs	p.P608fs	ITIH4_uc011bel.1_Frame_Shift_Del_p.P338fs|ITIH4_uc003dfy.2_Frame_Shift_Del_p.P472fs|ITIH4_uc011bem.1_Frame_Shift_Del_p.P608fs|ITIH4_uc011ben.1_Frame_Shift_Del_p.P608fs	NM_002218	NP_002209	Q14624	ITIH4_HUMAN	inter-alpha (globulin) inhibitor H4	608					acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CGCCTTCCATGGGCTTCTCAG	0.547											OREG0015616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	37	50	---	---	---	---	
BTLA	151888	broad.mit.edu	37	3	112218320	112218320	+	5'UTR	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112218320delA	uc003dza.3	-	1					BTLA_uc003dzb.3_5'UTR	NM_181780	NP_861445	Q7Z6A9	BTLA_HUMAN	B and T lymphocyte associated isoform 1						T cell costimulation		receptor activity				0		Acute lymphoblastic leukemia(4;1.34e-07)|all_hematologic(4;0.000361)				TGAAATAACTAAAAAAAAAAA	0.413													8	5	---	---	---	---	
SLC12A8	84561	broad.mit.edu	37	3	124896475	124896476	+	Intron	INS	-	GGTAAAGCCTAT	GGTAAAGCCTAT	rs143015454	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124896475_124896476insGGTAAAGCCTAT	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc010hrz.1_Intron	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0						CACCAATTGTAGGTAAAGCCTA	0.510													5	4	---	---	---	---	
ATP13A4	84239	broad.mit.edu	37	3	193249086	193249089	+	Intron	DEL	AGGA	-	-	rs2458122	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193249086_193249089delAGGA	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ggagggagggaggaaggaaggaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3699162	3699162	+	IGR	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3699162delA								LRPAP1 (164938 upstream) : ADRA2C (68913 downstream)																							tgagggaatgagggcacgaag	0.000													4	2	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6513274	6513282	+	Intron	DEL	TGGTGGTGG	-	-	rs62286140		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6513274_6513282delTGGTGGTGG	uc011bwd.1	-						PPP2R2C_uc011bwe.1_Intron	NM_181876	NP_870991	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						gtggtggtgatggtggtggtggtggtggt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15929349	15929351	+	IGR	DEL	TTT	-	-	rs139421865		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15929349_15929351delTTT								CD38 (78643 upstream) : FGFBP1 (7844 downstream)																							tcAATGTCTCttttttttttttt	0.084													4	2	---	---	---	---	
PI4K2B	55300	broad.mit.edu	37	4	25262254	25262267	+	Intron	DEL	ATATATATATACAC	-	-	rs71600578		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25262254_25262267delATATATATATACAC	uc003grk.2	+						PI4K2B_uc011bxs.1_Intron	NM_018323	NP_060793	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta							cytoplasm|membrane	1-phosphatidylinositol 4-kinase activity|ATP binding			ovary(2)|skin(2)	4		Breast(46;0.173)				atatatatatatatatatatacacacacacacac	0.136													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	38387897	38387900	+	IGR	DEL	AAGC	-	-	rs6812640	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38387897_38387900delAAGC								TBC1D1 (247104 upstream) : FLJ13197 (226422 downstream)																							ggaaggaaggaagcaaggaaggaa	0.123													3	3	---	---	---	---	
SPATA18	132671	broad.mit.edu	37	4	52928527	52928527	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52928527delA	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron	NM_145263	NP_660306	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			ATCTTTTTCCAAAAAGAATTG	0.343													40	39	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63021050	63021051	+	IGR	DEL	AC	-	-	rs147946009		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63021050_63021051delAC								LPHN3 (82883 upstream) : None (None downstream)																							acatataaatacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68214271	68214278	+	IGR	DEL	AGGAAGGA	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68214271_68214278delAGGAAGGA								None (None upstream) : CENPC1 (123711 downstream)																							agagagagagaggaaggaaggaaggaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174596492	174596496	+	IGR	DEL	CTTTT	-	-	rs139835286	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174596492_174596496delCTTTT								MORF4 (58698 upstream) : FBXO8 (561316 downstream)																							ttcctccctccttttcttttctttt	0.132													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8050493	8050497	+	IGR	DEL	AAGGA	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8050493_8050497delAAGGA								MTRR (149260 upstream) : SEMA5A (984641 downstream)																							ggaaggaaggaaggaaaggaaagga	0.000													3	4	---	---	---	---	
LOC441089	441089	broad.mit.edu	37	5	79646840	79646840	+	RNA	DEL	T	-	-	rs34240292		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79646840delT	uc010jaj.1	-	1		c.946delA				NR_003665				Homo sapiens CRSP8 pseudogene (LOC441089), non-coding RNA.												0						GCGTGGGGGCTTACTGCCGGC	0.632													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85703814	85703815	+	IGR	INS	-	AAGG	AAGG	rs149876942	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85703814_85703815insAAGG								NBPF22P (110452 upstream) : COX7C (209969 downstream)																							ggaaggaaggaaggaaggaagg	0.089													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174170410	174170413	+	IGR	DEL	CCTT	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174170410_174170413delCCTT								MSX2 (12509 upstream) : DRD1 (697263 downstream)																							ccttccttccccttccttccttcc	0.000													6	4	---	---	---	---	
SFXN1	94081	broad.mit.edu	37	5	174919392	174919392	+	Intron	DEL	A	-	-	rs35883400		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174919392delA	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591	Q9H9B4	SFXN1_HUMAN	sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCTTTTGACCAAAAAAAAAAA	0.154													4	2	---	---	---	---	
UIMC1	51720	broad.mit.edu	37	5	176395373	176395374	+	Intron	INS	-	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176395373_176395374insA	uc011dfp.1	-						UIMC1_uc003mfc.1_Intron|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfg.1_Intron|UIMC1_uc003mff.1_Intron	NM_016290	NP_057374	Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|negative regulation of transcription, DNA-dependent|positive regulation of DNA repair|response to ionizing radiation|transcription, DNA-dependent	BRCA1-A complex	histone binding|K63-linked polyubiquitin binding			ovary(3)|skin(1)	4	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gactccaactcaaaaaaaaaaa	0.045													3	4	---	---	---	---	
HLA-C	3107	broad.mit.edu	37	6	31237576	31237577	+	Intron	DEL	CA	-	-	rs72558156		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31237576_31237577delCA	uc003nsy.2	-						HLA-C_uc011dnj.1_Intron|HLA-C_uc003nsx.2_Intron|HLA-C_uc003nsz.2_Intron|HLA-C_uc010jsl.2_Intron|HLA-C_uc003nta.2_Intron|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						CCTTCATTGTCACATGTGCTTC	0.520													3	4	---	---	---	---	
HLA-DQB2	3120	broad.mit.edu	37	6	32725441	32725442	+	Intron	INS	-	CCTCCAGCTCAGTTTT	CCTCCAGCTCAGTTTT	rs143697066	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32725441_32725442insCCTCCAGCTCAGTTTT	uc003oby.3	-						HLA-DQB2_uc003obz.2_Intron	NR_003937		Q5SR06	Q5SR06_HUMAN	SubName: Full=Major histocompatibility complex, class II, DQ beta 2; SubName: Full=Putative uncharacterized protein ENSP00000372579;						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex					0						GTCTCCTCGCACTTCCTCTCAG	0.515													4	2	---	---	---	---	
COL9A1	1297	broad.mit.edu	37	6	71011908	71011916	+	Intron	DEL	TTTTTTTTT	-	-	rs71801341		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71011908_71011916delTTTTTTTTT	uc003pfg.3	-							NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor						axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4						TTTTCAtttcttttttttttttttttttt	0.158													3	3	---	---	---	---	
TPBG	7162	broad.mit.edu	37	6	83074572	83074572	+	5'UTR	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83074572delT	uc003pjn.3	+	3					TPBG_uc010kbj.2_5'UTR|TPBG_uc003pjo.2_5'UTR	NM_006670	NP_006661	Q13641	TPBG_HUMAN	trophoblast glycoprotein precursor						cell adhesion	integral to plasma membrane				central_nervous_system(1)	1		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		GAGAGGAAAGTTTTTTTTTTC	0.701													4	2	---	---	---	---	
PREP	5550	broad.mit.edu	37	6	105777031	105777031	+	Intron	DEL	T	-	-	rs11345908		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105777031delT	uc003prc.2	-							NM_002726	NP_002717	P48147	PPCE_HUMAN	prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CACTTTTACAttttttttttt	0.169													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64755430	64755437	+	IGR	DEL	CCTTCCTT	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64755430_64755437delCCTTCCTT								INTS4L1 (60831 upstream) : ZNF92 (83331 downstream)																							ttcttttctcccttccttccttccttcc	0.106													4	3	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70786853	70786853	+	Intron	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70786853delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ccttccttcctttccttcctt	0.000													4	4	---	---	---	---	
LRWD1	222229	broad.mit.edu	37	7	102106858	102106861	+	Intron	DEL	TTTA	-	-	rs66463732		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102106858_102106861delTTTA	uc003uzn.2	+						ALKBH4_uc003uzl.2_5'Flank|ALKBH4_uc003uzm.2_5'Flank|LRWD1_uc003uzo.2_Intron	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain						chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1						GATGTGCTACtttatttatttatt	0.260													2	4	---	---	---	---	
ADAM28	10863	broad.mit.edu	37	8	24211051	24211052	+	Intron	INS	-	ACTG	ACTG			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24211051_24211052insACTG	uc003xdy.2	+						ADAM28_uc011laa.1_Intron|ADAM28_uc010lua.2_Intron	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1						proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		AGACGAGTGACACTGACAGGAA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84526647	84526648	+	IGR	DEL	TC	-	-	rs144135500	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84526647_84526648delTC								None (None upstream) : RALYL (568805 downstream)																							tttctttctttctctctctttc	0.000													4	2	---	---	---	---	
RFK	55312	broad.mit.edu	37	9	79003685	79003685	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79003685delA	uc004akd.2	-						RFK_uc004ake.2_Intron	NM_018339	NP_060809	Q969G6	RIFK_HUMAN	riboflavin kinase						riboflavin biosynthetic process	cytosol	ATP binding|metal ion binding|riboflavin kinase activity				0					Riboflavin(DB00140)	AACACTCCTTAAACTTTTAAA	0.328													9	5	---	---	---	---	
ZBTB43	23099	broad.mit.edu	37	9	129595818	129595818	+	Frame_Shift_Del	DEL	G	-	-	rs141489057		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129595818delG	uc004bql.2	+	3	1303	c.1030delG	c.(1030-1032)GCAfs	p.A344fs	ZBTB43_uc010mxf.2_Frame_Shift_Del_p.A344fs	NM_014007	NP_054726	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	344					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GGCTGCCCTCGCAGCAGGTTA	0.468													63	46	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	130209778	130209778	+	IGR	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130209778delA								ZNF79 (2128 upstream) : RPL12 (177 downstream)																							actctgtctcaaaaaaaaaaa	0.209													6	3	---	---	---	---	
DHTKD1	55526	broad.mit.edu	37	10	12132367	12132370	+	Intron	DEL	CCTT	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12132367_12132370delCCTT	uc001ild.3	+							NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			GCcctccctcccttccttccttcc	0.167													4	2	---	---	---	---	
MCM10	55388	broad.mit.edu	37	10	13233564	13233567	+	Intron	DEL	AAGC	-	-	rs112703555		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13233564_13233567delAAGC	uc001ima.2	+						MCM10_uc001imb.2_Intron|MCM10_uc001imc.2_Intron	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						ATAAATAAATaagcaagcaagcaa	0.137													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	16454809	16454810	+	IGR	DEL	AG	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16454809_16454810delAG								FAM188A (552290 upstream) : PTER (24157 downstream)																							gaagaaagaaaggaaggaagga	0.010													4	2	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61444172	61444173	+	Intron	DEL	AA	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61444172_61444173delAA	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						TCCTAAAGTGAAAAAAAAAAAA	0.322													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63251406	63251409	+	Intron	DEL	GAAG	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63251406_63251409delGAAG	uc001jlr.2	+											Homo sapiens, clone IMAGE:5222445, mRNA.																		aggagggaaagaaggaaggaagga	0.103													4	2	---	---	---	---	
KCNIP2	30819	broad.mit.edu	37	10	103592054	103592057	+	Intron	DEL	TGTG	-	-	rs72317507		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103592054_103592057delTGTG	uc001kub.2	-						KCNIP2_uc001ktx.2_5'Flank|KCNIP2_uc001kty.2_5'Flank|KCNIP2_uc001ktz.2_Intron|KCNIP2_uc009xwu.2_Intron|KCNIP2_uc009xwv.2_Intron|KCNIP2_uc001kuc.2_Intron|KCNIP2_uc001kue.2_Intron|KCNIP2_uc001kud.2_Intron|KCNIP2_uc001kuf.2_Intron|KCNIP2_uc001kua.2_Intron|KCNIP2_uc009xww.2_Intron|KCNIP2_uc010qqh.1_Intron|KCNIP2_uc010qqi.1_Intron	NM_173191	NP_775283	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2 isoform 2						clustering of voltage-gated potassium channels|detection of calcium ion|muscle contraction|regulation of heart contraction|signal transduction|synaptic transmission	cytoplasm|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|calcium ion binding|ER retention sequence binding|identical protein binding|protein N-terminus binding				0		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		TCAGTGTTACtgtgtgtgtgtgtg	0.407													4	3	---	---	---	---	
TUBGCP2	10844	broad.mit.edu	37	10	135097228	135097228	+	Intron	DEL	G	-	-	rs67681147		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135097228delG	uc001lmg.1	-						TUBGCP2_uc001lmf.1_Intron|TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		tgcctctcccgcactccctgc	0.055													7	4	---	---	---	---	
NUP160	23279	broad.mit.edu	37	11	47833875	47833875	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47833875delT	uc001ngm.2	-	16	2144	c.2059delA	c.(2059-2061)ATGfs	p.M687fs	NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa	687					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						CCCTTTTCCATTTCCACTTCT	0.358													254	112	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48548379	48548380	+	IGR	INS	-	AT	AT			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48548379_48548380insAT								OR4A47 (37107 upstream) : FOLH1 (619808 downstream)																							CCTGTAGTTTCATGTATGTTAG	0.371													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68412201	68412201	+	IGR	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68412201delA								SAPS3 (29402 upstream) : GAL (39782 downstream)																							ggaaggaaagaaaggaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74140694	74140694	+	IGR	DEL	T	-	-	rs34117754		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74140694delT								PGM2L1 (31192 upstream) : KCNE3 (25194 downstream)																							tccttctttcttttttttttt	0.005													3	3	---	---	---	---	
MYO7A	4647	broad.mit.edu	37	11	76892815	76892816	+	Intron	INS	-	TTG	TTG			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76892815_76892816insTTG	uc001oyb.2	+						MYO7A_uc010rsl.1_Intron|MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc001oyd.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						CTTCTCAAGtttttttttttgt	0.297													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111759853	111759853	+	IGR	DEL	T	-	-	rs150833390		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111759853delT								C11orf1 (5058 upstream) : CRYAB (19497 downstream)																							tctctctctcttttttttttt	0.144													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112332121	112332121	+	IGR	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112332121delT								PTS (191444 upstream) : NCAM1 (499874 downstream)																							TGATTTTATGTTTTTTTTTTT	0.378													4	2	---	---	---	---	
CD3G	917	broad.mit.edu	37	11	118221605	118221605	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118221605delA	uc001psu.2	+						CD3G_uc009zaa.1_Intron	NM_000073	NP_000064	P09693	CD3G_HUMAN	CD3G antigen, gamma polypeptide precursor						establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity				0	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;3.04e-05)		TCCCTCTGTGAAAAAAAAAAA	0.239													10	5	---	---	---	---	
CAPRIN2	65981	broad.mit.edu	37	12	30881470	30881477	+	Intron	DEL	CAGAGTGT	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30881470_30881477delCAGAGTGT	uc001rji.1	-						CAPRIN2_uc001rjf.1_Intron|CAPRIN2_uc001rjg.1_Intron|CAPRIN2_uc001rjh.1_Intron|CAPRIN2_uc001rjj.1_Intron|CAPRIN2_uc001rjk.3_Intron|CAPRIN2_uc001rjl.3_Intron|CAPRIN2_uc001rjm.1_Intron|CAPRIN2_uc001rjn.1_3'UTR	NM_001002259	NP_001002259	Q6IMN6	CAPR2_HUMAN	C1q domain containing 1 isoform 1						negative regulation of cell growth|negative regulation of translation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of transcription from RNA polymerase II promoter	mitochondrion|receptor complex	receptor binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					gcctgggtaacagagtgtttctccatct	0.115													10	5	---	---	---	---	
ESYT1	23344	broad.mit.edu	37	12	56530374	56530375	+	Intron	INS	-	AA	AA			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56530374_56530375insAA	uc001sjq.2	+						ESYT1_uc001sjr.2_Intron	NM_015292	NP_056107	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1							integral to membrane				ovary(4)|skin(1)	5						gactctgtctcaaaaaaaaaaa	0.183													4	3	---	---	---	---	
GLT1D1	144423	broad.mit.edu	37	12	129428712	129428712	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129428712delA	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270	Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		TATAATTTTCAAAGAATTCAT	0.333													12	10	---	---	---	---	
RNF17	56163	broad.mit.edu	37	13	25448552	25448553	+	Intron	INS	-	T	T	rs142376691		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25448552_25448553insT	uc001upr.2	+						RNF17_uc010aab.2_Intron|RNF17_uc010tde.1_Intron|RNF17_uc001ups.2_Intron|RNF17_uc010aac.2_Intron|RNF17_uc010aad.2_Intron	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17						multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		accattgtagcttttttttttt	0.074													5	3	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33275733	33275734	+	Intron	INS	-	CA	CA	rs145247314	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33275733_33275734insCA	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ATTTGTATATGcacacacacac	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66497435	66497436	+	IGR	INS	-	AG	AG	rs142611026	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66497435_66497436insAG								None (None upstream) : PCDH9 (379531 downstream)																							GGAAAAAGAGAgaaggaaggaa	0.025													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	99760095	99760102	+	IGR	DEL	GAGGAAGC	-	-	rs146743357	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99760095_99760102delGAGGAAGC								DOCK9 (21435 upstream) : UBAC2 (92577 downstream)																							gggaggaggggaggaagcgaggaagcga	0.000													6	6	---	---	---	---	
MMP14	4323	broad.mit.edu	37	14	23313394	23313394	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23313394delA	uc001whc.2	+							NM_004995	NP_004986	P50281	MMP14_HUMAN	matrix metalloproteinase 14 preproprotein							extracellular matrix|integral to plasma membrane|melanosome	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		caacagtgtgagactccatct	0.209													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31745926	31745926	+	IGR	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31745926delT								HECTD1 (69011 upstream) : HEATR5A (15069 downstream)																							ccttccttcctttccttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101576872	101576874	+	IGR	DEL	GAG	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101576872_101576874delGAG								MIR656 (43734 upstream) : DIO3OS (441686 downstream)																							CAGGGCCAGAGAGGAGGCCGTGC	0.404													4	2	---	---	---	---	
DENND4A	10260	broad.mit.edu	37	15	65959941	65959942	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65959941_65959942delTC	uc002aph.2	-	28	5332_5333	c.4954_4955delGA	c.(4954-4956)GAAfs	p.E1652fs	DENND4A_uc002api.2_Frame_Shift_Del_p.E1695fs	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2	1652					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						ACCTTCATTTTCCAATAAGCTT	0.416													127	62	---	---	---	---	
MYO9A	4649	broad.mit.edu	37	15	72120536	72120537	+	Intron	INS	-	A	A	rs139814275	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72120536_72120537insA	uc002atl.3	-						MYO9A_uc002atj.2_Intron|MYO9A_uc002atk.2_Intron	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3						TGGTGAAGGCTAAAACTATATG	0.426													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79456059	79456060	+	IGR	DEL	TC	-	-	rs10592832		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79456059_79456060delTC								RASGRF1 (72844 upstream) : MIR184 (46070 downstream)																							tccttccttTtctctctctctc	0.104													3	3	---	---	---	---	
MYH3	4621	broad.mit.edu	37	17	10547483	10547486	+	Intron	DEL	AAAC	-	-	rs147605554		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10547483_10547486delAAAC	uc002gmq.1	-							NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,						muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						caaaaaaaaaaaacaaacaaaaaa	0.201													4	4	---	---	---	---	
SLFN11	91607	broad.mit.edu	37	17	33689643	33689644	+	Intron	INS	-	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33689643_33689644insA	uc010ctp.2	-						SLFN11_uc010ctq.2_Intron|SLFN11_uc002hjh.3_Intron|SLFN11_uc002hjg.3_Intron|SLFN11_uc010ctr.2_Intron	NM_001104588	NP_001098058	Q7Z7L1	SLN11_HUMAN	schlafen family member 11							nucleus	ATP binding			large_intestine(1)|ovary(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGATTCAAAATAAAGTGTTCAG	0.371													8	9	---	---	---	---	
THRA	7067	broad.mit.edu	37	17	38243312	38243313	+	Intron	DEL	AC	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38243312_38243313delAC	uc002htw.2	+						THRA_uc010cwp.1_Intron|THRA_uc002htv.2_Intron|THRA_uc002htx.2_Intron	NM_003250	NP_003241	P10827	THA_HUMAN	thyroid hormone receptor, alpha isoform 2						negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|negative regulation of transcription initiation, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter	cytosol|nucleoplasm	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|TBP-class protein binding|thyroid hormone binding|thyroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding				0	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Levothyroxine(DB00451)|Liothyronine(DB00279)	acatacacggacacacacacac	0.030													4	2	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42289911	42289912	+	Intron	INS	-	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42289911_42289912insT	uc002igb.2	-						UBTF_uc002igc.2_Intron|UBTF_uc010czs.2_Intron|UBTF_uc002igd.2_Intron|UBTF_uc010czt.2_Intron|UBTF_uc002ige.2_Intron	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CCCCCGCCCCCTCAGGCCATGG	0.688													4	2	---	---	---	---	
ITGB3	3690	broad.mit.edu	37	17	45377700	45377701	+	Intron	INS	-	GC	GC	rs113076632		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45377700_45377701insGC	uc002ilj.2	+						ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	TTGTCTTACAGGCGCGCGCGCG	0.525													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53458579	53458582	+	IGR	DEL	CTTT	-	-	rs10545207	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53458579_53458582delCTTT								HLF (56153 upstream) : MMD (11393 downstream)																							tctttctttcctttcttccttcct	0.000													4	2	---	---	---	---	
ANKRD12	23253	broad.mit.edu	37	18	9256041	9256042	+	Frame_Shift_Del	DEL	AA	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9256041_9256042delAA	uc002knv.2	+	9	3033_3034	c.2776_2777delAA	c.(2776-2778)AAAfs	p.K926fs	ANKRD12_uc002knw.2_Frame_Shift_Del_p.K903fs|ANKRD12_uc002knx.2_Frame_Shift_Del_p.K903fs|ANKRD12_uc010dkx.1_Frame_Shift_Del_p.K633fs	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	926						nucleus				ovary(2)|central_nervous_system(1)	3						AGCAGAAAGCAAAGAAAAGCAC	0.327													16	18	---	---	---	---	
TXNL1	9352	broad.mit.edu	37	18	54283363	54283363	+	Intron	DEL	A	-	-	rs35834292		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54283363delA	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron|TXNL1_uc002lgj.1_Intron	NM_004786	NP_004777	O43396	TXNL1_HUMAN	thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		actctgtctcaaaaaaaaaaa	0.100													9	4	---	---	---	---	
CTDP1	9150	broad.mit.edu	37	18	77474315	77474323	+	Intron	DEL	GCACTTCAG	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77474315_77474323delGCACTTCAG	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		ctggtcccacgcacttcaggtaaggggtg	0.225													3	3	---	---	---	---	
GNA11	2767	broad.mit.edu	37	19	3121300	3121300	+	3'UTR	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3121300delT	uc002lxd.2	+	7					uc010xhe.1_5'Flank	NM_002067	NP_002058	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein),						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			eye(70)|skin(16)	86		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		CGGGAGGAGATTTTTTTTTTT	0.557			Mis		uveal melanoma								4	2	---	---	---	---	
CARD8	22900	broad.mit.edu	37	19	48724211	48724211	+	Intron	DEL	A	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48724211delA	uc002pie.3	-						CARD8_uc002pii.3_Intron|CARD8_uc002pid.1_5'Flank|CARD8_uc010xzi.1_Intron|CARD8_uc010els.2_Intron|CARD8_uc010xzj.1_Intron|CARD8_uc010xzk.1_Intron|CARD8_uc002pif.3_Intron|CARD8_uc002pig.3_Intron|CARD8_uc002pih.3_Intron|CARD8_uc010xzl.1_Intron|CARD8_uc010xzm.1_Intron	NM_014959	NP_055774	Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8						negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		aaaggaaaggaaaggaaggaa	0.000													3	3	---	---	---	---	
CGB	1082	broad.mit.edu	37	19	49532322	49532322	+	Intron	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49532322delT	uc010yad.1	-						CGB2_uc002plw.2_5'Flank|CGB2_uc010yaf.1_5'Flank	NM_033183	NP_149439	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 8						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	tctttctttcttttttttttt	0.244													8	4	---	---	---	---	
TARM1	441864	broad.mit.edu	37	19	54583284	54583285	+	Intron	INS	-	GGAA	GGAA			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54583284_54583285insGGAA	uc010yei.1	-							NM_001135686	NP_001129158	B6A8C7	TARM1_HUMAN	OSCAR-like transcript-2							integral to membrane					0						aggaaaaggagggaaggaagga	0.000													3	3	---	---	---	---	
NOP56	10528	broad.mit.edu	37	20	2633378	2633379	+	Intron	INS	-	GAGCCTGGGCCT	GAGCCTGGGCCT	rs149713688	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2633378_2633379insGAGCCTGGGCCT	uc002wgh.2	+						NOP56_uc010zpy.1_Intron|MIR1292_hsa-mir-1292|MI0006433_5'Flank|NOP56_uc002wgi.2_5'Flank|SNORD110_uc002wgj.2_5'Flank|SNORA51_uc002wgk.1_5'Flank|NOP56_uc002wgm.1_5'Flank	NM_006392	NP_006383	O00567	NOP56_HUMAN	nucleolar protein 5A						rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2						GGCCGCAGACAgggcctgggcc	0.550													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9042357	9042358	+	IGR	INS	-	TTCT	TTCT	rs142004450	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9042357_9042358insTTCT								PLCB1 (176812 upstream) : PLCB4 (7343 downstream)																							tctttctttccttctttctctt	0.054													4	2	---	---	---	---	
SEC23B	10483	broad.mit.edu	37	20	18485750	18485751	+	5'Flank	INS	-	A	A	rs74180905		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18485750_18485751insA	uc002wqz.1	+						SEC23B_uc002wra.1_5'Flank|SEC23B_uc002wrb.1_5'Flank|SEC23B_uc010zsb.1_5'Flank|SEC23B_uc002wrc.1_5'Flank	NM_006363	NP_006354	Q15437	SC23B_HUMAN	Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1						GCCTCATTCAGAAAAAAAAAAA	0.371													9	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11085955	11085957	+	Intron	DEL	CAT	-	-	rs75434111	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11085955_11085957delCAT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccaccaccaccatcaacaccacA	0.177													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	30274437	30274444	+	IGR	DEL	CCATCTCG	-	-	rs2776223	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30274437_30274444delCCATCTCG								N6AMT1 (16744 upstream) : RNF160 (26022 downstream)																							tgcaatggcaccatctcgccatctcagc	0.087													4	2	---	---	---	---	
DNAJC28	54943	broad.mit.edu	37	21	34861875	34861875	+	Intron	DEL	T	-	-	rs77181674		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34861875delT	uc002yrv.2	-						DNAJC28_uc002yrw.2_Intron	NM_017833	NP_060303	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28								heat shock protein binding				0						AACTTTttccttttttttttt	0.154													4	4	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	18003413	18003413	+	Intron	DEL	C	-	-	rs695465		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18003413delC	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		CCGGCAATTTCtttttttttt	0.279													5	3	---	---	---	---	
TFIP11	24144	broad.mit.edu	37	22	26892602	26892603	+	Intron	INS	-	A	A			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26892602_26892603insA	uc003acr.2	-						TFIP11_uc003acq.2_5'Flank|TFIP11_uc003acs.2_Intron|TFIP11_uc003act.2_Intron	NM_012143	NP_036275	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11						biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0						CCAGGCGTTTTAACAGCACTGA	0.450													37	21	---	---	---	---	
GAL3ST1	9514	broad.mit.edu	37	22	30952062	30952062	+	Frame_Shift_Del	DEL	C	-	-	rs73394272	by1000genomes	TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30952062delC	uc003aig.1	-	4	290	c.150delG	c.(148-150)GCGfs	p.A50fs	GAL3ST1_uc003aih.1_Frame_Shift_Del_p.A50fs|GAL3ST1_uc003aii.1_Frame_Shift_Del_p.A50fs|GAL3ST1_uc010gvz.1_Frame_Shift_Del_p.A50fs	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	50	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0						GAGAGCAGGACGCTGCGGCCT	0.662													64	41	---	---	---	---	
CFP	5199	broad.mit.edu	37	X	47483959	47483960	+	Intron	INS	-	T	T			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47483959_47483960insT	uc004dig.3	-						CFP_uc004dih.2_Intron|CFP_uc004dii.1_3'UTR|CFP_uc010nhu.2_3'UTR	NM_001145252	NP_001138724	P27918	PROP_HUMAN	complement factor properdin precursor						complement activation, alternative pathway|defense response to bacterium	extracellular space				breast(2)|lung(1)	3						tttttttttccttttttttttt	0.094													6	3	---	---	---	---	
FAAH2	158584	broad.mit.edu	37	X	57458220	57458220	+	Intron	DEL	G	-	-	rs6521622		TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57458220delG	uc004dvc.2	+							NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3						ttgtttttttgttttttttgg	0.060										HNSCC(52;0.14)			4	2	---	---	---	---	
DLG3	1741	broad.mit.edu	37	X	69713144	69713144	+	Intron	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69713144delT	uc004dyi.1	+						DLG3_uc004dyj.1_Intron|DLG3_uc011mpn.1_Intron	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)					TCCATTTTAGTTTTTCTTGCA	0.338													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13483364	13483364	+	IGR	DEL	T	-	-			TCGA-BP-5185-01A-01D-1429-08	TCGA-BP-5185-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13483364delT								None (None upstream) : None (None downstream)																							tctgtcacaattcccctttag	0.000													5	3	---	---	---	---	
