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
ACADM	34	broad.mit.edu	37	1	76228484	76228484	+	3'UTR	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76228484C>A	uc001dgw.3	+	12					ACADM_uc009wbp.2_3'UTR|ACADM_uc009wbr.2_3'UTR|ACADM_uc010ore.1_3'UTR|ACADM_uc010orf.1_3'UTR|ACADM_uc001dgx.3_3'UTR|ACADM_uc010org.1_3'UTR	NM_000016	NP_000007	P11310	ACADM_HUMAN	medium-chain acyl-CoA dehydrogenase isoform a						carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)|skin(1)	4						AACTAGAACACAAGCCACTGT	0.308													8	14	---	---	---	---	PASS
NGF	4803	broad.mit.edu	37	1	115828691	115828691	+	Nonstop_Mutation	SNP	T	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115828691T>G	uc001efu.1	-	3	895	c.726A>C	c.(724-726)TGA>TGC	p.*242C		NM_002506	NP_002497	P01138	NGF_HUMAN	nerve growth factor, beta polypeptide precursor	242					activation of MAPKK activity|activation of phospholipase C activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of cell cycle|nerve growth factor processing|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|Golgi lumen	growth factor activity|nerve growth factor receptor binding			upper_aerodigestive_tract(2)	2	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)	Clenbuterol(DB01407)	TGTCGGCAGGTCAGGCTCTTC	0.552													5	49	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201079330	201079330	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201079330T>G	uc001gvv.2	-	2	447	c.220A>C	c.(220-222)ATG>CTG	p.M74L		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	74	I.|Extracellular (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TCTTCCGGCATGGGCAGGTAC	0.602													27	84	---	---	---	---	PASS
ATF3	467	broad.mit.edu	37	1	212792385	212792385	+	Intron	SNP	C	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212792385C>G	uc001hjf.2	+						ATF3_uc001hjj.2_3'UTR|ATF3_uc009xdg.1_Intron|ATF3_uc001hjh.2_Intron|ATF3_uc001hji.2_Intron|ATF3_uc010ptg.1_Intron	NM_001030287	NP_001025458	P18847	ATF3_HUMAN	activating transcription factor 3 isoform 1							nucleolus	identical protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)		GATTTCTCCCCAGCTCCCAAG	0.458													20	40	---	---	---	---	PASS
TFB2M	64216	broad.mit.edu	37	1	246729284	246729284	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246729284G>A	uc001ibn.2	-	1	282	c.157C>T	c.(157-159)CCC>TCC	p.P53S	CNST_uc001ibo.3_5'Flank|CNST_uc001ibp.2_5'Flank|TFB2M_uc010pys.1_RNA	NM_022366	NP_071761	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	53					positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			TCCGGTTCGGGCCACAGCTGC	0.577													4	117	---	---	---	---	PASS
ZNF669	79862	broad.mit.edu	37	1	247265092	247265092	+	Silent	SNP	T	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247265092T>C	uc001ice.2	-	3	563	c.390A>G	c.(388-390)GGA>GGG	p.G130G	ZNF669_uc001icf.2_Silent_p.G44G	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	130	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			TCCATTGGCTTCCTAAAATGC	0.358													25	69	---	---	---	---	PASS
ZNF669	79862	broad.mit.edu	37	1	247265093	247265093	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247265093C>A	uc001ice.2	-	3	562	c.389G>T	c.(388-390)GGA>GTA	p.G130V	ZNF669_uc001icf.2_Missense_Mutation_p.G44V	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	130	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CCATTGGCTTCCTAAAATGCA	0.358													26	69	---	---	---	---	PASS
NLRC4	58484	broad.mit.edu	37	2	32476580	32476580	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32476580T>A	uc002roi.2	-	4	599	c.353A>T	c.(352-354)TAT>TTT	p.Y118F	NLRC4_uc002roj.1_Missense_Mutation_p.Y118F|NLRC4_uc010ezt.1_Intron	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12	118					activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ACCAAGGGGATAAAAGTTCAG	0.428													33	60	---	---	---	---	PASS
POTEF	728378	broad.mit.edu	37	2	130831636	130831636	+	3'UTR	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130831636C>T	uc010fmh.2	-	17						NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						TTGGAGGAAGCTTCCTCCAAC	0.368													3	9	---	---	---	---	PASS
CACNB4	785	broad.mit.edu	37	2	152709962	152709962	+	Silent	SNP	T	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152709962T>C	uc002tya.2	-	12	1184	c.1116A>G	c.(1114-1116)CCA>CCG	p.P372P	CACNB4_uc002txy.2_Silent_p.P338P|CACNB4_uc002txz.2_Silent_p.P354P|CACNB4_uc010fnz.2_Silent_p.P372P	NM_000726	NP_000717	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4	372					axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)	TCATACTTACTGGGGGGCATT	0.358													7	15	---	---	---	---	PASS
SCLY	51540	broad.mit.edu	37	2	238999918	238999918	+	Intron	SNP	A	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238999918A>T	uc010fyv.2	+						SCLY_uc002vxm.3_Intron|SCLY_uc002vxn.2_Missense_Mutation_p.E315V|SCLY_uc010znq.1_Intron|SCLY_uc010znr.1_Intron	NM_016510	NP_057594	Q96I15	SCLY_HUMAN	selenocysteine lyase						cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GAGCTTGAGGAGATGAGTTGA	0.473													44	102	---	---	---	---	PASS
LAMB2	3913	broad.mit.edu	37	3	49158615	49158615	+	3'UTR	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49158615C>T	uc003cwe.2	-	32					USP19_uc003cvz.3_5'Flank|USP19_uc011bcg.1_5'Flank|USP19_uc003cwb.2_5'Flank|USP19_uc003cwd.1_5'Flank|USP19_uc011bch.1_5'Flank|USP19_uc011bci.1_5'Flank	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor						cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGCAGACATGCATGTGGGGCA	0.592													12	10	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113115391	113115391	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113115391G>A	uc003eae.1	-	14	1799	c.1753C>T	c.(1753-1755)CGT>TGT	p.R585C		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	585	WD 7.									central_nervous_system(1)	1						TCCCCATCACGTTCATAAGCT	0.383													4	77	---	---	---	---	PASS
SIDT1	54847	broad.mit.edu	37	3	113325904	113325904	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113325904G>C	uc003eak.2	+	15	2072	c.1421G>C	c.(1420-1422)GGC>GCC	p.G474A	SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Missense_Mutation_p.G474A|SIDT1_uc011big.1_Missense_Mutation_p.G227A|SIDT1_uc011bih.1_Intron|SIDT1_uc011bii.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor	474	Extracellular (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						AATGTCACTGGCAACCAGGAC	0.512													40	57	---	---	---	---	PASS
PEX5L	51555	broad.mit.edu	37	3	179526182	179526182	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179526182G>A	uc003fki.1	-	13	1526	c.1396C>T	c.(1396-1398)CAC>TAC	p.H466Y	PEX5L_uc011bqd.1_Missense_Mutation_p.H423Y|PEX5L_uc011bqe.1_Missense_Mutation_p.H274Y|PEX5L_uc011bqf.1_Missense_Mutation_p.H358Y|PEX5L_uc003fkj.1_Missense_Mutation_p.H431Y|PEX5L_uc010hxd.1_Missense_Mutation_p.H464Y|PEX5L_uc011bqg.1_Missense_Mutation_p.H442Y|PEX5L_uc011bqh.1_Missense_Mutation_p.H407Y	NM_016559	NP_057643	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	466					protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			CCATTTTGGTGGGCAGCTTCC	0.398													43	73	---	---	---	---	PASS
KIAA0232	9778	broad.mit.edu	37	4	6843902	6843902	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6843902G>A	uc003gjr.3	+	4	803	c.340G>A	c.(340-342)GTC>ATC	p.V114I	KIAA0232_uc003gjq.3_Missense_Mutation_p.V114I	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	114							ATP binding			ovary(2)	2						ACAGGCTGCTGTCCAGTGTCT	0.353													44	65	---	---	---	---	PASS
ZNF518B	85460	broad.mit.edu	37	4	10447375	10447375	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10447375T>C	uc003gmn.2	-	3	1065	c.578A>G	c.(577-579)GAG>GGG	p.E193G		NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	193	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4						GTCACAATACTCACACTGATA	0.403													33	185	---	---	---	---	PASS
ADAMTS3	9508	broad.mit.edu	37	4	73169737	73169737	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73169737G>T	uc003hgk.1	-	17	2358	c.2321C>A	c.(2320-2322)TCG>TAG	p.S774*	ADAMTS3_uc003hgl.2_Nonsense_Mutation_p.S115*	NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	774	Spacer.				collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAAGGTCCGCGACTTGGCTTC	0.393													8	282	---	---	---	---	PASS
HEXB	3074	broad.mit.edu	37	5	74001196	74001196	+	Intron	SNP	A	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74001196A>C	uc003kdf.3	+						HEXB_uc003kdd.2_Intron|HEXB_uc003kde.2_Silent_p.S274S|HEXB_uc010izh.2_Intron	NM_000521	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B preproprotein						cell death	lysosome	cation binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		GTATAGTTTCATTACAAGTTT	0.308													16	9	---	---	---	---	PASS
HSPA9	3313	broad.mit.edu	37	5	137910976	137910976	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137910976C>A	uc003ldf.2	-	1	140	c.32G>T	c.(31-33)CGT>CTT	p.R11L	HSPA9_uc011cyw.1_5'UTR	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor	11					anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GCCCACGAGACGGGCTGCTGC	0.682													8	15	---	---	---	---	PASS
NDST1	3340	broad.mit.edu	37	5	149933065	149933065	+	3'UTR	SNP	C	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149933065C>G	uc003lsk.3	+	15					NDST1_uc011dcj.1_3'UTR	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan						heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGCAAGCACCTCGGAGCACC	0.657													12	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	161178692	161178692	+	IGR	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161178692C>T								GABRA6 (49094 upstream) : GABRA1 (95505 downstream)																							CTCTTGGGCCCTCCTGCAGTA	0.488													34	96	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56483775	56483775	+	Intron	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56483775G>A	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Missense_Mutation_p.A1686V	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATTCAGTTCCGCATTCAGATT	0.393													52	138	---	---	---	---	PASS
PRIM2	5558	broad.mit.edu	37	6	57372299	57372299	+	Silent	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57372299G>A	uc003pdx.2	+	8	792	c.705G>A	c.(703-705)AGG>AGA	p.R235R		NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	235					DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TAACAGCCAGGTCCTTGCCTG	0.423													8	63	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90572760	90572760	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572760A>C	uc003pnr.2	+	7	1528	c.1332A>C	c.(1330-1332)AAA>AAC	p.K444N	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.K444N|CASP8AP2_uc011dzz.1_Missense_Mutation_p.K444N	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	444					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GAACTCACAAAAACATTGACT	0.368													5	160	---	---	---	---	PASS
ZNF107	51427	broad.mit.edu	37	7	64168953	64168953	+	Silent	SNP	C	T	T	rs139989226		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64168953C>T	uc003ttd.2	+	7	3057	c.2271C>T	c.(2269-2271)TTC>TTT	p.F757F	ZNF107_uc003tte.2_Silent_p.F757F	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107	757	C2H2-type 25; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)				GCAGAGCTTTCAACCTATCCT	0.348													14	20	---	---	---	---	PASS
CLN8	2055	broad.mit.edu	37	8	1728612	1728612	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1728612C>T	uc003wpo.3	+	3	1045	c.740C>T	c.(739-741)CCA>CTA	p.P247L		NM_018941	NP_061764	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8	247	TLC.				cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		ATCATTAATCCATATTGGACC	0.537													49	114	---	---	---	---	PASS
FLJ10661	286042	broad.mit.edu	37	8	8088411	8088411	+	RNA	SNP	A	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8088411A>G	uc011kwt.1	+	2		c.275A>G			FLJ10661_uc010lrq.2_RNA|FLJ10661_uc003wsf.3_RNA	NR_024362				Homo sapiens cDNA FLJ60033 complete cds, highly similar to Protein FAM86A.												0						GAGCTGCTGCAGGATATTTTG	0.488													4	27	---	---	---	---	PASS
TNFRSF10B	8795	broad.mit.edu	37	8	22880052	22880052	+	3'UTR	SNP	T	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22880052T>A	uc003xcu.2	-	9					TNFRSF10B_uc003xcs.1_3'UTR|TNFRSF10B_uc003xct.2_3'UTR|TNFRSF10B_uc011kzq.1_3'UTR|TNFRSF10B_uc003xcv.2_3'UTR	NM_003842	NP_003833	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily,						activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade	plasma membrane	caspase activator activity|receptor activity|TRAIL binding				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		TGGGTGATGTTGGATGGGAGA	0.423													3	8	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	119413893	119413893	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119413893C>G	uc004bjs.1	-	17	3087	c.2986G>C	c.(2986-2988)GAG>CAG	p.E996Q	ASTN2_uc004bjr.1_Missense_Mutation_p.E992Q|ASTN2_uc004bjt.1_Missense_Mutation_p.E945Q|ASTN2_uc004bjp.1_Missense_Mutation_p.E89Q|ASTN2_uc004bjq.1_Missense_Mutation_p.E48Q|ASTN2_uc011lxr.1_Missense_Mutation_p.E48Q|ASTN2_uc011lxs.1_Missense_Mutation_p.E48Q|ASTN2_uc011lxt.1_Missense_Mutation_p.E48Q|ASTN2_uc004bjv.1_Missense_Mutation_p.E48Q	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	996	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						CTCAGCTGCTCCTTGCCTGGC	0.572													33	53	---	---	---	---	PASS
KCNMA1	3778	broad.mit.edu	37	10	78872137	78872137	+	Silent	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78872137C>A	uc001jxn.2	-	7	1125	c.948G>T	c.(946-948)GGG>GGT	p.G316G	KCNMA1_uc001jxj.2_Silent_p.G316G|KCNMA1_uc001jxk.1_5'UTR|KCNMA1_uc009xrt.1_Silent_p.G136G|KCNMA1_uc001jxl.1_5'Flank|KCNMA1_uc001jxo.2_Silent_p.G316G|KCNMA1_uc001jxm.2_Silent_p.G316G|KCNMA1_uc001jxq.2_Silent_p.G316G	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	316	Helical; Name=Segment S5; (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	AATGGATGAACCCGGCTGCAG	0.458											OREG0020286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	39	---	---	---	---	PASS
KCNMA1	3778	broad.mit.edu	37	10	78872140	78872140	+	Silent	SNP	G	A	A	rs79713097	byFrequency	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78872140G>A	uc001jxn.2	-	7	1122	c.945C>T	c.(943-945)GCC>GCT	p.A315A	KCNMA1_uc001jxj.2_Silent_p.A315A|KCNMA1_uc001jxk.1_5'UTR|KCNMA1_uc009xrt.1_Silent_p.A135A|KCNMA1_uc001jxl.1_5'Flank|KCNMA1_uc001jxo.2_Silent_p.A315A|KCNMA1_uc001jxm.2_Silent_p.A315A|KCNMA1_uc001jxq.2_Silent_p.A315A	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	315	Helical; Name=Segment S5; (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	GGATGAACCCGGCTGCAGTCA	0.453											OREG0020286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	41	---	---	---	---	PASS
FAM45A	404636	broad.mit.edu	37	10	120877121	120877121	+	Silent	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120877121C>A	uc001ldw.2	+	4	467	c.423C>A	c.(421-423)GGC>GGA	p.G141G	FAM45A_uc010qsv.1_Silent_p.G133G|FAM45A_uc010qsw.1_Intron|FAM45A_uc010qsx.1_RNA|FAM45A_uc010qsy.1_Silent_p.G68G|FAM45A_uc010qsz.1_Silent_p.G30G	NM_207009	NP_996892	Q8TCE6	FA45A_HUMAN	hypothetical protein LOC404636	141										ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		AAGAAAACGGCTCTTTCCTTA	0.378													38	76	---	---	---	---	PASS
TIAL1	7073	broad.mit.edu	37	10	121336683	121336683	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121336683A>G	uc001lei.1	-	10	1334	c.770T>C	c.(769-771)ATT>ACT	p.I257T	TIAL1_uc001leh.1_Missense_Mutation_p.I235T|TIAL1_uc001lej.1_Missense_Mutation_p.I274T|TIAL1_uc001lek.1_Missense_Mutation_p.I134T|TIAL1_uc009xzi.1_Missense_Mutation_p.I126T|TIAL1_uc010qtb.1_Missense_Mutation_p.I134T	NM_003252	NP_003243	Q01085	TIAR_HUMAN	TIA-1 related protein isoform 1	257	RRM 3.				apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		CACCGAAACAATGGCATGGGC	0.348													3	55	---	---	---	---	PASS
LRRC55	219527	broad.mit.edu	37	11	56954876	56954876	+	Silent	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56954876G>A	uc001njl.1	+	2	1095	c.948G>A	c.(946-948)GTG>GTA	p.V316V	LRRC55_uc001njm.1_5'Flank	NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	286	Helical; (Potential).					integral to membrane					0						TTGCTTCTGTGGCCACCAACT	0.572													20	47	---	---	---	---	PASS
CCDC82	79780	broad.mit.edu	37	11	96092231	96092231	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96092231C>T	uc009ywp.2	-	6	1735	c.1492G>A	c.(1492-1494)GTT>ATT	p.V498I	CCDC82_uc009ywq.2_Missense_Mutation_p.V498I|CCDC82_uc001pfx.3_Missense_Mutation_p.V498I|CCDC82_uc009ywr.2_Missense_Mutation_p.V498I	NM_024725	NP_079001	Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	498							protein binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		TCATCTTCAACTTCTTCTGTC	0.353													55	128	---	---	---	---	PASS
OVCH1	341350	broad.mit.edu	37	12	29640641	29640641	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29640641G>C	uc001rix.1	-	7	877	c.877C>G	c.(877-879)CAA>GAA	p.Q293E		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	293	Peptidase S1 1.|CUB 1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AACAGGTTTtgagtgataaaa	0.274													7	4	---	---	---	---	PASS
DDX11	1663	broad.mit.edu	37	12	31237922	31237922	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31237922G>C	uc001rjt.1	+	5	751	c.500G>C	c.(499-501)AGA>ACA	p.R167T	DDX11_uc010sjw.1_Missense_Mutation_p.R167T|DDX11_uc010sjx.1_RNA|DDX11_uc001rjr.1_Missense_Mutation_p.R167T|DDX11_uc001rjs.1_Missense_Mutation_p.R167T|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Missense_Mutation_p.R167T|DDX11_uc001rjw.1_Missense_Mutation_p.R141T|DDX11_uc001rjx.1_5'Flank	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	167	Glu-rich.|Helicase ATP-binding.				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GAAGAAGAAAGAGAGAATCTC	0.612										Multiple Myeloma(12;0.14)			3	14	---	---	---	---	PASS
DDX11	1663	broad.mit.edu	37	12	31242861	31242861	+	Silent	SNP	A	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31242861A>C	uc001rjt.1	+	9	1173	c.922A>C	c.(922-924)AGG>CGG	p.R308R	DDX11_uc010sjw.1_3'UTR|DDX11_uc010sjx.1_RNA|DDX11_uc001rjr.1_Silent_p.R308R|DDX11_uc001rjs.1_Silent_p.R308R|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Silent_p.R308R|DDX11_uc001rjw.1_Silent_p.R282R|DDX11_uc001rjx.1_5'UTR|DDX11_uc009zjn.1_RNA	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	308	Helicase ATP-binding.				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AAAGAGGAGGAGGCAGGAGAA	0.587										Multiple Myeloma(12;0.14)			3	7	---	---	---	---	PASS
ASB8	140461	broad.mit.edu	37	12	48543458	48543458	+	Silent	SNP	T	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48543458T>C	uc001rrh.2	-	4	727	c.558A>G	c.(556-558)ACA>ACG	p.T186T	ASB8_uc010slr.1_Silent_p.T182T	NM_024095	NP_077000	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box-containing 8	186					intracellular signal transduction	cytoplasm|nucleus				kidney(1)	1						GGGAGATGGGTGTCTGGCCTA	0.532													31	43	---	---	---	---	PASS
ERBB3	2065	broad.mit.edu	37	12	56487900	56487900	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56487900C>T	uc001sjh.2	+	14	1824	c.1631C>T	c.(1630-1632)GCC>GTC	p.A544V	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.A485V|ERBB3_uc009zok.2_5'UTR|ERBB3_uc001sjk.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	544	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CGAGAATTTGCCCATGAGGCC	0.562													3	72	---	---	---	---	PASS
C13orf34	79866	broad.mit.edu	37	13	73303218	73303218	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73303218C>A	uc001viv.1	+	2	259	c.140C>A	c.(139-141)TCA>TAA	p.S47*	C13orf37_uc001viu.2_5'Flank|C13orf34_uc010thq.1_5'UTR|C13orf34_uc010aen.1_Nonsense_Mutation_p.S122*|C13orf34_uc010thr.1_Missense_Mutation_p.Q13K|C13orf34_uc001viw.1_Nonsense_Mutation_p.S47*	NM_024808	NP_079084	Q6PGQ7	BORA_HUMAN	aurora borealis	47					cell division|mitosis|regulation of mitosis|regulation of mitotic spindle organization|regulation of protein localization		protein kinase binding				0		Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.000227)		GTTTTTAAATCAACAAAATTA	0.303													6	290	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21875113	21875113	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21875113G>C	uc001was.1	-	14	2066	c.1972C>G	c.(1972-1974)CTT>GTT	p.L658V	CHD8_uc001war.1_Missense_Mutation_p.L554V|CHD8_uc001wav.1_Missense_Mutation_p.L100V	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	937	Helicase ATP-binding.				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		ATTTCACGAAGCTCAGGACAA	0.453													10	16	---	---	---	---	PASS
ARF6	382	broad.mit.edu	37	14	50360965	50360965	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50360965T>A	uc001wxg.3	+	2	1132	c.511T>A	c.(511-513)TCT>ACT	p.S171T		NM_001663	NP_001654	P62330	ARF6_HUMAN	ADP-ribosylation factor 6	171					cell adhesion|cellular component movement|cortical actin cytoskeleton organization|negative regulation of receptor-mediated endocytosis|positive regulation of actin filament polymerization|positive regulation of establishment of protein localization in plasma membrane|protein localization at cell surface|protein transport|regulation of dendritic spine development|regulation of filopodium assembly|regulation of Rac protein signal transduction|ruffle organization|small GTPase mediated signal transduction|vesicle-mediated transport	cell cortex|endosome membrane|filopodium membrane|Golgi apparatus|membrane fraction|ruffle	GTP binding|GTPase activity|thioesterase binding				0	all_epithelial(31;0.000822)|Breast(41;0.0117)					ATGGTTAACCTCTAACTACAA	0.502													16	12	---	---	---	---	PASS
CDAN1	146059	broad.mit.edu	37	15	43026449	43026449	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43026449G>C	uc001zql.2	-	7	1349	c.1232C>G	c.(1231-1233)GCT>GGT	p.A411G	CDAN1_uc001zqk.2_5'UTR|CDAN1_uc010bcx.1_Intron	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	411						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		CTCATAGGCAGCTCGAAGGCG	0.552													40	71	---	---	---	---	PASS
LIPC	3990	broad.mit.edu	37	15	58834808	58834808	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58834808G>A	uc010bga.1	+	6	1140	c.532G>A	c.(532-534)GGC>AGC	p.G178S	LIPC_uc010bfz.1_Missense_Mutation_p.G178S|LIPC_uc002afa.1_Missense_Mutation_p.G178S|LIPC_uc010bgb.1_Missense_Mutation_p.G76S|LIPC_uc010ugy.1_Missense_Mutation_p.G117S	NM_000236	NP_000227	P11150	LIPC_HUMAN	lipase C precursor	178					cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity			ovary(1)	1		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		AGGATTTGCCGGCAGTTCCAT	0.532													51	90	---	---	---	---	PASS
SH2D7	646892	broad.mit.edu	37	15	78393416	78393416	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78393416A>G	uc010blb.1	+	5	821	c.821A>G	c.(820-822)TAC>TGC	p.Y274C		NM_001101404	NP_001094874	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	274											0						AGCCAGGCCTACTCCCCAGGC	0.627													9	16	---	---	---	---	PASS
CPEB1	64506	broad.mit.edu	37	15	83215272	83215272	+	Splice_Site	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83215272C>A	uc002bit.2	-	11	1827	c.1690_splice	c.e11-1	p.V564_splice	CPEB1_uc002biq.2_Splice_Site_p.V424_splice|CPEB1_uc002bir.2_Splice_Site_p.V429_splice|CPEB1_uc002bis.2_Splice_Site_p.V424_splice|CPEB1_uc010uod.1_Splice_Site_p.V273_splice|CPEB1_uc010uoe.1_Splice_Site_p.V502_splice|CPEB1_uc002biu.2_Splice_Site_p.V526_splice|CPEB1_uc010uof.1_Splice_Site_p.V424_splice|CPEB1_uc002biv.2_Splice_Site_p.V499_splice|CPEB1_uc002bip.2_Splice_Site_p.V273_splice	NM_001079533	NP_001073001	Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding						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)			CAATCTGAACCTGCACAAAGG	0.483													28	54	---	---	---	---	PASS
GOLGA6L5	374650	broad.mit.edu	37	15	85053142	85053142	+	RNA	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85053142C>T	uc002bkm.2	-	9		c.1905G>A			uc002bkl.1_5'Flank	NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						TTTTTCAATTCCTTGACCCGC	0.393													3	6	---	---	---	---	PASS
IGF1R	3480	broad.mit.edu	37	15	99465636	99465636	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99465636G>T	uc002bul.2	+	11	2511	c.2461G>T	c.(2461-2463)GTC>TTC	p.V821F	IGF1R_uc010urq.1_Missense_Mutation_p.V821F|IGF1R_uc010bon.2_Missense_Mutation_p.V821F|IGF1R_uc010boo.1_5'Flank	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor	821	Extracellular (Potential).				anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	CTCCAACTTCGTCTTTGCAAG	0.522													6	82	---	---	---	---	PASS
ATP2A1	487	broad.mit.edu	37	16	28898565	28898565	+	Silent	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28898565C>A	uc002dro.1	+	7	784	c.600C>A	c.(598-600)GTC>GTA	p.V200V	uc010vct.1_Intron|ATP2A1_uc002drn.1_Silent_p.V200V|ATP2A1_uc002drp.1_Silent_p.V75V|ATP2A1_uc010bym.1_5'Flank	NM_173201	NP_775293	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, fast twitch 1 isoform	200	Cytoplasmic (By similarity).				apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CCCGAGCTGTCAACCAGGACA	0.557													29	45	---	---	---	---	PASS
USP6	9098	broad.mit.edu	37	17	5037336	5037336	+	Intron	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5037336C>T	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron|USP6_uc002gaw.2_3'UTR|uc002gay.1_5'Flank|uc002gba.2_5'Flank|uc002gbb.2_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						ATGGGGTGAACGAGAGGGATG	0.607			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								10	14	---	---	---	---	PASS
SREBF1	6720	broad.mit.edu	37	17	17723754	17723754	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17723754C>T	uc002gru.1	-	2	367	c.173G>A	c.(172-174)GGC>GAC	p.G58D	SREBF1_uc002grp.1_5'Flank|SREBF1_uc002grq.1_5'UTR|SREBF1_uc002grr.1_5'UTR|SREBF1_uc002grs.1_Missense_Mutation_p.G34D|SREBF1_uc002grt.1_Missense_Mutation_p.G88D|SREBF1_uc010cpp.1_Missense_Mutation_p.G34D|SREBF1_uc010cpq.1_Missense_Mutation_p.G58D	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	58	Cytoplasmic (Potential).|Transcriptional activation (acidic).				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1						AGGGTCTGTGCCCCCTGCCCC	0.587													15	31	---	---	---	---	PASS
WFIKKN2	124857	broad.mit.edu	37	17	48918256	48918256	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48918256G>A	uc002isv.3	+	2	2301	c.1607G>A	c.(1606-1608)GGC>GAC	p.G536D	WFIKKN2_uc010dbu.2_Missense_Mutation_p.G443D	NM_175575	NP_783165	Q8TEU8	WFKN2_HUMAN	WFIKKN2 protein	536	NTR.					extracellular region	metalloendopeptidase inhibitor activity|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GTGGACGGCGGCATGGCCATG	0.632													3	42	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60028244	60028244	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60028244G>C	uc002izo.2	-	28	6310	c.6233C>G	c.(6232-6234)CCT>CGT	p.P2078R		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2078					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						GAACCAGTCAGGTAATGGACC	0.428													52	101	---	---	---	---	PASS
EVPL	2125	broad.mit.edu	37	17	74018281	74018281	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74018281G>A	uc002jqi.2	-	6	862	c.634C>T	c.(634-636)CGA>TGA	p.R212*	EVPL_uc010wss.1_Nonsense_Mutation_p.R212*|EVPL_uc010wst.1_5'UTR	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	212	Globular 1.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4						AGTAGGTCTCGGTATTGGCTC	0.697													7	14	---	---	---	---	PASS
ABHD8	79575	broad.mit.edu	37	19	17405546	17405546	+	Silent	SNP	G	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17405546G>T	uc002ngb.3	-	3	1110	c.870C>A	c.(868-870)ATC>ATA	p.I290I		NM_024527	NP_078803	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	290							hydrolase activity				0						GCATGTTGAAGATTGAGCAGA	0.597													19	43	---	---	---	---	PASS
GPATCH1	55094	broad.mit.edu	37	19	33579085	33579085	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33579085G>T	uc002nug.1	+	2	433	c.119G>T	c.(118-120)AGA>ATA	p.R40I		NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	40						catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					CAGACTGTCAGAGATGAAAAA	0.368													3	42	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58385546G>T	uc002qqo.2	-	3	1484	c.1212C>A	c.(1210-1212)GAC>GAA	p.D404E	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						AATGTTTTTTGTCAGTGTGAA	0.393													4	8	---	---	---	---	PASS
LOC100132288	100132288	broad.mit.edu	37	21	9907346	9907346	+	3'UTR	SNP	G	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9907346G>A	uc002zka.1	-	4					LOC100132288_uc010gqn.1_RNA	NM_001033515	NP_001028687			hypothetical protein LOC100132288												0						TGGCAGTGACGTCCTTCTCCA	0.572													7	28	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23006960	23006960	+	RNA	SNP	C	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23006960C>A	uc011aim.1	+	119		c.7563C>A								Parts of antibodies, mostly variable regions.												0						GGGCTCTGCTCCTCCTCACCC	0.627													3	8	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23006961	23006961	+	RNA	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23006961C>T	uc011aim.1	+	119		c.7564C>T								Parts of antibodies, mostly variable regions.												0						GGCTCTGCTCCTCCTCACCCT	0.627													3	8	---	---	---	---	PASS
ZBED4	9889	broad.mit.edu	37	22	50279076	50279076	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50279076G>C	uc003bix.2	+	2	2236	c.1766G>C	c.(1765-1767)GGG>GCG	p.G589A		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	589	BED-type 4.					cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		ATCAGCCGGGGGAAGAAGCCG	0.522													33	61	---	---	---	---	PASS
TBC1D8B	54885	broad.mit.edu	37	X	106066596	106066596	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106066596C>T	uc004emo.2	+	5	892	c.727C>T	c.(727-729)CTT>TTT	p.L243F	MORC4_uc004emp.3_Intron|TBC1D8B_uc004emm.2_Missense_Mutation_p.L243F|TBC1D8B_uc004emn.2_Missense_Mutation_p.L243F	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	243						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						AACATACCTTCTTATGGAACA	0.363													8	159	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1600092	1600093	+	Intron	DEL	TG	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1600092_1600093delTG	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc009vkl.1_Intron|SLC35E2B_uc001ahe.3_Intron|SLC35E2B_uc001ahf.3_Intron|SLC35E2B_uc001ahg.3_Intron|SLC35E2B_uc001ahh.3_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						CTGTTTTTTTTGTTTGTTTGTT	0.317													3	3	---	---	---	---	
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	Frame_Shift_Ins	INS	-	AGCT	AGCT	rs141324796	by1000genomes	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17034125_17034126insAGCT	uc001azn.1	-	3	478_479	c.364_365insAGCT	c.(364-366)TGGfs	p.W122fs	ESPNP_uc010ocj.1_Frame_Shift_Ins_p.W52fs	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						CAGCAGCAGCCAGCTGAGCACC	0.663													12	6	---	---	---	---	
MCOLN2	255231	broad.mit.edu	37	1	85412990	85412991	+	Intron	DEL	CA	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85412990_85412991delCA	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN	mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		caccccccaccacacacacaca	0.069													3	3	---	---	---	---	
TMEM183A	92703	broad.mit.edu	37	1	202991831	202991831	+	Intron	DEL	A	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202991831delA	uc001gyu.1	+						TMEM183A_uc001gyv.1_Intron|TMEM183A_uc001gyw.1_Intron|TMEM183A_uc001gyx.1_Intron|TMEM183A_uc001gyy.2_5'Flank	NM_001079809	NP_001073277	Q8IXX5	T183A_HUMAN	transmembrane protein 183B							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)			gtcctttctcaaaaaaaaaaa	0.144													3	4	---	---	---	---	
ACTN2	88	broad.mit.edu	37	1	236926030	236926030	+	3'UTR	DEL	A	-	-	rs1051251	by1000genomes	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236926030delA	uc001hyf.2	+	21					ACTN2_uc001hyg.2_3'UTR|ACTN2_uc009xgi.1_3'UTR|ACTN2_uc010pxu.1_3'UTR|ACTN2_uc001hyh.2_3'UTR	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2						focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			GAGAGAGGGGAAAAAAAAAAG	0.363													4	2	---	---	---	---	
LOC654342	654342	broad.mit.edu	37	2	91843055	91843056	+	Intron	INS	-	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91843055_91843056insA	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0						GTCACAAGGGCAGACCCCTGGA	0.569													4	2	---	---	---	---	
NCKAP1	10787	broad.mit.edu	37	2	183867819	183867822	+	Intron	DEL	ACAA	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183867819_183867822delACAA	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TTCAGAAAACACAAACAAATAAGG	0.265													11	9	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225661983	225661983	+	Intron	DEL	T	-	-	rs113535092		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225661983delT	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)		ACTTGGTCTATTTTTTTTTTT	0.308													6	4	---	---	---	---	
EOMES	8320	broad.mit.edu	37	3	27763289	27763289	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27763289delT	uc003cdx.2	-	1	497	c.497delA	c.(496-498)CAGfs	p.Q166fs	EOMES_uc003cdy.3_Frame_Shift_Del_p.Q166fs|EOMES_uc010hfn.2_Frame_Shift_Del_p.Q166fs|EOMES_uc011axc.1_Intron	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	166					CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4						AGCCGCCGCCTGGTACGGGAA	0.721													4	2	---	---	---	---	
TOMM70A	9868	broad.mit.edu	37	3	100100774	100100775	+	Intron	INS	-	T	T	rs149548888	by1000genomes	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100100774_100100775insT	uc003dtw.2	-							NM_014820	NP_055635	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1						AAAGGTGAAGCTGCCAGTCCCA	0.376													6	5	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39279672	39279672	+	Intron	DEL	A	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39279672delA	uc003gtv.2	+						WDR19_uc011byi.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						agattccgtcaaaaaaaaaaa	0.144													3	3	---	---	---	---	
ANP32C	23520	broad.mit.edu	37	4	165118171	165118172	+	Frame_Shift_Ins	INS	-	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165118171_165118172insT	uc011cjk.1	-	1	692_693	c.692_693insA	c.(691-693)CAGfs	p.Q231fs	MARCH1_uc003iqs.1_Intron	NM_012403	NP_036535	O43423	AN32C_HUMAN	acidic nuclear phosphoprotein 32C	231											0	all_hematologic(180;0.203)	Prostate(90;0.0138)|Melanoma(52;0.18)|all_neural(102;0.223)		KIRC - Kidney renal clear cell carcinoma(143;0.242)		attttcgcttctgacccctttc	0.064													43	19	---	---	---	---	
SYNCRIP	10492	broad.mit.edu	37	6	86329254	86329254	+	Intron	DEL	A	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86329254delA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA						CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		GTCAGAATATAAAAAAAAAAA	0.189													6	3	---	---	---	---	
GABRR1	2569	broad.mit.edu	37	6	89899765	89899765	+	Intron	DEL	A	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89899765delA	uc003pna.2	-						GABRR1_uc011dzv.1_Intron	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)	actccatctcaaaaaaaaaaa	0.204													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141083119	141083120	+	IGR	INS	-	C	C			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141083119_141083120insC								None (None upstream) : None (None downstream)																							GATACAGAAGACCTCTTATTCT	0.371													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33066270	33066270	+	Intron	DEL	T	-	-	rs34317509		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33066270delT	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						tgcccggccAttttttttttt	0.000													4	2	---	---	---	---	
GUSB	2990	broad.mit.edu	37	7	65440854	65440854	+	Intron	DEL	G	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65440854delG	uc003tun.2	-						GUSB_uc011kdt.1_Intron|GUSB_uc010kzw.1_Frame_Shift_Del_p.L187fs	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						aaaaaaaaaagaaaaTGGGCC	0.284													4	5	---	---	---	---	
BAIAP2L1	55971	broad.mit.edu	37	7	97946299	97946300	+	Intron	INS	-	T	T	rs143087564	by1000genomes	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97946299_97946300insT	uc003upj.2	-							NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			cctcagcctccgagtagctgtg	0.000													2	7	---	---	---	---	
FOXP2	93986	broad.mit.edu	37	7	114330185	114330185	+	3'UTR	DEL	T	-	-	rs143759073		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114330185delT	uc003vhb.2	+	17					FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_3'UTR|FOXP2_uc003vha.2_3'UTR|FOXP2_uc011kmu.1_3'UTR|FOXP2_uc011kmv.1_3'UTR|FOXP2_uc010ljz.1_3'UTR	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						cttcttcttcttttttttttt	0.289													4	2	---	---	---	---	
BRAF	673	broad.mit.edu	37	7	140487125	140487125	+	Intron	DEL	G	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140487125delG	uc003vwc.3	-							NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	aaaaaaaaaaGACTTCCTTTT	0.134		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				5	3	---	---	---	---	
NUB1	51667	broad.mit.edu	37	7	151066098	151066099	+	Intron	INS	-	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151066098_151066099insT	uc003wjx.2	+						NUB1_uc003wjw.2_Intron|NUB1_uc010lqc.2_Intron|uc003wjz.1_5'Flank	NM_016118	NP_057202	Q9Y5A7	NUB1_HUMAN	NEDD8 ultimate buster-1						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|response to interferon-gamma|response to tumor necrosis factor|ubiquitin-dependent protein catabolic process	nucleus	protein binding				0			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GAAACTTGTCCttttttttttc	0.193													4	2	---	---	---	---	
CNOT7	29883	broad.mit.edu	37	8	17088039	17088040	+	3'UTR	INS	-	T	T	rs112850424		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17088039_17088040insT	uc003wxf.1	-	7					CNOT7_uc003wxg.1_3'UTR	NM_013354	NP_037486	Q9UIV1	CNOT7_HUMAN	CCR4-NOT transcription complex, subunit 7						carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)		ACCTGAATGCGTTTTTTTTTTT	0.356													3	3	---	---	---	---	
INTS8	55656	broad.mit.edu	37	8	95869299	95869300	+	Intron	INS	-	T	T			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95869299_95869300insT	uc003yhb.2	+						INTS8_uc003yha.1_Intron|INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334	Q75QN2	INT8_HUMAN	integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)					AGTTTGTAATCttttttttttt	0.173													5	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139774832	139774833	+	Intron	DEL	CA	-	-	rs34749309		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139774832_139774833delCA	uc003yvd.2	-						COL22A1_uc011ljo.1_5'Flank	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			AACGCACGTGcacacacacaca	0.302										HNSCC(7;0.00092)			9	4	---	---	---	---	
LOC100129066	100129066	broad.mit.edu	37	9	92286492	92286494	+	Intron	DEL	GGC	-	-	rs144940722	by1000genomes	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92286492_92286494delGGC	uc004aqs.2	+							NR_024280				Homo sapiens cDNA FLJ42342 fis, clone UTERU2000794.												0						tggtggtggtggcggtgatggag	0.010													3	4	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	17875520	17875520	+	Intron	DEL	A	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17875520delA	uc001ipk.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						actctgtctcaaaaaaaaaaa	0.085													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	48862227	48862228	+	Intron	INS	-	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48862227_48862228insA	uc001jfy.3	-						FRMPD2L1_uc001jfz.3_Intron	NM_001042525	NP_001035990			FERM and PDZ domain containing 2 like 1 isoform																		AAATGGAAGAGAAAAAAAAAAA	0.421													4	2	---	---	---	---	
SLC22A9	114571	broad.mit.edu	37	11	63141417	63141418	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63141417_63141418delTG	uc001nww.2	+	4	981_982	c.713_714delTG	c.(712-714)ATGfs	p.M238fs	SLC22A9_uc001nwx.2_RNA	NM_080866	NP_543142	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion/cation	238	Helical; (Potential).				transmembrane transport	integral to membrane				breast(2)|large_intestine(1)	3						ACATTGGGAATGTGCCCTTCTG	0.475													51	25	---	---	---	---	
ACTN3	89	broad.mit.edu	37	11	66321927	66321928	+	Intron	INS	-	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66321927_66321928insA	uc001oio.1	+						ACTN3_uc010rpi.1_Intron	NM_001104	NP_001095	Q08043	ACTN3_HUMAN	actinin, alpha 3						focal adhesion assembly|muscle filament sliding|regulation of apoptosis	actin filament|cytosol|focal adhesion|pseudopodium	actin binding|calcium ion binding|integrin binding|protein homodimerization activity|structural constituent of muscle				0						gaccctgtctcaaaaaaaaaaa	0.248													4	3	---	---	---	---	
MLL2	8085	broad.mit.edu	37	12	49427700	49427700	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49427700delC	uc001rta.3	-	39	10788	c.10788delG	c.(10786-10788)CGGfs	p.R3596fs		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	3596	Potential.|Gln-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						gctgctTGTTCCGATATTCTG	0.458			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	129497863	129497864	+	IGR	INS	-	TT	TT	rs10655206		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129497863_129497864insTT								GLT1D1 (28354 upstream) : TMEM132D (58407 downstream)																							TGGCAGAATCCTTTTTTTTTTT	0.371													4	2	---	---	---	---	
ISM2	145501	broad.mit.edu	37	14	77948468	77948469	+	Intron	INS	-	A	A			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77948468_77948469insA	uc001xtz.2	-						ISM2_uc001xua.2_Intron|ISM2_uc001xty.2_Intron|ISM2_uc010tvl.1_Intron	NM_199296	NP_954993	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1							extracellular region				skin(1)	1						attaaaaaattaaaaaaaaaaa	0.173													6	3	---	---	---	---	
KLC1	3831	broad.mit.edu	37	14	104053849	104053850	+	Intron	INS	-	C	C	rs2896487	by1000genomes	TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104053849_104053850insC	uc010tyd.1	+						C14orf153_uc001ynl.3_Intron|C14orf153_uc010tyc.1_Intron	NM_005552	NP_005543	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 1						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)				ttttttcttttttttttttttt	0.129													4	2	---	---	---	---	
NETO2	81831	broad.mit.edu	37	16	47156542	47156542	+	Intron	DEL	T	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47156542delT	uc002eer.1	-						NETO2_uc010vgf.1_Intron|NETO2_uc002ees.1_Intron	NM_018092	NP_060562	Q8NC67	NETO2_HUMAN	neuropilin- and tolloid-like protein 2							integral to membrane	receptor activity				0		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				TGTTCTTCTCTGAAGCGACTC	0.343										HNSCC(25;0.065)			118	75	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80525803	80525808	+	Intron	DEL	TTTTTT	-	-	rs5822539		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80525803_80525808delTTTTTT	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ATTCTCTTCCtttttttttttttttt	0.325													4	2	---	---	---	---	
DPP9	91039	broad.mit.edu	37	19	4682879	4682880	+	Intron	DEL	AG	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4682879_4682880delAG	uc002mba.2	-							NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9						proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		AGATGGGGGCAGAGAGAGAGAG	0.663													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42107427	42107428	+	IGR	INS	-	CA	CA	rs71928647		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42107427_42107428insCA								CEACAM21 (14231 upstream) : CEACAM4 (17916 downstream)																							gcgcgcgcgcgcacacacacac	0.213													4	2	---	---	---	---	
ZNF816A	125893	broad.mit.edu	37	19	53454915	53454915	+	Intron	DEL	T	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53454915delT	uc002qal.1	-						ZNF321_uc010eqj.2_Intron|ZNF321_uc002qak.1_Intron|ZNF816A_uc002qam.1_Intron	NM_001031665	NP_001026835	Q0VGE8	ZN816_HUMAN	zinc finger protein 816A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0313)		TGTGTAAAAATTACACAAAAA	0.209													28	13	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45390749	45390750	+	Intron	INS	-	A	A	rs112823395		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45390749_45390750insA	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_Intron	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		GTGATTTCTTTAAAAAAAAAAA	0.540													8	5	---	---	---	---	
SEZ6L	23544	broad.mit.edu	37	22	26709538	26709539	+	Intron	DEL	AC	-	-	rs68081834		TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26709538_26709539delAC	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_Intron	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						TTTAATCATTacacacacacac	0.401													6	4	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31985765	31985768	+	Intron	DEL	TTTA	-	-			TCGA-B8-4146-01B-11D-1669-08	TCGA-B8-4146-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31985765_31985768delTTTA	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron|SFI1_uc010gwi.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						TTTGTCCATCTTTATTTATTTATT	0.333													4	2	---	---	---	---	
