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
MYCL1	4610	broad.mit.edu	37	1	40362819	40362819	+	3'UTR	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40362819G>T	uc001cer.1	-	3					MYCL1_uc001ces.1_3'UTR	NM_001033082	NP_001028254	P12524	MYCL1_HUMAN	l-myc-1 proto-oncogene isoform 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|liver(1)	2	all_cancers(7;1.73e-14)|all_lung(5;2.77e-17)|all_epithelial(6;6.81e-17)|Lung SC(1;2.85e-13)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.51e-19)|Epithelial(16;3.36e-18)|all cancers(16;8.43e-17)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AAAGGCGCCAGAGAACATACA	0.537			A		small cell lung 								3	12	---	---	---	---	PASS
KIAA0467	23334	broad.mit.edu	37	1	43895716	43895716	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43895716G>A	uc001cjk.1	+	15	2108	c.1646G>A	c.(1645-1647)CGC>CAC	p.R549H		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1448						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCCACTTCCGCACAGTGCCT	0.527													5	246	---	---	---	---	PASS
PTGER3	5733	broad.mit.edu	37	1	71437325	71437325	+	Intron	SNP	A	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71437325A>C	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron|PTGER3_uc009wbo.2_Intron|PTGER3_uc001dfo.2_Intron|PTGER3_uc001dfp.1_3'UTR	NM_198714	NP_942007	P43115	PE2R3_HUMAN	prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)	TCCAAATTAAAATATATAATT	0.289													32	88	---	---	---	---	PASS
MIA3	375056	broad.mit.edu	37	1	222794531	222794531	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222794531A>C	uc001hnl.2	+	2	173	c.164A>C	c.(163-165)GAT>GCT	p.D55A		NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	55	SH3.|Extracellular (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)		GCTCTTGAAGATTTCACAGGC	0.388													25	135	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229633944	229633944	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229633944G>T	uc001htn.2	-	6	850	c.758C>A	c.(757-759)TCA>TAA	p.S253*		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	253					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				ACCAATTCCTGAAAGCATGCC	0.363													4	198	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233136189	233136189	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233136189C>G	uc001hvl.2	-	30	5425	c.5190G>C	c.(5188-5190)GAG>GAC	p.E1730D	PCNXL2_uc001hvk.1_Missense_Mutation_p.E382D|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1730						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				CCGGGTCGCCCTCGTGGCAGA	0.622													4	140	---	---	---	---	PASS
MTR	4548	broad.mit.edu	37	1	237057790	237057790	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237057790C>A	uc001hyi.3	+	30	3761	c.3338C>A	c.(3337-3339)GCC>GAC	p.A1113D	MTR_uc010pxw.1_Missense_Mutation_p.A706D|MTR_uc010pxx.1_Missense_Mutation_p.A1062D|MTR_uc010pxy.1_Missense_Mutation_p.A967D	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	1113	AdoMet activation.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	CTGAGCAAGGCCTATGAGGAT	0.592													8	168	---	---	---	---	PASS
OR2L8	391190	broad.mit.edu	37	1	248112971	248112971	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248112971A>T	uc001idt.1	+	1	812	c.812A>T	c.(811-813)AAG>ATG	p.K271M	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	271	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ACAGAGGACAAGGTTCTGGCT	0.507													26	176	---	---	---	---	PASS
OR2T1	26696	broad.mit.edu	37	1	248569981	248569981	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248569981G>T	uc010pzm.1	+	1	686	c.686G>T	c.(685-687)TGT>TTT	p.C229F		NM_030904	NP_112166	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T,	229	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACTTCTTCTGTGAGGCACCA	0.517													4	200	---	---	---	---	PASS
FBXO11	80204	broad.mit.edu	37	2	48066061	48066061	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48066061T>C	uc010fbl.2	-	4	386	c.272A>G	c.(271-273)GAT>GGT	p.D91G	FBXO11_uc002rwe.2_Missense_Mutation_p.D91G|FBXO11_uc002rwf.2_Missense_Mutation_p.D91G|FBXO11_uc002rwg.1_Missense_Mutation_p.D91G	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	175	F-box.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCTACAAAGATCCTGTTCCAG	0.368													32	128	---	---	---	---	PASS
RGPD3	653489	broad.mit.edu	37	2	107049631	107049631	+	Silent	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107049631C>T	uc010ywi.1	-	16	2373	c.2316G>A	c.(2314-2316)GCG>GCA	p.A772A		NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	772					intracellular transport		binding			ovary(1)	1						TTTCTGAATCCGCATTTCGCA	0.373													5	477	---	---	---	---	PASS
CCDC93	54520	broad.mit.edu	37	2	118766138	118766138	+	Silent	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118766138A>G	uc002tlj.2	-	2	265	c.139T>C	c.(139-141)TTA>CTA	p.L47L	CCDC93_uc010fld.1_Silent_p.L47L	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	47										large_intestine(1)|ovary(1)	2						AAGGGTGATAAGCCTTTAATT	0.388													43	228	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141116420	141116420	+	Missense_Mutation	SNP	C	T	T	rs150879175	byFrequency	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141116420C>T	uc002tvj.1	-	73	12199	c.11227G>A	c.(11227-11229)GGT>AGT	p.G3743S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3743	Extracellular (Potential).|LDL-receptor class A 31.				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)		GAATTGTCACCGCATTCATCA	0.398										TSP Lung(27;0.18)			57	251	---	---	---	---	PASS
ITGAV	3685	broad.mit.edu	37	2	187500900	187500900	+	Silent	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187500900G>A	uc002upq.2	+	7	999	c.723G>A	c.(721-723)CGG>CGA	p.R241R	ITGAV_uc010frs.2_Silent_p.R205R|ITGAV_uc010zfv.1_Silent_p.R195R	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor	241	FG-GAP 4.|Extracellular (Potential).				angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|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|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)		TAGCAACTCGGACTGCACAAG	0.353													34	228	---	---	---	---	PASS
XRCC5	7520	broad.mit.edu	37	2	217005911	217005911	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217005911G>A	uc002vfy.2	+	13	1485	c.1345G>A	c.(1345-1347)GCA>ACA	p.A449T	XRCC5_uc002vfz.2_Missense_Mutation_p.A335T	NM_021141	NP_066964	P13010	XRCC5_HUMAN	ATP-dependent DNA helicase II	449	Ku.				double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		TGTTTAAGAGGCACAGTTGAA	0.393								Direct_reversal_of_damage|NHEJ					50	175	---	---	---	---	PASS
STK36	27148	broad.mit.edu	37	2	219561786	219561786	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219561786G>T	uc002viu.2	+	23	2877	c.2611G>T	c.(2611-2613)GAT>TAT	p.D871Y	STK36_uc002viv.2_Missense_Mutation_p.D850Y|STK36_uc002viw.2_Missense_Mutation_p.D49Y|STK36_uc002vix.2_5'UTR	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	871					cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CCTAATCAGGGATATGTCCAG	0.522													91	436	---	---	---	---	PASS
ANKZF1	55139	broad.mit.edu	37	2	220097312	220097312	+	Silent	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220097312C>T	uc002vkg.2	+	5	639	c.465C>T	c.(463-465)AGC>AGT	p.S155S	ATG9A_uc002vke.1_5'Flank|ATG9A_uc002vkf.1_5'Flank|ANKZF1_uc010zkv.1_Silent_p.S99S|ANKZF1_uc010zkw.1_5'UTR|ANKZF1_uc002vkh.2_5'UTR|ANKZF1_uc002vki.2_Silent_p.S155S|ANKZF1_uc002vkj.1_Silent_p.S143S	NM_018089	NP_060559	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing	155						intracellular	zinc ion binding			ovary(2)	2		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAAGTTGAGCCGACCCCCAG	0.537													4	158	---	---	---	---	PASS
IL17RC	84818	broad.mit.edu	37	3	9970113	9970113	+	Silent	SNP	T	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9970113T>G	uc003bua.2	+	11	1451	c.1215T>G	c.(1213-1215)GGT>GGG	p.G405G	CIDEC_uc003bto.2_Intron|IL17RC_uc011ato.1_RNA|IL17RC_uc010hcs.2_Silent_p.G309G|IL17RC_uc003btz.2_Silent_p.G334G|IL17RC_uc011atp.1_Silent_p.G190G|IL17RC_uc003bud.2_5'UTR|IL17RC_uc003bub.2_Silent_p.G319G|IL17RC_uc010hct.2_Silent_p.G334G|IL17RC_uc010hcu.2_Silent_p.G334G|IL17RC_uc010hcv.2_Silent_p.G319G|IL17RC_uc011atq.1_Silent_p.G319G|IL17RC_uc003buc.2_5'UTR|IL17RC_uc003bue.2_5'Flank	NM_153461	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C isoform 1 precursor	405	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)|pancreas(1)	2						GGGCTCCGGGTGGGGACCCCT	0.682													11	66	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38802744	38802744	+	Silent	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38802744A>G	uc003ciq.2	-	6	822	c.822T>C	c.(820-822)AAT>AAC	p.N274N		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	274	I.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	TGACACATTTATTTTTGAGGT	0.463													32	118	---	---	---	---	PASS
CADPS	8618	broad.mit.edu	37	3	62478037	62478037	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62478037C>A	uc003dll.2	-	20	3172	c.2812G>T	c.(2812-2814)GAG>TAG	p.E938*	CADPS_uc003dlk.1_Nonsense_Mutation_p.E435*|CADPS_uc003dlm.2_Nonsense_Mutation_p.E948*|CADPS_uc003dln.2_Nonsense_Mutation_p.E908*	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	938	MHD1.|Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GGTTGCACCTCTAAGGCTGCA	0.453													6	462	---	---	---	---	PASS
CRYBG3	131544	broad.mit.edu	37	3	97614877	97614877	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97614877A>T	uc003drx.2	+	9	1869	c.1805A>T	c.(1804-1806)AAT>ATT	p.N602I		NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0						GAAGACAGTAATGCTTGTGGT	0.393													56	201	---	---	---	---	PASS
GPR128	84873	broad.mit.edu	37	3	100354672	100354672	+	Splice_Site	SNP	T	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100354672T>A	uc003duc.2	+	5	865	c.597_splice	c.e5+2	p.E199_splice	GPR128_uc011bhc.1_Splice_Site	NM_032787	NP_116176	Q96K78	GP128_HUMAN	G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4						TCACCTGAGGTAAAACTCACA	0.368													10	73	---	---	---	---	PASS
ALDH1L1	10840	broad.mit.edu	37	3	125872361	125872361	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125872361G>A	uc003eim.1	-	7	974	c.784C>T	c.(784-786)CCC>TCC	p.P262S	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Missense_Mutation_p.P161S|ALDH1L1_uc003eio.2_5'UTR|ALDH1L1_uc010hsf.1_Missense_Mutation_p.P288S|ALDH1L1_uc003eip.1_Missense_Mutation_p.P169S|ALDH1L1_uc011bkj.1_Missense_Mutation_p.P87S	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	262					10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CCTGGGATGGGCAAAGCGTCT	0.537													5	149	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164755814	164755814	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164755814T>C	uc003fei.2	-	21	2364	c.2302_splice	c.e21-1	p.G768_splice		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	TTTTGCACCCTAATAATTGGA	0.318										HNSCC(35;0.089)			3	200	---	---	---	---	PASS
AHSG	197	broad.mit.edu	37	3	186335070	186335070	+	Silent	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186335070G>T	uc003fqk.3	+	4	585	c.504G>T	c.(502-504)CTG>CTT	p.L168L	AHSG_uc003fqj.2_Silent_p.L168L|AHSG_uc003fql.3_Silent_p.L169L|AHSG_uc003fqm.3_Silent_p.L167L|AHSG_uc010hyp.2_Silent_p.L131L	NM_001622	NP_001613	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	168	Cystatin fetuin-A-type 2.			PLLAPLNDTRVVHAAKAALAAFNAQNNGSNFQL -> MVGW QEGANHKNGAGRSQKQEMAEKMVPEVASG (in Ref. 12; AAF69649).	acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		AAGCTGCCCTGGCCGCCTTCA	0.597											OREG0015968	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	24	138	---	---	---	---	PASS
PHF17	79960	broad.mit.edu	37	4	129789065	129789065	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129789065T>A	uc003igk.2	+	10	1838	c.1558T>A	c.(1558-1560)TGC>AGC	p.C520S	PHF17_uc003igl.2_Missense_Mutation_p.C508S|PHF17_uc011cgy.1_Missense_Mutation_p.C520S	NM_199320	NP_955352	Q6IE81	JADE1_HUMAN	PHD finger protein 17 long isoform	520					apoptosis|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell growth|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	histone acetyltransferase complex|mitochondrion	protein binding|zinc ion binding				0						ACGGTCTGTGTGCAAAGTCCA	0.403													18	113	---	---	---	---	PASS
ACTBL2	345651	broad.mit.edu	37	5	56777710	56777710	+	Silent	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56777710G>A	uc003jrm.2	-	1	927	c.825C>T	c.(823-825)ATC>ATT	p.I275I		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	275						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		TTGTCTCATGGATCCCACTGG	0.502													23	92	---	---	---	---	PASS
CCND3	896	broad.mit.edu	37	6	41904303	41904303	+	Silent	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41904303A>G	uc003orn.2	-	4	870	c.705T>C	c.(703-705)ACT>ACC	p.T235T	CCND3_uc003orp.2_Silent_p.T154T|CCND3_uc011duk.1_Silent_p.T39T|CCND3_uc003orm.2_Silent_p.T185T|CCND3_uc003oro.2_Silent_p.T163T	NM_001760	NP_001751	P30281	CCND3_HUMAN	cyclin D3 isoform 2	235					cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding				0	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCACCACTTCAGTGCCAGTGA	0.602			T	IGH@	MM						OREG0017437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	71	---	---	---	---	PASS
ZNF117	51351	broad.mit.edu	37	7	64439363	64439363	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64439363C>A	uc003ttr.2	-	4	1871	c.586G>T	c.(586-588)GAA>TAA	p.E196*		NM_015852	NP_056936	Q03924	ZN117_HUMAN	zinc finger protein 117	196	C2H2-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)				CCACATTCTTCACATTTGTAG	0.368													7	180	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100680821	100680821	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100680821C>T	uc003uxp.1	+	3	6177	c.6124C>T	c.(6124-6126)CGG>TGG	p.R2042W	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2042	Extracellular (Potential).|32.|59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCTAGTGAACGGACCACTCC	0.502													6	312	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116339927	116339927	+	Silent	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116339927G>T	uc003vij.2	+	2	976	c.789G>T	c.(787-789)ACG>ACT	p.T263T	MET_uc010lkh.2_Silent_p.T263T|MET_uc011knc.1_Silent_p.T263T|MET_uc011knd.1_Silent_p.T263T|MET_uc011kne.1_Silent_p.T263T|MET_uc011knf.1_Silent_p.T263T|MET_uc011kng.1_Silent_p.T263T|MET_uc011knh.1_Silent_p.T263T|MET_uc011kni.1_Silent_p.T263T|MET_uc003vii.1_Silent_p.T282T|MET_uc010lkg.2_Silent_p.T263T|MET_uc011kmz.1_Silent_p.T263T|MET_uc011kna.1_Silent_p.T263T|MET_uc011knb.1_Silent_p.T263T	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	263	Extracellular (Potential).|Sema.				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			ACTTCTTGACGGTCCAAAGGG	0.403			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				70	356	---	---	---	---	PASS
INTS9	55756	broad.mit.edu	37	8	28651299	28651299	+	Intron	SNP	A	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28651299A>C	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron|INTS9_uc003xhb.2_Missense_Mutation_p.F354L	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		AAATTCACAAAAAAAAAAAAA	0.368													3	30	---	---	---	---	PASS
FAM91A1	157769	broad.mit.edu	37	8	124817571	124817571	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124817571T>A	uc003yqv.2	+	19	1935	c.1874T>A	c.(1873-1875)CTA>CAA	p.L625Q	FAM91A1_uc011lik.1_Missense_Mutation_p.L625Q|FAM91A1_uc011lil.1_Missense_Mutation_p.L383Q	NM_144963	NP_659400	Q658Y4	F91A1_HUMAN	hypothetical protein LOC157769	625										ovary(1)|central_nervous_system(1)	2	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			GAAACAGAACTACAAGGAGGT	0.338													14	58	---	---	---	---	PASS
VLDLR	7436	broad.mit.edu	37	9	2646492	2646492	+	Missense_Mutation	SNP	A	C	C	rs148487944		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2646492A>C	uc003zhk.1	+	11	2040	c.1643A>C	c.(1642-1644)AAG>ACG	p.K548T	VLDLR_uc003zhl.1_Missense_Mutation_p.K548T|VLDLR_uc003zhm.1_RNA|VLDLR_uc003zhn.1_Missense_Mutation_p.K507T	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a	548	LDL-receptor class B 3.|Extracellular (Potential).				cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		ACCAAGAGGAAGTTCCTGTTT	0.478													23	106	---	---	---	---	PASS
SMC5	23137	broad.mit.edu	37	9	72933592	72933592	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72933592G>A	uc004ahr.2	+	14	2086	c.1969G>A	c.(1969-1971)GAA>AAA	p.E657K	uc004ahs.1_5'Flank	NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein	657	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						ACACTTAGAAGAACAGCTAAA	0.303													29	137	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77435221	77435221	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77435221C>A	uc004ajl.1	-	9	1371	c.1133G>T	c.(1132-1134)TGT>TTT	p.C378F	TRPM6_uc004ajk.1_Missense_Mutation_p.C373F|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.C378F|TRPM6_uc010mpd.1_Missense_Mutation_p.C378F|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	378	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						CATACTCACACAATCCCTGTG	0.323													4	155	---	---	---	---	PASS
ZWINT	11130	broad.mit.edu	37	10	58120095	58120095	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58120095C>G	uc001jjx.1	-	2	128	c.91G>C	c.(91-93)GAG>CAG	p.E31Q	ZWINT_uc001jjy.1_Missense_Mutation_p.E31Q|ZWINT_uc001jka.1_Missense_Mutation_p.E31Q|ZWINT_uc009xoy.1_RNA	NM_007057	NP_008988	O95229	ZWINT_HUMAN	ZW10 interactor isoform a	31					cell division|establishment of localization in cell|mitotic cell cycle checkpoint|mitotic prometaphase|mitotic sister chromatid segregation|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytosol|nucleus	protein N-terminus binding				0						AGTTCTGCCTCCTCCTGCAGG	0.547													12	74	---	---	---	---	PASS
PPP3CB	5532	broad.mit.edu	37	10	75231247	75231247	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75231247G>C	uc001jue.2	-	5	783	c.648C>G	c.(646-648)CAC>CAG	p.H216Q	PPP3CB_uc001juf.2_Missense_Mutation_p.H216Q|PPP3CB_uc001jug.2_Missense_Mutation_p.H216Q|PPP3CB_uc001jui.2_Missense_Mutation_p.H234Q|PPP3CB_uc001juh.2_Missense_Mutation_p.H130Q	NM_021132	NP_066955	P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta	216	Catalytic.									skin(1)	1	Prostate(51;0.0119)					CATCCAGTGTGTGTATTTCTG	0.348													4	216	---	---	---	---	PASS
BTAF1	9044	broad.mit.edu	37	10	93784657	93784657	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93784657C>T	uc001khr.2	+	35	5106	c.5008C>T	c.(5008-5010)CCC>TCC	p.P1670S		NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription	1670	Helicase C-terminal.				negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				ACCTCACTTGCCCTCTGTCAC	0.443													59	215	---	---	---	---	PASS
SLIT1	6585	broad.mit.edu	37	10	98945307	98945307	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98945307C>G	uc001kmw.2	-	1	377	c.125G>C	c.(124-126)GGA>GCA	p.G42A	SLIT1_uc009xvh.1_Missense_Mutation_p.G42A|ARHGAP19_uc001kmy.2_Intron|SLIT1_uc001kmz.2_Missense_Mutation_p.G42A	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	42	LRRNT.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CACCGTGGTTCCGGTGCAGGT	0.721													8	27	---	---	---	---	PASS
HABP2	3026	broad.mit.edu	37	10	115327282	115327282	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115327282C>A	uc001lai.3	+	2	207	c.104C>A	c.(103-105)CCA>CAA	p.P35Q	HABP2_uc010qrz.1_RNA|HABP2_uc010qry.1_5'UTR	NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	35					cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)		AGCCTGGACCCAGGTAAGTGT	0.532													3	50	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6661620	6661620	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6661620C>T	uc001mem.1	-	2	1635	c.1225G>A	c.(1225-1227)GAG>AAG	p.E409K		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	409	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAGTGGCCCTCTCCACCTTCC	0.577													9	39	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57087711	57087711	+	Silent	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57087711G>A	uc001njr.2	-	2	882	c.570C>T	c.(568-570)AAC>AAT	p.N190N	TNKS1BP1_uc001njs.2_Silent_p.N190N|TNKS1BP1_uc009ymd.1_5'UTR	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	190	Pro-rich.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				TGCCATCGTGGTTAAAGGTGA	0.647													28	89	---	---	---	---	PASS
GLYAT	10249	broad.mit.edu	37	11	58477917	58477917	+	Intron	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58477917A>G	uc001nnb.2	-						GLYAT_uc001nnc.2_3'UTR	NM_201648	NP_964011	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase isoform a						acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process	mitochondrial matrix	glycine N-acyltransferase activity|glycine N-benzoyltransferase activity				0		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	ggagagaaacatgttctgagt	0.000													6	28	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62284360	62284360	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62284360A>T	uc001ntl.2	-	5	17829	c.17529T>A	c.(17527-17529)GAT>GAA	p.D5843E	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	5843					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				TGCCTGTCTCATCATCGCTCC	0.512													17	327	---	---	---	---	PASS
CADM1	23705	broad.mit.edu	37	11	115049400	115049400	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115049400G>A	uc001ppi.3	-	9	1303	c.1174C>T	c.(1174-1176)CTC>TTC	p.L392F	CADM1_uc001ppf.3_Missense_Mutation_p.L364F|CADM1_uc001ppk.3_Missense_Mutation_p.L364F|CADM1_uc001ppj.3_Missense_Mutation_p.L393F|CADM1_uc001pph.3_Missense_Mutation_p.L155F	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	392	Helical; (Potential).				adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		AGAATGATGAGCAAGCACAGC	0.547													4	231	---	---	---	---	PASS
FBXL14	144699	broad.mit.edu	37	12	1702196	1702196	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1702196T>C	uc001qjh.2	-	1	1136	c.1037A>G	c.(1036-1038)AAG>AGG	p.K346R	WNT5B_uc009zdq.2_Intron|FBXL14_uc001qji.2_Missense_Mutation_p.K258R	NM_152441	NP_689654	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	346						cytoplasm				ovary(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			CTCCAGGCCCTTGTCCGTGAT	0.617													37	139	---	---	---	---	PASS
SLC38A2	54407	broad.mit.edu	37	12	46754875	46754875	+	3'UTR	SNP	T	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46754875T>G	uc001rpg.2	-	16					SLC38A2_uc010sli.1_3'UTR|SLC38A2_uc001rph.2_3'UTR	NM_018976	NP_061849	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2						cellular nitrogen compound metabolic process|glutamate secretion|neurotransmitter secretion|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			urinary_tract(1)|skin(1)	2	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		GGACTGAGTTTGAGTTTGAGT	0.438													10	54	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104107503	104107503	+	Silent	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104107503C>T	uc001tjw.2	+	42	4680	c.4494C>T	c.(4492-4494)TGC>TGT	p.C1498C	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1498	Extracellular (Potential).|EGF-like 12.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						GGCGAGTGTGCACGTGCAAAG	0.512													6	450	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109702175	109702175	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109702175A>G	uc001tob.2	+	50	7045	c.6926A>G	c.(6925-6927)GAG>GGG	p.E2309G	ACACB_uc001toc.2_Missense_Mutation_p.E2309G|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.E975G	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	2309					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	CGGATGCTGGAGAAGGGCGTC	0.627											OREG0022102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	24	100	---	---	---	---	PASS
PITPNM2	57605	broad.mit.edu	37	12	123471023	123471023	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123471023A>G	uc001uej.1	-	24	3825	c.3686T>C	c.(3685-3687)ATC>ACC	p.I1229T	PITPNM2_uc001uek.1_Missense_Mutation_p.I1223T	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,	1229					metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CCGGCCCACGATGTAGATCTG	0.682													6	6	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124270368	124270368	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124270368T>A	uc001uft.3	+	9	1148	c.1123T>A	c.(1123-1125)TGG>AGG	p.W375R		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	375	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCGGATGGTGTGGATCATCTC	0.577													29	113	---	---	---	---	PASS
FAM179B	23116	broad.mit.edu	37	14	45433179	45433179	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45433179C>G	uc001wvv.2	+	1	1764	c.1555C>G	c.(1555-1557)CTT>GTT	p.L519V	FAM179B_uc001wvw.2_Missense_Mutation_p.L519V|FAM179B_uc010anc.2_RNA|KLHL28_uc001wvq.2_5'Flank|KLHL28_uc001wvr.2_5'Flank|FAM179B_uc010anb.1_Missense_Mutation_p.L519V|FAM179B_uc001wvu.2_Missense_Mutation_p.L519V	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	519	HEAT 4.						binding			skin(2)|upper_aerodigestive_tract(1)	3						TGCCCCAGCTCTTGTAGATAG	0.478													67	181	---	---	---	---	PASS
PELI2	57161	broad.mit.edu	37	14	56757051	56757051	+	Silent	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56757051G>T	uc001xch.2	+	5	859	c.573G>T	c.(571-573)CTG>CTT	p.L191L		NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2	191					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1						ATGGCGTCCTGGTGATGCATC	0.557													44	169	---	---	---	---	PASS
PELI2	57161	broad.mit.edu	37	14	56757052	56757052	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56757052G>T	uc001xch.2	+	5	860	c.574G>T	c.(574-576)GTG>TTG	p.V192L		NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2	192					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1						TGGCGTCCTGGTGATGCATCC	0.562													43	173	---	---	---	---	PASS
TMEM87A	25963	broad.mit.edu	37	15	42529648	42529648	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42529648G>A	uc010udd.1	-	9	1009	c.850C>T	c.(850-852)CGA>TGA	p.R284*	TMEM87A_uc001zpf.3_Nonsense_Mutation_p.R223*|TMEM87A_uc010bcu.1_Nonsense_Mutation_p.R223*	NM_015497	NP_056312	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A isoform 1	284						integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		CCTTTGTATCGGATATTCTGA	0.418													4	156	---	---	---	---	PASS
SPATA5L1	79029	broad.mit.edu	37	15	45695510	45695510	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45695510C>T	uc001zve.2	+	1	992	c.883C>T	c.(883-885)CGC>TGC	p.R295C	uc001zvd.2_5'Flank|SPATA5L1_uc001zvf.2_RNA	NM_024063	NP_076968	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	295						cytoplasm	ATP binding|nucleoside-triphosphatase activity			ovary(3)|skin(1)	4		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		ACTGGCCAGCCGCGGACCCAG	0.716													3	8	---	---	---	---	PASS
CPEB1	64506	broad.mit.edu	37	15	83218246	83218246	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83218246C>A	uc002bit.2	-	9	1695	c.1558G>T	c.(1558-1560)GCC>TCC	p.A520S	CPEB1_uc002biq.2_Missense_Mutation_p.A380S|CPEB1_uc002bir.2_Missense_Mutation_p.A385S|CPEB1_uc002bis.2_Missense_Mutation_p.A380S|CPEB1_uc010uod.1_Missense_Mutation_p.A229S|CPEB1_uc010uoe.1_Missense_Mutation_p.A458S|CPEB1_uc002biu.2_Missense_Mutation_p.A482S|CPEB1_uc010uof.1_Missense_Mutation_p.A380S|CPEB1_uc002biv.2_Missense_Mutation_p.A455S|CPEB1_uc002bip.2_Missense_Mutation_p.A229S	NM_001079533	NP_001073001	Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding	460	RRM 2.|Necessary for stress granule assembly and correct localization in dcp1 bodies.				mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)			TCAATCCCGGCATACACCACT	0.522													3	70	---	---	---	---	PASS
MKL2	57496	broad.mit.edu	37	16	14306227	14306227	+	Silent	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14306227G>A	uc010uza.1	+	5	392	c.237G>A	c.(235-237)GCG>GCA	p.A79A	MKL2_uc002dcg.2_Silent_p.A79A|MKL2_uc002dch.2_Silent_p.A68A|MKL2_uc010uzb.1_Silent_p.A28A	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	68					cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						AGAGCCCAGCGGCATTCCATG	0.378													5	186	---	---	---	---	PASS
ZNF688	146542	broad.mit.edu	37	16	30581153	30581153	+	3'UTR	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30581153G>A	uc002dyt.2	-	3					ZNF688_uc002dys.2_3'UTR|uc002dyu.2_5'Flank	NM_145271	NP_660314	P0C7X2	ZN688_HUMAN	zinc finger protein 688 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTTCAGTTCCGGAGTCCCCGA	0.537													9	69	---	---	---	---	PASS
ZNF423	23090	broad.mit.edu	37	16	49670844	49670844	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49670844G>A	uc002efs.2	-	5	2517	c.2219C>T	c.(2218-2220)GCG>GTG	p.A740V	ZNF423_uc010vgn.1_Missense_Mutation_p.A623V	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	740	C2H2-type 17.				cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)				GTGCTTCACCGCCAGGTGCAC	0.577													12	60	---	---	---	---	PASS
TAF1C	9013	broad.mit.edu	37	16	84216939	84216939	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84216939T>C	uc002fhn.2	-	5	547	c.319A>G	c.(319-321)ATC>GTC	p.I107V	TAF1C_uc002fhm.2_Missense_Mutation_p.I40V|TAF1C_uc010vnx.1_Missense_Mutation_p.I107V|TAF1C_uc010vny.1_5'UTR|TAF1C_uc010vnz.1_5'UTR|TAF1C_uc002fho.2_Intron|TAF1C_uc010voa.1_Intron|TAF1C_uc002fhp.1_RNA|TAF1C_uc010vob.1_Missense_Mutation_p.I107V	NM_005679	NP_005670	Q15572	TAF1C_HUMAN	TBP-associated factor 1C isoform 1	107					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1						AACCGGCTGATCTGGGGAGAA	0.617													16	72	---	---	---	---	PASS
MAP1LC3B	81631	broad.mit.edu	37	16	87436734	87436734	+	3'UTR	SNP	G	T	T	rs115646842	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87436734G>T	uc002fjx.2	+	4					MAP1LC3B_uc010chs.2_RNA	NM_022818	NP_073729	Q9GZQ8	MLP3B_HUMAN	microtubule-associated proteins 1A/1B light						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0249)		TTCTAGAATTGTTTAAACCCT	0.413													4	138	---	---	---	---	PASS
RICH2	9912	broad.mit.edu	37	17	12893542	12893542	+	3'UTR	SNP	G	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12893542G>C	uc002gnr.3	+	21					RICH2_uc010vvk.1_3'UTR|RICH2_uc010vvl.1_3'UTR|RICH2_uc002gns.3_3'UTR|RICH2_uc010vvm.1_3'UTR|RICH2_uc010vvn.1_RNA	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						CCCTAGGAACGCCGCCAGGAG	0.577													3	16	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630635	44630635	+	3'UTR	SNP	A	G	G	rs150521815	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630635A>G	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						TACACAGCATACAATTCCTGT	0.239													3	39	---	---	---	---	PASS
ABCC3	8714	broad.mit.edu	37	17	48765031	48765031	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48765031T>C	uc002isl.2	+	30	4495	c.4415T>C	c.(4414-4416)TTT>TCT	p.F1472S	ABCC3_uc002isn.2_Missense_Mutation_p.F226S	NM_003786	NP_003777	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C, member 3	1472	Cytoplasmic (By similarity).|ABC transporter 2.				bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity			skin(3)|central_nervous_system(1)	4			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Glibenclamide(DB01016)	CGCACCCAGTTTGATACCTGC	0.582													4	232	---	---	---	---	PASS
C17orf47	284083	broad.mit.edu	37	17	56620818	56620818	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56620818G>T	uc002iwq.1	-	1	866	c.730C>A	c.(730-732)CCT>ACT	p.P244T	SEPT4_uc010wnx.1_5'Flank|SEPT4_uc010wny.1_5'Flank	NM_001038704	NP_001033793	Q8NEP4	CQ047_HUMAN	hypothetical protein LOC284083	244										breast(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCTTCTACAGGGACCCTTCTC	0.478													56	238	---	---	---	---	PASS
SKA2	348235	broad.mit.edu	37	17	57232526	57232526	+	5'UTR	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57232526T>C	uc002ixd.2	-	1					PRR11_uc002ixf.1_5'Flank|PRR11_uc002ixg.1_5'Flank|SKA2_uc010dde.1_5'UTR|SKA2_uc002ixe.2_RNA	NM_182620	NP_872426	Q8WVK7	SKA2_HUMAN	spindle and KT associated 2 isoform 1						cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0						CGCCTCCATGTTGAATAGTTG	0.557													13	259	---	---	---	---	PASS
STRADA	92335	broad.mit.edu	37	17	61791458	61791458	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61791458G>A	uc002jbm.2	-	5	293	c.134C>T	c.(133-135)GCG>GTG	p.A45V	STRADA_uc002jbn.2_5'UTR|STRADA_uc002jbo.2_Missense_Mutation_p.A8V|STRADA_uc002jbp.2_Missense_Mutation_p.A8V|STRADA_uc002jbq.2_5'UTR|STRADA_uc010wpq.1_Intron|STRADA_uc010wpr.1_Missense_Mutation_p.A16V|STRADA_uc010ddw.2_Missense_Mutation_p.A16V|STRADA_uc002jbr.2_5'UTR	NM_001003787	NP_001003787	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha isoform 1	45					activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|kinase binding|protein kinase activity			ovary(1)	1						CTCTGAGCTCGCATCATTGGT	0.473													4	143	---	---	---	---	PASS
TTYH2	94015	broad.mit.edu	37	17	72233486	72233486	+	Silent	SNP	G	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72233486G>T	uc002jkc.2	+	4	499	c.468G>T	c.(466-468)CGG>CGT	p.R156R	TTYH2_uc010wqw.1_Silent_p.R135R	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1	156	Extracellular (Potential).					chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						ACCTGGCCCGGCTCAGTGAGA	0.577													39	206	---	---	---	---	PASS
DTNA	1837	broad.mit.edu	37	18	32459638	32459638	+	Missense_Mutation	SNP	G	T	T	rs150410546		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32459638G>T	uc010dmn.1	+	19	2037	c.2036G>T	c.(2035-2037)GGG>GTG	p.G679V	DTNA_uc002kxw.2_Missense_Mutation_p.G622V|DTNA_uc010dmj.2_Missense_Mutation_p.G619V|DTNA_uc002kxz.2_Missense_Mutation_p.G626V|DTNA_uc002kxy.2_Missense_Mutation_p.G619V|DTNA_uc010xby.1_Missense_Mutation_p.G369V|DTNA_uc010xbz.1_Missense_Mutation_p.G388V|DTNA_uc010xca.1_Missense_Mutation_p.G331V|DTNA_uc002kye.2_Missense_Mutation_p.G327V	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	679					neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						CGAAAACCTGGGTACATTCAC	0.458													22	82	---	---	---	---	PASS
SERPINB10	5273	broad.mit.edu	37	18	61600419	61600419	+	Silent	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61600419C>T	uc010xev.1	+	7	861	c.771C>T	c.(769-771)GAC>GAT	p.D257D	SERPINB10_uc010xew.1_Silent_p.D257D	NM_005024	NP_005015	P48595	SPB10_HUMAN	serine (or cysteine) proteinase inhibitor, clade	257						cytoplasm|nucleus	serine-type endopeptidase inhibitor activity			lung(1)|kidney(1)|skin(1)	3		Esophageal squamous(42;0.131)				TGCCAGAAGACATTAATGGGC	0.428													46	187	---	---	---	---	PASS
ZNF490	57474	broad.mit.edu	37	19	12692483	12692483	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12692483T>C	uc002mtz.2	-	5	535	c.406A>G	c.(406-408)AGC>GGC	p.S136G		NM_020714	NP_065765	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	136					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGGCTAGTGCTTTTTCCACAT	0.383													3	229	---	---	---	---	PASS
GAPDHS	26330	broad.mit.edu	37	19	36029250	36029250	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36029250A>G	uc002oaf.1	+	3	403	c.287A>G	c.(286-288)GAG>GGG	p.E96G		NM_014364	NP_055179	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase,	96					gluconeogenesis|glycolysis|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)	GCCTGCATGGAGAAGGGTGTT	0.592													9	31	---	---	---	---	PASS
PRX	57716	broad.mit.edu	37	19	40903142	40903142	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40903142C>A	uc002onr.2	-	7	1386	c.1117G>T	c.(1117-1119)GCT>TCT	p.A373S	PRX_uc002onq.2_Missense_Mutation_p.A234S|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	373					axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TTGGCCTCAGCAACTTCCTTT	0.642													4	198	---	---	---	---	PASS
AXL	558	broad.mit.edu	37	19	41727096	41727096	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41727096G>C	uc010ehj.2	+	3	544	c.354G>C	c.(352-354)TTG>TTC	p.L118F	CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Missense_Mutation_p.L118F|AXL_uc010ehk.2_Missense_Mutation_p.L118F	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1	118	Extracellular (Potential).|Ig-like C2-type 1.					integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						ACCAGTGTTTGGTGTTTCTGG	0.587													19	78	---	---	---	---	PASS
PPP1R13L	10848	broad.mit.edu	37	19	45901534	45901534	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45901534T>C	uc002pbn.2	-	2	120	c.43A>G	c.(43-45)ATG>GTG	p.M15V	PPP1R13L_uc002pbo.2_Missense_Mutation_p.M15V|PPP1R13L_uc002pbp.2_Missense_Mutation_p.M15V	NM_006663	NP_006654	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13	15					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription corepressor activity|transcription factor binding			skin(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		TGGAAGTTCATGTCCAGAAAG	0.711													16	66	---	---	---	---	PASS
KDELR1	10945	broad.mit.edu	37	19	48893818	48893818	+	Intron	SNP	G	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48893818G>C	uc002pjb.1	-						KDELR1_uc002pja.1_5'UTR	NM_006801	NP_006792	P24390	ERD21_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum						intracellular protein transport|protein retention in ER lumen|vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane|membrane fraction	KDEL sequence binding|protein binding|receptor activity				0		all_epithelial(76;2.48e-06)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Prostate(7;0.122)|Breast(70;0.203)		all cancers(93;0.000114)|OV - Ovarian serous cystadenocarcinoma(262;0.000136)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.0145)		gagagagagagacagagagag	0.348													3	39	---	---	---	---	PASS
NTF4	4909	broad.mit.edu	37	19	49564851	49564851	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49564851T>C	uc002pmf.3	-	2	545	c.404A>G	c.(403-405)TAC>TGC	p.Y135C	CGB7_uc010yah.1_Intron	NM_006179	NP_006170	P34130	NTF4_HUMAN	neurotrophin 5 preproprotein	135					adult locomotory behavior|epidermis development|ganglion mother cell fate determination|long-term memory|sensory organ boundary specification	endoplasmic reticulum lumen|extracellular region	growth factor activity				0		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-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)		TTCAAAGAAGTACTGGCGGAG	0.677													13	88	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56569658	56569658	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56569658C>A	uc002qmj.2	+	14	3352	c.3352C>A	c.(3352-3354)CTT>ATT	p.L1118I	NLRP5_uc002qmi.2_Missense_Mutation_p.L1099I	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	1118						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CTCCTTGGCCCTTTCCTGCAA	0.517													4	207	---	---	---	---	PASS
MYT1	4661	broad.mit.edu	37	20	62839353	62839353	+	Silent	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62839353A>G	uc002yii.2	+	7	1168	c.804A>G	c.(802-804)GAA>GAG	p.E268E	MYT1_uc002yih.2_Intron|MYT1_uc002yij.2_5'UTR	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	268	Glu-rich.				cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					aggaggaggaagaggaggagg	0.199													3	29	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587													4	86	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24659578	24659578	+	RNA	SNP	A	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24659578A>G	uc002zzs.3	+	7		c.3310A>G			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						TGCGCAGGCCAACACTCACTG	0.617													7	38	---	---	---	---	PASS
APOL4	80832	broad.mit.edu	37	22	36586051	36586051	+	3'UTR	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36586051C>A	uc003aox.2	-	6					APOL4_uc003aow.2_3'UTR|APOL4_uc010gww.2_3'UTR	NM_145660	NP_663693	Q9BPW4	APOL4_HUMAN	apolipoprotein L4 isoform 2 precursor						lipid metabolic process|lipid transport|lipoprotein metabolic process	extracellular region	lipid binding				0						tatcggggaacctgccccgat	0.244													9	19	---	---	---	---	PASS
POLR3H	171568	broad.mit.edu	37	22	41923557	41923557	+	3'UTR	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41923557C>T	uc003baf.2	-	7					ACO2_uc003bac.2_Intron|ACO2_uc003bad.2_Intron|POLR3H_uc003bae.2_RNA|POLR3H_uc003bag.2_3'UTR|POLR3H_uc003bai.2_3'UTR	NM_138338	NP_612211	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide						innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			skin(1)	1						CAGCCTCTTGCCCCTTCTTAG	0.612											OREG0026589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	14	---	---	---	---	PASS
KAL1	3730	broad.mit.edu	37	X	8504907	8504907	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8504907C>A	uc004csf.2	-	11	1676	c.1526G>T	c.(1525-1527)AGT>ATT	p.S509I		NM_000216	NP_000207	P23352	KALM_HUMAN	Kallmann syndrome 1 protein precursor	509	Fibronectin type-III 3.				axon guidance|cell adhesion|cellular component movement	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|serine-type endopeptidase inhibitor activity			ovary(3)|pancreas(1)	4						CTTGGAGTGACTTTTTGGCCG	0.453													26	78	---	---	---	---	PASS
CENPI	2491	broad.mit.edu	37	X	100381784	100381784	+	Silent	SNP	G	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100381784G>A	uc004egx.2	+	8	1044	c.774G>A	c.(772-774)AAG>AAA	p.K258K	CENPI_uc011mrg.1_Silent_p.K258K|CENPI_uc004egy.2_Silent_p.K258K	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I	258					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1						CTGTAAGGAAGAAGGTAAGGG	0.343													104	431	---	---	---	---	PASS
TCEAL2	140597	broad.mit.edu	37	X	101382231	101382231	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101382231C>A	uc004eip.2	+	3	648	c.429C>A	c.(427-429)AAC>AAA	p.N143K		NM_080390	NP_525129	Q9H3H9	TCAL2_HUMAN	transcription elongation factor A (SII)-like 2	143					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						GAAAAACCAACAAGGGGCTGG	0.398													44	165	---	---	---	---	PASS
C1GALT1C1	29071	broad.mit.edu	37	X	119760539	119760539	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119760539C>A	uc004esy.2	-	3	830	c.483G>T	c.(481-483)AAG>AAT	p.K161N	C1GALT1C1_uc004esz.2_Missense_Mutation_p.K161N	NM_152692	NP_689905	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	161	Lumenal (Potential).					integral to membrane					0						GTGATGGATCCTTTTTTAACA	0.383													15	239	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123179154	123179154	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123179154T>G	uc004etz.3	+	7	942	c.603T>G	c.(601-603)ATT>ATG	p.I201M	STAG2_uc004eua.2_Missense_Mutation_p.I201M|STAG2_uc004eub.2_Missense_Mutation_p.I201M|STAG2_uc004euc.2_Missense_Mutation_p.I201M|STAG2_uc004eud.2_Missense_Mutation_p.I201M|STAG2_uc004eue.2_Missense_Mutation_p.I201M	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	201					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						ATACAGTCATTTCACTTCTTA	0.368													118	429	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130220540	130220540	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130220540C>T	uc004evz.2	+	11	1732	c.1387C>T	c.(1387-1389)CGC>TGC	p.R463C	ARHGAP36_uc004ewa.2_Missense_Mutation_p.R451C|ARHGAP36_uc004ewb.2_Missense_Mutation_p.R432C|ARHGAP36_uc004ewc.2_Missense_Mutation_p.R327C	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	463					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						CAGGAGTGCACGCATAAAGAT	0.458													5	233	---	---	---	---	PASS
UTS2	10911	broad.mit.edu	37	1	7907620	7907621	+	Intron	INS	-	TAAT	TAAT	rs143440682	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7907620_7907621insTAAT	uc001aoq.2	-							NM_006786	NP_006777	O95399	UTS2_HUMAN	urotensin 2 isoform b preproprotein						muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		GAAGAAAAGAATAATTATAAAT	0.297													8	6	---	---	---	---	
GBP1	2633	broad.mit.edu	37	1	89518866	89518866	+	3'UTR	DEL	T	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89518866delT	uc001dmx.2	-	11						NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		ATTTACAGTCTTTTTTTTTTT	0.318													4	2	---	---	---	---	
ARHGAP29	9411	broad.mit.edu	37	1	94669700	94669701	+	Intron	INS	-	T	T	rs77020055		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94669700_94669701insT	uc001dqj.3	-						ARHGAP29_uc009wdq.1_Intron|ARHGAP29_uc001dql.2_Intron	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TTCTTTCTTCCttttttttttt	0.153													4	2	---	---	---	---	
CAPZA1	829	broad.mit.edu	37	1	113202204	113202208	+	Intron	DEL	CTCTC	-	-	rs60025142	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113202204_113202208delCTCTC	uc001ecj.1	+							NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTTCTCTCTCTCTCTTTTTTTTTT	0.395													3	7	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237806919	237806920	+	Intron	INS	-	T	T	rs113722212		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237806919_237806920insT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TAAttttttccttttttttttt	0.119													3	3	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237850666	237850667	+	Intron	INS	-	TT	TT	rs41267515		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237850666_237850667insTT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ttttcttcttcttttttttttt	0.327													6	3	---	---	---	---	
ASXL2	55252	broad.mit.edu	37	2	26079232	26079233	+	Intron	INS	-	TTT	TTT	rs143352675		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26079232_26079233insTTT	uc002rgs.2	-							NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ctggccTATACttttttttttt	0.218													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139045443	139045444	+	3'UTR	INS	-	A	A	rs76535811		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139045443_139045444insA	uc010zbk.1	-	1										SubName: Full=cDNA, FLJ79100, highly similar to 14-3-3 protein epsilon (14-3-3E);																		AAACTGtttttttaaaaaaaaa	0.371													4	2	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225668718	225668719	+	Intron	DEL	TG	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225668718_225668719delTG	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002voa.2_Intron|DOCK10_uc002voc.2_Intron	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AATAGAAATAtgtgtgtgtgtg	0.282													9	7	---	---	---	---	
DNAJC13	23317	broad.mit.edu	37	3	132220414	132220414	+	Intron	DEL	A	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132220414delA	uc003eor.2	+							NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2						actctgtctcaaaaaaaaaaa	0.179													6	3	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	151011751	151011762	+	Intron	DEL	GCCATTAACCCT	-	-	rs67834444		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151011751_151011762delGCCATTAACCCT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAGACTTCCAGCCATTAACCCTGCCATTCACC	0.443													1	5	---	---	---	---	
GUCY1A3	2982	broad.mit.edu	37	4	156651536	156651539	+	3'UTR	DEL	ATGT	-	-	rs146677644		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156651536_156651539delATGT	uc003iov.2	+	11					GUCY1A3_uc003iow.2_3'UTR|GUCY1A3_uc010iqd.2_3'UTR|GUCY1A3_uc003iox.2_3'UTR|GUCY1A3_uc003ioz.2_3'UTR|GUCY1A3_uc003ioy.2_3'UTR|GUCY1A3_uc010iqe.2_3'UTR|GUCY1A3_uc003ipa.2_RNA|GUCY1A3_uc003ipb.2_3'UTR	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A						blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		ACATGACAAAATGTATGTACTCAC	0.338													5	3	---	---	---	---	
XPO5	57510	broad.mit.edu	37	6	43538049	43538049	+	Intron	DEL	A	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43538049delA	uc003ovp.2	-							NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5						gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			cctccgtctcaaaaaaaaaaa	0.095													8	4	---	---	---	---	
OOEP	441161	broad.mit.edu	37	6	74082632	74082632	+	Intron	DEL	T	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74082632delT	uc003pgv.3	-							NM_001080507	NP_001073976	A6NGQ2	OOEP_HUMAN	oocyte expressed protein homolog							cytoplasm					0						ttttctttccttttttttttt	0.378													3	6	---	---	---	---	
SLC17A5	26503	broad.mit.edu	37	6	74320415	74320415	+	Intron	DEL	A	-	-	rs10707321		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74320415delA	uc003phn.3	-						SLC17A5_uc010kax.2_Intron|SLC17A5_uc010kay.2_Intron|SLC17A5_uc011dyo.1_Intron	NM_012434	NP_036566	Q9NRA2	S17A5_HUMAN	sialin						anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6						ATTTCATGAGAAAAAAAAAAT	0.308													4	3	---	---	---	---	
AMD1	262	broad.mit.edu	37	6	111196178	111196179	+	5'UTR	INS	-	A	A			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111196178_111196179insA	uc003puk.1	+	1					AMD1_uc011eay.1_Intron|AMD1_uc011eaz.1_5'UTR|AMD1_uc011eba.1_5'UTR|AMD1_uc003pul.1_5'UTR	NM_001634	NP_001625	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1 isoform 1						spermidine biosynthetic process|spermine biosynthetic process	cytosol	adenosylmethionine decarboxylase activity			upper_aerodigestive_tract(1)	1		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	aaaattataGCAAAAAAAAAAA	0.376													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124676686	124676686	+	Intron	DEL	C	-	-	rs144139894		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124676686delC	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		TGTACTTTTTCTTAAGCAAAA	0.308													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158195269	158195270	+	IGR	INS	-	G	G	rs150472202	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158195269_158195270insG								ZDHHC14 (100293 upstream) : SNX9 (49024 downstream)																							gaggtggaggagtggaggaggt	0.322													4	4	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38543104	38543105	+	Intron	INS	-	C	C	rs139707552	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38543104_38543105insC	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						GCGGGGGGGTGGGTGGTGGAAT	0.426													5	8	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100230357	100230357	+	Intron	DEL	G	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100230357delG	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					aaaaaaaaaagaacctttttt	0.000													4	3	---	---	---	---	
ADAM32	203102	broad.mit.edu	37	8	39009194	39009195	+	Intron	INS	-	T	T	rs67270213		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39009194_39009195insT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			AACATCTTATCttttttttttt	0.124													4	2	---	---	---	---	
TMEM2	23670	broad.mit.edu	37	9	74337571	74337571	+	Intron	DEL	A	-	-	rs72034909		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74337571delA	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AAGGTACTGTAAAAAAAAAAA	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90460050	90460051	+	IGR	DEL	GA	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90460050_90460051delGA								CTSL3 (58251 upstream) : C9orf79 (37690 downstream)																							tgtgtgtgtgGATATCAGCTTT	0.302													4	2	---	---	---	---	
LOC100129066	100129066	broad.mit.edu	37	9	92286637	92286645	+	Intron	DEL	ATGGTGGTT	-	-	rs138909303	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92286637_92286645delATGGTGGTT	uc004aqs.2	+							NR_024280				Homo sapiens cDNA FLJ42342 fis, clone UTERU2000794.												0						ggtggtggtgatggtggttatggtggtga	0.033													9	4	---	---	---	---	
RBM18	92400	broad.mit.edu	37	9	125010064	125010065	+	Intron	INS	-	T	T	rs34974193		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125010064_125010065insT	uc004bma.2	-						RBM18_uc004blz.2_Intron|RBM18_uc010mvy.2_Intron|RBM18_uc011lyp.1_Intron	NM_033117	NP_149108	Q96H35	RBM18_HUMAN	RNA binding motif protein 18								nucleotide binding|RNA binding				0						tttttttgttgttttttttttt	0.149													4	2	---	---	---	---	
SAPS3	55291	broad.mit.edu	37	11	68305521	68305522	+	Intron	INS	-	T	T	rs147520180	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68305521_68305522insT	uc001onw.2	+						SAPS3_uc010rqb.1_Intron|SAPS3_uc001onv.2_Intron|SAPS3_uc001ony.3_Intron|SAPS3_uc001onx.2_Intron|SAPS3_uc009ysh.2_Intron|SAPS3_uc001onu.2_Intron|SAPS3_uc010rqc.1_Intron	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6						regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)			CATTCTAGCAGTAAGTCCAGGG	0.406													3	4	---	---	---	---	
C1S	716	broad.mit.edu	37	12	7171339	7171340	+	Intron	INS	-	ACACACACAC	ACACACACAC			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7171339_7171340insACACACACAC	uc001qsj.2	+						C1S_uc001qsk.2_Intron|C1S_uc001qsl.2_Intron|C1S_uc009zfr.2_Intron|C1S_uc009zfs.2_Intron	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	ctatgtcACTTACACACACACA	0.228													5	3	---	---	---	---	
ARHGDIB	397	broad.mit.edu	37	12	15095807	15095807	+	Intron	DEL	T	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15095807delT	uc001rcq.1	-						ARHGDIB_uc001rcp.1_Intron	NM_001175	NP_001166	P52566	GDIR2_HUMAN	Rho GDP dissociation inhibitor (GDI) beta						actin cytoskeleton organization|cellular component movement|immune response|multicellular organismal development|negative regulation of cell adhesion|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoplasmic membrane-bounded vesicle|cytoskeleton|cytosol	GTPase activator activity|Rho GDP-dissociation inhibitor activity				0						CTGAGGCATCttttttttttt	0.199													4	2	---	---	---	---	
AVPR1A	552	broad.mit.edu	37	12	63543437	63543437	+	Intron	DEL	T	-	-	rs111634582		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63543437delT	uc001sro.1	-							NM_000706	NP_000697	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A						activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)	AGGAATATGCTTTTTTTTTTT	0.264													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	129497863	129497864	+	IGR	INS	-	TT	TT	rs10655206		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129497863_129497864insTT								GLT1D1 (28354 upstream) : TMEM132D (58407 downstream)																							TGGCAGAATCCTTTTTTTTTTT	0.371													11	5	---	---	---	---	
KL	9365	broad.mit.edu	37	13	33637746	33637746	+	Intron	DEL	A	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33637746delA	uc001uus.2	+							NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor						aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		catctctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19408019	19408019	+	IGR	DEL	A	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19408019delA								OR11H12 (29447 upstream) : POTEG (145346 downstream)																							CTGTGGAGCCAAAAAAAAAAT	0.393													4	2	---	---	---	---	
PCNX	22990	broad.mit.edu	37	14	71572271	71572271	+	Intron	DEL	T	-	-	rs79334123		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71572271delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron|PCNX_uc001xmp.2_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AGAAATAGAAttttttttttt	0.169													5	3	---	---	---	---	
SEL1L	6400	broad.mit.edu	37	14	81943647	81943648	+	Intron	INS	-	TGTG	TGTG	rs140905448	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81943647_81943648insTGTG	uc010tvv.1	-							NM_005065	NP_005056	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like precursor						Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)		ACGTTTTGCAAtgtgtgtgtgt	0.257													3	3	---	---	---	---	
EML5	161436	broad.mit.edu	37	14	89124421	89124423	+	Intron	DEL	ACC	-	-	rs143248735		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89124421_89124423delACC	uc001xxg.2	-						EML5_uc001xxf.2_Intron|EML5_uc001xxh.1_Intron	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3						TAAAAACAGTACCACTACAATTA	0.266													8	5	---	---	---	---	
TJP1	7082	broad.mit.edu	37	15	30020390	30020390	+	Intron	DEL	T	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30020390delT	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		CATACTTCCCTTTTTTTTTTT	0.164													4	2	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74394379	74394380	+	Intron	INS	-	A	A	rs142790741	by1000genomes	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74394379_74394380insA	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						TAGTCATCCTTAAACAAAATTC	0.327													4	4	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2888574	2888574	+	Intron	DEL	T	-	-	rs71377564		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888574delT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						AACAGTGATGTTTTTTTTTTT	0.398													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45156257	45156258	+	IGR	INS	-	T	T			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45156257_45156258insT								IER3IP1 (453512 upstream) : SMAD2 (203209 downstream)																							AGGGACATCCATATATAAATCA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3131446	3131446	+	IGR	DEL	C	-	-	rs66993077		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3131446delC								GNA11 (9994 upstream) : GNA15 (4745 downstream)																							aaaaaaaaaacaaaaaaaaaa	0.348													8	4	---	---	---	---	
ZNF557	79230	broad.mit.edu	37	19	7082210	7082214	+	Intron	DEL	AGGTC	-	-	rs140739902		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7082210_7082214delAGGTC	uc002mgb.2	+						ZNF557_uc002mga.2_Intron|ZNF557_uc002mgc.2_Intron	NM_001044388	NP_001037853	Q8N988	ZN557_HUMAN	zinc finger protein 557 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2				Lung(535;0.179)		ttggatcatgaggtcaggtcaggag	0.083													7	5	---	---	---	---	
SLC9A8	23315	broad.mit.edu	37	20	48494743	48494743	+	Intron	DEL	A	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48494743delA	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010gic.2_Intron|SLC9A8_uc010gid.2_Intron	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TTCTTTTGTTAAAAAAAAAAA	0.303													5	3	---	---	---	---	
MKL1	57591	broad.mit.edu	37	22	40813065	40813066	+	Intron	DEL	AA	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40813065_40813066delAA	uc003ayv.1	-						MKL1_uc003ayw.1_Intron|MKL1_uc010gye.1_Intron|MKL1_uc010gyf.1_Intron	NM_020831	NP_065882	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia 1 protein						positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						GGGACAAAGGAAAAAAAAAAAA	0.520			T	RBM15	acute megakaryocytic leukemia								10	5	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43227348	43227348	+	Intron	DEL	T	-	-	rs71754335		TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43227348delT	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						TAGGTTTCAGttttttttttt	0.045													4	3	---	---	---	---	
NUP50	10762	broad.mit.edu	37	22	45577373	45577410	+	Intron	DEL	CAAGTGGAACAGGAAAGAATTCTTGGCCAGTTTATTTA	-	-	rs75217739	byFrequency	TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45577373_45577410delCAAGTGGAACAGGAAAGAATTCTTGGCCAGTTTATTTA	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron|NUP50_uc011aqo.1_Intron	NM_007172	NP_009103	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGCCTGCTCTCAAGTGGAACAGGAAAGAATTCTTGGCCAGTTTATTTAAAAATCCAGT	0.466													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	44335201	44335201	+	IGR	DEL	T	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44335201delT								EFHC2 (132278 upstream) : FUNDC1 (47685 downstream)																							Atttcttttcttttttttttt	0.274													7	4	---	---	---	---	
CD40LG	959	broad.mit.edu	37	X	135730206	135730206	+	5'Flank	DEL	A	-	-			TCGA-CJ-4916-01A-01D-1429-08	TCGA-CJ-4916-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135730206delA	uc004faa.2	+						CD40LG_uc010nsd.2_5'Flank|CD40LG_uc010nse.1_5'Flank	NM_000074	NP_000065	P29965	CD40L_HUMAN	CD40 ligand						anti-apoptosis|B cell proliferation|inflammatory response|isotype switching|leukocyte cell-cell adhesion|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of interleukin-12 production	extracellular space|integral to plasma membrane|soluble fraction	CD40 receptor binding|cytokine activity|tumor necrosis factor receptor binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)				Atorvastatin(DB01076)	GGGTATAATTaaaaaaaaaaa	0.338									Immune_Deficiency_with_Hyper-IgM				8	4	---	---	---	---	
