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
CROCCL1	84809	broad.mit.edu	37	1	16946434	16946434	+	RNA	SNP	C	T	T	rs367060		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946434C>T	uc010ocf.1	-	3		c.464G>A			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CTCAGCCTTCCGCCGGGCCAG	0.672													4	25	---	---	---	---	PASS
FCN3	8547	broad.mit.edu	37	1	27697177	27697177	+	Missense_Mutation	SNP	G	A	A	rs150694369	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27697177G>A	uc001boa.2	-	7	574	c.568C>T	c.(568-570)CGT>TGT	p.R190C	FCN3_uc001bob.2_Missense_Mutation_p.R179C	NM_003665	NP_003656	O75636	FCN3_HUMAN	ficolin 3 isoform 1 precursor	190	Fibrinogen C-terminal.				complement activation, lectin pathway|signal transduction	collagen|extracellular space	receptor binding|sugar binding				0		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCGAAAGTACGGTTACCATTA	0.537													4	82	---	---	---	---	PASS
TRIM62	55223	broad.mit.edu	37	1	33612870	33612870	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33612870G>A	uc001bxb.2	-	5	1974	c.1336C>T	c.(1336-1338)CCT>TCT	p.P446S		NM_018207	NP_060677	Q9BVG3	TRI62_HUMAN	tripartite motif-containing 62	446	B30.2/SPRY.					intracellular	zinc ion binding				0		Myeloproliferative disorder(586;0.0393)				AGCTTGCCAGGGAACTTCTCG	0.557													12	27	---	---	---	---	PASS
CLSPN	63967	broad.mit.edu	37	1	36226519	36226519	+	Splice_Site	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36226519T>C	uc001bzi.2	-	8	1085	c.1005_splice	c.e8-1	p.K335_splice	CLSPN_uc009vux.2_Splice_Site_p.K335_splice	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin						activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTAGATGACCTAGAGAAGAGA	0.348													3	39	---	---	---	---	PASS
SLC44A3	126969	broad.mit.edu	37	1	95357883	95357883	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95357883A>C	uc001dqv.3	+	14	1774	c.1667A>C	c.(1666-1668)AAC>ACC	p.N556T	SLC44A3_uc001dqx.3_Missense_Mutation_p.N555T|SLC44A3_uc010otq.1_Missense_Mutation_p.N488T|SLC44A3_uc010otr.1_Missense_Mutation_p.N520T|SLC44A3_uc001dqw.3_Missense_Mutation_p.N508T|SLC44A3_uc010ots.1_Missense_Mutation_p.N476T|SLC44A3_uc009wds.2_Missense_Mutation_p.N459T|SLC44A3_uc010ott.1_Missense_Mutation_p.N475T	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1	556						integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	ATGGCTTTTAACTACAATCGG	0.393													194	329	---	---	---	---	PASS
DENND2D	79961	broad.mit.edu	37	1	111743023	111743023	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111743023A>T	uc001eak.1	-	1	259	c.59T>A	c.(58-60)CTC>CAC	p.L20H	DENND2D_uc001eal.1_Intron	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	20										ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		ACCTGCTCGGAGTTGAAGCAG	0.557													24	34	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145296373	145296373	+	Missense_Mutation	SNP	G	T	T	rs3969711		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145296373G>T	uc001end.3	+	3	330	c.295G>T	c.(295-297)GTT>TTT	p.V99F	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.V99F|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	99											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TAAAGTCCTAGTTCACTCTCA	0.473													4	62	---	---	---	---	PASS
FLAD1	80308	broad.mit.edu	37	1	154962043	154962043	+	Silent	SNP	T	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154962043T>G	uc001fgf.1	+	3	1479	c.1125T>G	c.(1123-1125)TCT>TCG	p.S375S	FLAD1_uc001fgd.1_Silent_p.S375S|FLAD1_uc001fge.1_Silent_p.S278S|FLAD1_uc001fgg.1_Silent_p.S278S|FLAD1_uc001fgh.1_Intron	NM_025207	NP_079483	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase isoform	375					FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)|skin(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGGGTCTTCTTTGGGGAAAA	0.463													19	32	---	---	---	---	PASS
RUSC1	23623	broad.mit.edu	37	1	155300500	155300500	+	3'UTR	SNP	A	G	G	rs111866473		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155300500A>G	uc001fkj.2	+	10					RAG1AP1_uc010pey.1_Intron|RUSC1_uc001fkk.2_3'UTR|RUSC1_uc009wqn.1_RNA|RUSC1_uc009wqo.1_3'UTR|RUSC1_uc001fkl.2_3'UTR|RUSC1_uc001fkp.2_3'UTR|RUSC1_uc001fkq.2_3'UTR|RUSC1_uc010pgb.1_3'UTR|RUSC1_uc009wqp.1_3'UTR|RUSC1_uc001fkn.2_3'UTR|RUSC1_uc001fko.2_RNA|RUSC1_uc001fkr.2_3'UTR|RUSC1_uc001fks.2_3'UTR	NM_001105203	NP_001098673	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1 isoform a							cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			TATTTAAAATAAACTTTCCTT	0.413													7	9	---	---	---	---	PASS
VSIG8	391123	broad.mit.edu	37	1	159827560	159827560	+	Silent	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159827560C>T	uc001fuh.2	-	4	763	c.627G>A	c.(625-627)GAG>GAA	p.E209E	C1orf204_uc001fuf.1_5'Flank|C1orf204_uc001fug.1_5'Flank	NM_001013661	NP_001013683	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	209	Extracellular (Potential).|Ig-like V-type 2.					integral to membrane				central_nervous_system(1)	1	all_hematologic(112;0.0597)					TGTGGAAGGACTCCTGGTAGG	0.572													25	38	---	---	---	---	PASS
C1orf14	81626	broad.mit.edu	37	1	182869151	182869151	+	Silent	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182869151G>A	uc001gpu.2	-	10	2214	c.1929C>T	c.(1927-1929)AAC>AAT	p.N643N	C1orf14_uc001gpv.2_Silent_p.N524N|C1orf14_uc010pnz.1_Silent_p.N501N|C1orf14_uc001gpw.2_Silent_p.N363N	NM_030933	NP_112195	Q9BZQ2	SHP1L_HUMAN	chromosome 1 open reading frame 14	715											0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)		CCCCCTTGACGTTTGCTTCTA	0.308													49	94	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216166458	216166458	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216166458C>A	uc001hku.1	-	35	7096	c.6709G>T	c.(6709-6711)GAC>TAC	p.D2237Y		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2237	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATGTCCTCGTCAGTTAGGGCC	0.507										HNSCC(13;0.011)	OREG0014251	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	44	54	---	---	---	---	PASS
DEGS1	8560	broad.mit.edu	37	1	224363513	224363513	+	5'UTR	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224363513G>T	uc001hoi.2	+	1						NM_144780	NP_659004	O15121	DEGS1_HUMAN	degenerative spermatocyte homolog 1, lipid						sphingolipid metabolic process|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	electron carrier activity|protein binding|sphingolipid delta-4 desaturase activity				0	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		CATCGCTTGGGCCTCCTCCAC	0.701													10	36	---	---	---	---	PASS
C1orf131	128061	broad.mit.edu	37	1	231374536	231374536	+	Intron	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231374536A>G	uc001hun.1	-						C1orf131_uc001hul.2_Intron|C1orf131_uc001hum.2_Intron|C1orf131_uc010pwd.1_Intron|C1orf131_uc001huo.1_3'UTR|GNPAT_uc009xfo.1_5'Flank|GNPAT_uc001hup.3_5'Flank|GNPAT_uc009xfp.2_5'Flank	NM_152379	NP_689592	Q8NDD1	CA131_HUMAN	hypothetical protein LOC128061											central_nervous_system(1)|skin(1)	2	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				caGTCTAAAGAGCTATTCACC	0.219													4	61	---	---	---	---	PASS
RASGRP3	25780	broad.mit.edu	37	2	33783285	33783285	+	Silent	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33783285A>G	uc002rox.2	+	17	2214	c.1587A>G	c.(1585-1587)GGA>GGG	p.G529G	RASGRP3_uc010ync.1_Silent_p.G529G|RASGRP3_uc002roy.2_Silent_p.G528G	NM_170672	NP_733772	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and	529	Phorbol-ester/DAG-type.				MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)					CAGACTGTGGAGCCAATTGTC	0.537													5	128	---	---	---	---	PASS
GGT8P	645367	broad.mit.edu	37	2	91968965	91968965	+	RNA	SNP	T	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91968965T>G	uc010fho.1	+	2		c.1296T>G				NR_003503				Homo sapiens cDNA FLJ31276 fis, clone KIDNE2006376, weakly similar to GAMMA-GLUTAMYLTRANSPEPTIDASE 1 PRECURSOR (EC 2.3.2.2).												0						GGTGTGGGGGTTGGTCTAGCT	0.637													4	6	---	---	---	---	PASS
C2orf29	55571	broad.mit.edu	37	2	101885856	101885856	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101885856A>C	uc002taw.3	+	7	1596	c.1514A>C	c.(1513-1515)GAG>GCG	p.E505A		NM_017546	NP_060016	Q9UKZ1	CB029_HUMAN	hypothetical protein LOC55571	505					cell proliferation|nuclear-transcribed mRNA poly(A) tail shortening	cytosol				ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						ACACCTTCTGAGACCAAAATG	0.413													57	79	---	---	---	---	PASS
ACVR2A	92	broad.mit.edu	37	2	148677842	148677842	+	Missense_Mutation	SNP	G	T	T	rs111862877		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148677842G>T	uc002twg.2	+	9	1275	c.1006G>T	c.(1006-1008)GCT>TCT	p.A336S	ACVR2A_uc010zbn.1_Missense_Mutation_p.A228S|ACVR2A_uc002twh.2_Missense_Mutation_p.A336S	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	336	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CAACCTGACAGCTTGCATTGC	0.348													23	37	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196664105	196664105	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196664105T>C	uc002utj.3	-	55	10369	c.10268A>G	c.(10267-10269)GAC>GGC	p.D3423G		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3423	AAA 6 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						GCAGTTACTGTCTCCAAATGC	0.443													4	81	---	---	---	---	PASS
SP140	11262	broad.mit.edu	37	2	231090582	231090582	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231090582G>A	uc002vql.2	+	1	138	c.23G>A	c.(22-24)GGG>GAG	p.G8E	SP140_uc010zma.1_RNA|SP140_uc002vqj.2_Missense_Mutation_p.G8E|SP140_uc002vqk.2_Missense_Mutation_p.G8E|SP140_uc002vqn.2_Missense_Mutation_p.G8E|SP140_uc002vqm.2_Missense_Mutation_p.G8E|SP140_uc010fxl.2_Missense_Mutation_p.G8E	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1	8					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GGCCAGCAGGGGCAGATGGCA	0.552													38	69	---	---	---	---	PASS
NCL	4691	broad.mit.edu	37	2	232323070	232323070	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232323070T>C	uc002vru.2	-	8	1337	c.1196A>G	c.(1195-1197)AAT>AGT	p.N399S	SNORA75_uc002vrv.1_5'Flank|SNORD20_uc002vrw.1_5'Flank	NM_005381	NP_005372	P19338	NUCL_HUMAN	nucleolin	399	RRM 2.				angiogenesis	cell cortex|nucleolus|ribonucleoprotein complex	nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding			ovary(2)|pancreas(1)	3		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		GTAAGGGAGATTTTTAGCCAA	0.408													43	71	---	---	---	---	PASS
RUVBL1	8607	broad.mit.edu	37	3	127817748	127817748	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127817748T>C	uc003ekh.2	-	7	898	c.794A>G	c.(793-795)AAG>AGG	p.K265R	RUVBL1_uc003eke.2_Missense_Mutation_p.K6R|RUVBL1_uc003ekf.2_Missense_Mutation_p.K205R|RUVBL1_uc010hss.2_Missense_Mutation_p.K265R	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1	265					cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)		CTTCTTTGGCTTCATTAGCTG	0.527													4	94	---	---	---	---	PASS
PPP1R2	5504	broad.mit.edu	37	3	195269862	195269862	+	5'UTR	SNP	G	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195269862G>C	uc003fup.2	-	1					PPP1R2_uc003fuq.3_5'UTR	NM_006241	NP_006232	P41236	IPP2_HUMAN	protein phosphatase 1, regulatory subunit 2						glycogen metabolic process|regulation of phosphoprotein phosphatase activity|regulation of signal transduction		protein binding|protein serine/threonine phosphatase inhibitor activity			urinary_tract(1)	1	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)		CGGGCGCTCCGGCTGTCGGCT	0.662													18	16	---	---	---	---	PASS
KIAA0226	9711	broad.mit.edu	37	3	197403751	197403751	+	Intron	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197403751C>T	uc003fyc.2	-						KIAA0226_uc003fyd.3_Intron|MIR922_hsa-mir-922|MI0005714_5'Flank|KIAA0226_uc003fye.1_Missense_Mutation_p.R616K	NM_014687	NP_055502	Q92622	RUBIC_HUMAN	hypothetical protein LOC9711 isoform 2.						autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis	early endosome|late endosome|lysosome	protein binding				0	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GTGAGACTTTCTCACCATGCA	0.577													14	47	---	---	---	---	PASS
PDS5A	23244	broad.mit.edu	37	4	39905797	39905797	+	Silent	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39905797T>C	uc003guv.3	-	12	1788	c.1248A>G	c.(1246-1248)AAA>AAG	p.K416K	PDS5A_uc010ifo.2_Silent_p.K376K|PDS5A_uc003guw.3_Silent_p.K416K	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog	416	HEAT.				cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						TCATAGCTTCTTTTCTTACTC	0.388													4	72	---	---	---	---	PASS
SCOC	60592	broad.mit.edu	37	4	141302257	141302257	+	Silent	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141302257A>G	uc003iif.2	+	4	506	c.479A>G	c.(478-480)TAA>TGA	p.*160*	SCOC_uc003iib.2_Silent_p.*123*|SCOC_uc011che.1_Silent_p.*123*|SCOC_uc003iid.2_Silent_p.*122*|SCOC_uc011chf.1_Silent_p.*123*|SCOC_uc011chg.1_Silent_p.*95*|SCOC_uc011chh.1_Silent_p.*159*|SCOC_uc003iig.2_Silent_p.*132*	NM_001153484	NP_001146956	Q9UIL1	SCOC_HUMAN	short coiled-coil protein isoform 1	160						Golgi apparatus|nucleus	protein binding				0	all_hematologic(180;0.162)					AAAAGAAAGTAAGGGATTGAC	0.333													14	25	---	---	---	---	PASS
RAPGEF2	9693	broad.mit.edu	37	4	160273849	160273849	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160273849C>T	uc003iqg.3	+	21	3705	c.3395C>T	c.(3394-3396)GCT>GTT	p.A1132V		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1132	Ser-rich.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TATACTTTGGCTCCCAGTGGT	0.373													47	53	---	---	---	---	PASS
KLKB1	3818	broad.mit.edu	37	4	187172722	187172722	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187172722T>A	uc003iyy.2	+	9	1021	c.950T>A	c.(949-951)GTT>GAT	p.V317D	KLKB1_uc011clc.1_Missense_Mutation_p.V115D|KLKB1_uc011cld.1_Missense_Mutation_p.V279D	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	317	Apple 4.				blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		GGAGTGAATGTTTGCCAAGAG	0.363													65	98	---	---	---	---	PASS
KDM3B	51780	broad.mit.edu	37	5	137761132	137761132	+	Silent	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137761132C>T	uc003lcy.1	+	17	4472	c.4272C>T	c.(4270-4272)CTC>CTT	p.L1424L	KDM3B_uc010jew.1_Silent_p.L1080L|KDM3B_uc011cys.1_Silent_p.L456L	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	1424					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						ATAAAAAGCTCAAGTCTGAGC	0.463													8	113	---	---	---	---	PASS
C6orf62	81688	broad.mit.edu	37	6	24706388	24706388	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24706388G>T	uc003nel.2	-	5	1174	c.667C>A	c.(667-669)CTC>ATC	p.L223I		NM_030939	NP_112201	Q9GZU0	CF062_HUMAN	hypothetical protein LOC81688	223						intracellular					0						TAAGGACGGAGGTGATCCTCT	0.443													51	90	---	---	---	---	PASS
TBP	6908	broad.mit.edu	37	6	170871067	170871067	+	Silent	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170871067G>A	uc003qxt.2	+	3	475	c.243G>A	c.(241-243)CAG>CAA	p.Q81Q	TBP_uc003qxu.2_Silent_p.Q81Q|TBP_uc011ehf.1_Silent_p.Q61Q|TBP_uc011ehg.1_Silent_p.Q81Q	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein	81	Poly-Gln.				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.174													9	19	---	---	---	---	PASS
EMID2	136227	broad.mit.edu	37	7	101063346	101063346	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101063346T>A	uc010lhy.1	+	2	439	c.247T>A	c.(247-249)TGC>AGC	p.C83S	EMID2_uc003uyo.1_Missense_Mutation_p.C83S	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2	83	EMI.					collagen				ovary(1)	1	Lung NSC(181;0.215)					GTACCAGAGCTGCCGGTGGCC	0.647													10	17	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136700327	136700327	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700327A>G	uc003vtf.1	+	4	1338	c.715A>G	c.(715-717)AGG>GGG	p.R239G	CHRM2_uc003vtg.1_Missense_Mutation_p.R239G|CHRM2_uc003vtj.1_Missense_Mutation_p.R239G|CHRM2_uc003vtk.1_Missense_Mutation_p.R239G|CHRM2_uc003vtl.1_Missense_Mutation_p.R239G|CHRM2_uc003vtm.1_Missense_Mutation_p.R239G|CHRM2_uc003vti.1_Missense_Mutation_p.R239G|CHRM2_uc003vto.1_Missense_Mutation_p.R239G|CHRM2_uc003vtn.1_Missense_Mutation_p.R239G|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	239	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	GGTACAAGGAAGGATAGTGAA	0.502													4	58	---	---	---	---	PASS
NAT1	9	broad.mit.edu	37	8	18074427	18074427	+	Intron	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18074427G>A	uc010ltd.2	+						NAT1_uc003wyt.2_Missense_Mutation_p.E9K|NAT1_uc003wyu.2_Intron|NAT1_uc003wyv.2_Intron|NAT1_uc010ltc.2_Intron|NAT1_uc003wys.2_Missense_Mutation_p.E9K|NAT1_uc003wyr.2_Intron|NAT1_uc003wyq.2_Intron	NM_001160179	NP_001153651	P18440	ARY1_HUMAN	N-acetyltransferase 1 isoform a						xenobiotic metabolic process	cytosol	arylamine N-acetyltransferase activity				0				Colorectal(111;0.0519)|COAD - Colon adenocarcinoma(73;0.208)		cttacacaaggaggcagccct	0.000													3	40	---	---	---	---	PASS
TRIM55	84675	broad.mit.edu	37	8	67047249	67047249	+	Silent	SNP	C	A	A	rs151067178		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67047249C>A	uc003xvv.2	+	3	592	c.366C>A	c.(364-366)CCC>CCA	p.P122P	TRIM55_uc003xvu.2_Silent_p.P122P|TRIM55_uc003xvw.2_Silent_p.P122P|TRIM55_uc003xvx.2_Silent_p.P122P	NM_184085	NP_908973	Q9BYV6	TRI55_HUMAN	tripartite motif-containing 55 isoform 1	122	B box-type.					cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			CCGACCAGCCCATGTGCGAGG	0.517													32	52	---	---	---	---	PASS
PABPC1	26986	broad.mit.edu	37	8	101724606	101724606	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101724606G>A	uc003yjs.1	-	7	1460	c.956C>T	c.(955-957)ACA>ATA	p.T319I	PABPC1_uc011lhc.1_Missense_Mutation_p.T287I|PABPC1_uc011lhd.1_Missense_Mutation_p.T274I|PABPC1_uc003yjt.1_Missense_Mutation_p.T316I|PABPC1_uc003yju.2_RNA	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	319	RRM 4.				mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ACTAGTGATTGTACCAAATGG	0.284													5	48	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20414340G>A	uc003zoe.2	-	5	763	c.504C>T	c.(502-504)AGC>AGT	p.S168S	MLLT3_uc011lne.1_Silent_p.S136S|MLLT3_uc011lnf.1_Silent_p.S165S|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Missense_Mutation_p.A130V	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	168	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctgctactgctgc	0.144			T	MLL	ALL								5	128	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20414343A>G	uc003zoe.2	-	5	760	c.501T>C	c.(499-501)AGT>AGC	p.S167S	MLLT3_uc011lne.1_Silent_p.S135S|MLLT3_uc011lnf.1_Silent_p.S164S|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Missense_Mutation_p.V129A	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	167	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.139			T	MLL	ALL								8	122	---	---	---	---	PASS
SMC2	10592	broad.mit.edu	37	9	106860765	106860765	+	Silent	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106860765A>G	uc004bbv.2	+	4	645	c.357A>G	c.(355-357)GGA>GGG	p.G119G	SMC2_uc004bbu.1_Silent_p.G119G|SMC2_uc004bbw.2_Silent_p.G119G|SMC2_uc011lvl.1_Silent_p.G119G|SMC2_uc010mtg.1_5'UTR|SMC2_uc010mth.1_Silent_p.G69G|SMC2_uc004bbx.2_Silent_p.G119G	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	119					cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						TAATCAATGGAGTCAATGCCA	0.353													4	60	---	---	---	---	PASS
REXO4	57109	broad.mit.edu	37	9	136279971	136279971	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136279971C>T	uc004cdm.2	-	2	586	c.386G>A	c.(385-387)AGG>AAG	p.R129K	ADAMTS13_uc004cdp.3_Intron|REXO4_uc011mde.1_Intron|REXO4_uc011mdf.1_Intron|REXO4_uc004cdn.2_Intron|REXO4_uc004cdo.2_Intron	NM_020385	NP_065118	Q9GZR2	REXO4_HUMAN	XPMC2 prevents mitotic catastrophe 2 homolog	129						nucleolus	exonuclease activity|nucleic acid binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		AACAGAGCCCCTGCTGGCCTC	0.522													73	99	---	---	---	---	PASS
FAM188A	80013	broad.mit.edu	37	10	15902340	15902340	+	5'UTR	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15902340G>T	uc001iod.1	-	1					FAM188A_uc001ioe.1_5'UTR|FAM188A_uc001iof.1_5'UTR	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1						GCGGACTCCTGCCCCGGAACA	0.617													10	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	30986423	30986423	+	Translation_Start_Site	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30986423C>T	uc010qdx.1	+	3	299	c.-243C>T	c.(-245--241)AACGC>AATGC							SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		AGTTCGCAAACGCCATAGAAA	0.527													6	80	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	49239581	49239581	+	5'UTR	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49239581C>T	uc001jgd.2	-	1										RecName: Full=Arf-GAP, GTPase, ANK repeat and PH domain-containing protein 11; AltName: Full=Centaurin-gamma-like protein KIAA1975;																		TCGAGGCTGACGCTAGGGTGC	0.622													5	47	---	---	---	---	PASS
NCOA4	8031	broad.mit.edu	37	10	51580556	51580556	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51580556G>T	uc001jis.3	+	3	345	c.142G>T	c.(142-144)GTC>TTC	p.V48F	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Missense_Mutation_p.V64F|NCOA4_uc010qhd.1_Missense_Mutation_p.V64F|NCOA4_uc010qhe.1_5'UTR|NCOA4_uc010qhf.1_Intron|NCOA4_uc001jit.2_Missense_Mutation_p.V48F|NCOA4_uc009xoo.2_Missense_Mutation_p.V48F	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	48					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						TGTTTCCTAGGTCAAAGCTCA	0.418			T	RET	papillary thyroid 								3	61	---	---	---	---	PASS
KCNMA1	3778	broad.mit.edu	37	10	78637476	78637476	+	3'UTR	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78637476A>G	uc001jxj.2	-	29					KCNMA1_uc001jxk.1_3'UTR|KCNMA1_uc009xrt.1_3'UTR	NM_001014797	NP_001014797	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						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)	CTTTAAAAAAATAGTTCTGGT	0.388													4	95	---	---	---	---	PASS
DHDPSL	112817	broad.mit.edu	37	10	99359576	99359576	+	Intron	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99359576G>T	uc001kny.2	+						DHDPSL_uc001knx.2_3'UTR|DHDPSL_uc001knz.2_Intron|PI4K2A_uc010qoy.1_Intron	NM_138413	NP_612422	Q86XE5	HOGA1_HUMAN	DHDPS-like protein isoform 1						glyoxylate catabolic process	mitochondrion	4-hydroxy-2-oxoglutarate aldolase activity				0						GGTGATGTGAGTGGCAGCAGC	0.587													20	32	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093204	1093204	+	Missense_Mutation	SNP	C	A	A	rs56299570		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093204C>A	uc001lsx.1	+	31	12136	c.12109C>A	c.(12109-12111)CCG>ACG	p.P4037T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4037						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gtccccaaccccaacagccat	0.015													12	415	---	---	---	---	PASS
KRTAP5-4	387267	broad.mit.edu	37	11	1643335	1643335	+	5'UTR	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1643335A>G	uc009ycy.1	-	1						NM_001012709	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4							keratin filament					0		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GTTCTGGTGGATTGAGGGTGG	0.403													5	20	---	---	---	---	PASS
MRVI1	10335	broad.mit.edu	37	11	10624763	10624763	+	Silent	SNP	C	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10624763C>G	uc010rcc.1	-	14	2165	c.1779G>C	c.(1777-1779)CGG>CGC	p.R593R	MRVI1_uc001miw.2_Silent_p.R584R|MRVI1_uc010rcb.1_Silent_p.R585R|MRVI1_uc009ygb.1_Silent_p.R278R|MRVI1_uc001mix.2_Silent_p.R278R|MRVI1_uc001miz.2_Silent_p.R502R|MRVI1_uc009ygc.1_Silent_p.R502R|MRVI1_uc010rcd.1_Silent_p.R387R|MRVI1_uc009ygd.1_Silent_p.R278R|MRVI1_uc010rce.1_RNA	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c	566	Potential.				platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GGTAGGTTTCCCGGTGCTCAC	0.557													8	47	---	---	---	---	PASS
SOX6	55553	broad.mit.edu	37	11	16424392	16424392	+	5'UTR	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16424392C>T	uc001mme.2	-	1					SOX6_uc001mmd.2_5'UTR|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_RNA|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						TTTCCTATCCCCAATGGTCTC	0.363													3	48	---	---	---	---	PASS
PAMR1	25891	broad.mit.edu	37	11	35492180	35492180	+	Silent	SNP	G	A	A	rs146476025		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35492180G>A	uc001mwg.2	-	5	724	c.681C>T	c.(679-681)GAC>GAT	p.D227D	PAMR1_uc001mwf.2_Silent_p.D227D|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Silent_p.D187D	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	227	CUB.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						CATGGAAACCGTCAAAATTCT	0.493													4	76	---	---	---	---	PASS
C11orf94	143678	broad.mit.edu	37	11	45928173	45928173	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45928173G>A	uc001nbs.3	-	3	281	c.244C>T	c.(244-246)CGC>TGC	p.R82C		NM_001080446	NP_001073915	C9JXX5	CK094_HUMAN	hypothetical protein LOC143678	82						extracellular region					0						TCCCGCTTGCGCTGCTGGGCC	0.577													9	52	---	---	---	---	PASS
SSSCA1	10534	broad.mit.edu	37	11	65338194	65338194	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65338194C>T	uc001oek.2	+	2	159	c.139C>T	c.(139-141)CGC>TGC	p.R47C	FAM89B_uc001oen.2_5'Flank|FAM89B_uc001oem.2_5'Flank|FAM89B_uc001oel.2_5'Flank	NM_006396	NP_006387	O60232	SSA27_HUMAN	Sjogren syndrome/scleroderma autoantigen 1	47					cell division|mitosis		protein binding			ovary(1)|skin(1)	2						GCGCGGTTACCGCATGCTGGG	0.711													21	29	---	---	---	---	PASS
PGR	5241	broad.mit.edu	37	11	100933375	100933375	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100933375C>G	uc001pgh.2	-	4	2758	c.2015G>C	c.(2014-2016)AGA>ACA	p.R672T	PGR_uc001pgg.2_Missense_Mutation_p.R53T|PGR_uc001pgi.2_Intron|PGR_uc009yww.1_Intron|PGR_uc001pgj.2_RNA|PGR_uc009ywx.1_RNA	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	672					cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)	AAAAGTGAATCTCTGGCTTAG	0.443													24	34	---	---	---	---	PASS
RAD51AP1	10635	broad.mit.edu	37	12	4668106	4668106	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4668106T>A	uc001qmw.2	+	10	1162	c.1006T>A	c.(1006-1008)TTG>ATG	p.L336M	RAD51AP1_uc001qmu.2_Missense_Mutation_p.L319M|RAD51AP1_uc001qmv.2_Missense_Mutation_p.L282M|RAD51AP1_uc010sep.1_Missense_Mutation_p.L217M|RAD51AP1_uc010seq.1_Missense_Mutation_p.L217M|RAD51AP1_uc009zeg.2_RNA	NM_001130862	NP_001124334	Q96B01	R51A1_HUMAN	RAD51 associated protein 1 isoform a	336	Interaction with RAD51.			L->Q: Strongly decreases interaction with RAD51; when associated with A-333; A-345 and A-346.	double-strand break repair via homologous recombination		double-stranded DNA binding|protein binding|protein binding|RNA binding|single-stranded DNA binding				0			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			CCGCCTTGGCTTGTCCAGATT	0.493													37	60	---	---	---	---	PASS
GDF3	9573	broad.mit.edu	37	12	7842617	7842617	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7842617G>T	uc001qte.2	-	2	988	c.952C>A	c.(952-954)CAT>AAT	p.H318N		NM_020634	NP_065685	Q9NR23	GDF3_HUMAN	growth differentiation factor 3 precursor	318					eye development|growth|skeletal system development	extracellular space	cytokine activity|growth factor activity			skin(3)|ovary(1)|lung(1)|central_nervous_system(1)	6						TCAACGGCATGCATCAGGGCT	0.507													31	54	---	---	---	---	PASS
GDF3	9573	broad.mit.edu	37	12	7842665	7842665	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7842665T>C	uc001qte.2	-	2	940	c.904A>G	c.(904-906)ACC>GCC	p.T302A		NM_020634	NP_065685	Q9NR23	GDF3_HUMAN	growth differentiation factor 3 precursor	302					eye development|growth|skeletal system development	extracellular space	cytokine activity|growth factor activity			skin(3)|ovary(1)|lung(1)|central_nervous_system(1)	6						AGAGAGATGGTCAGTGAGAAG	0.527													30	44	---	---	---	---	PASS
KLRC1	3821	broad.mit.edu	37	12	10603588	10603588	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10603588G>T	uc001qyl.2	-	2	332	c.168C>A	c.(166-168)GAC>GAA	p.D56E	KLRC1_uc009zhm.1_Missense_Mutation_p.D56E|KLRC1_uc001qym.2_Missense_Mutation_p.D56E|KLRC1_uc001qyn.2_Missense_Mutation_p.D56E|KLRC1_uc001qyo.2_Missense_Mutation_p.D56E	NM_002259	NP_002250	P26715	NKG2A_HUMAN	killer cell lectin-like receptor subfamily C,	56	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|regulation of immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0						GATAGGTTTTGTCATTCCCTT	0.388													45	222	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49427164	49427164	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49427164C>T	uc001rta.3	-	39	11324	c.11324G>A	c.(11323-11325)GGC>GAC	p.G3775D		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	3775	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	p.Q3775R(1)		kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						AGGCATAAGGCCCTGGGGCTT	0.607			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			19	33	---	---	---	---	PASS
ATP5G2	517	broad.mit.edu	37	12	54063038	54063038	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54063038C>A	uc009znc.2	-	5	906	c.205G>T	c.(205-207)GAC>TAC	p.D69Y	ATP5G2_uc001sec.2_Missense_Mutation_p.D126Y|ATP5G2_uc001sed.2_Missense_Mutation_p.D85Y	NM_001002031	NP_001002031	Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial F0	69					ATP hydrolysis coupled proton transport|ATP synthesis coupled proton transport	integral to membrane|mitochondrial proton-transporting ATP synthase complex|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity|lipid binding			ovary(1)	1						GCTGCTGTGTCGATGTCCCTT	0.547													52	45	---	---	---	---	PASS
TAC3	6866	broad.mit.edu	37	12	57409489	57409489	+	Silent	SNP	A	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57409489A>T	uc001smp.2	-	2	253	c.93T>A	c.(91-93)GTT>GTA	p.V31V	TAC3_uc001smr.2_RNA|TAC3_uc001smq.2_RNA|TAC3_uc001smt.2_RNA|TAC3_uc001sms.2_RNA|TAC3_uc010sqy.1_RNA|TAC3_uc001smu.2_RNA|TAC3_uc001smv.2_RNA|TAC3_uc001smo.2_Silent_p.V31V	NM_013251	NP_037383	Q9UHF0	TKNK_HUMAN	tachykinin 3 precursor	31					female pregnancy|neuropeptide signaling pathway|tachykinin receptor signaling pathway	extracellular space|soluble fraction	receptor binding			ovary(1)|skin(1)	2						CCCCGCCAGGAACCACCTCCT	0.587													18	30	---	---	---	---	PASS
PPFIA2	8499	broad.mit.edu	37	12	81688619	81688619	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81688619G>A	uc001szo.1	-	24	3081	c.2920C>T	c.(2920-2922)CGA>TGA	p.R974*	PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_RNA|PPFIA2_uc010suh.1_RNA|PPFIA2_uc010sui.1_RNA|PPFIA2_uc010suj.1_RNA|PPFIA2_uc009zsi.1_RNA|PPFIA2_uc010suf.1_RNA|PPFIA2_uc009zsh.2_RNA	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2	900										ovary(3)|lung(2)|pancreas(1)	6						CTCACAGTTCGAGATGTTGGA	0.453													8	123	---	---	---	---	PASS
FGF9	2254	broad.mit.edu	37	13	22275428	22275428	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22275428C>T	uc001uog.2	+	3	1318	c.481C>T	c.(481-483)CGA>TGA	p.R161*		NM_002010	NP_002001	P31371	FGF9_HUMAN	fibroblast growth factor 9 precursor	161					cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|male gonad development|positive regulation of cell division	extracellular space	growth factor activity|heparin binding				0		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		CACTGGAAGGCGATACTATGT	0.423													6	91	---	---	---	---	PASS
PLEKHG3	26030	broad.mit.edu	37	14	65204095	65204095	+	Splice_Site	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65204095T>C	uc001xho.1	+	14	1673	c.1404_splice	c.e14+2	p.K468_splice	PLEKHG3_uc001xhn.1_Splice_Site_p.K412_splice|PLEKHG3_uc001xhp.2_Splice_Site_p.K468_splice|PLEKHG3_uc010aqh.1_Splice_Site_p.K10_splice|PLEKHG3_uc001xhq.1_5'Flank	NM_015549	NP_056364	A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G,						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		GGAATGAAGGTAAAGGCCAGT	0.607													28	36	---	---	---	---	PASS
CYP46A1	10858	broad.mit.edu	37	14	100165841	100165841	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100165841G>C	uc001ygo.2	+	4	321	c.321G>C	c.(319-321)AAG>AAC	p.K107N	CYP46A1_uc001ygn.1_Missense_Mutation_p.K69N	NM_006668	NP_006659	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46	107					bile acid biosynthetic process|cholesterol catabolic process|nervous system development|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol 24-hydroxylase activity|electron carrier activity|heme binding|steroid hydroxylase activity				0		Melanoma(154;0.0866)|all_epithelial(191;0.179)				AGGACTCCAAGATGTACCGTG	0.522													10	157	---	---	---	---	PASS
GOLGA8C	729786	broad.mit.edu	37	15	20777925	20777925	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20777925G>T	uc010tzc.1	+	18	2181	c.1166G>T	c.(1165-1167)GGA>GTA	p.G389V	uc001ytq.2_5'Flank	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E											skin(1)	1						CCTGTGCAAGGAGAGACCAGG	0.617													4	35	---	---	---	---	PASS
ADAL	161823	broad.mit.edu	37	15	43628827	43628827	+	Silent	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43628827T>C	uc010udo.1	+	6	772	c.198T>C	c.(196-198)TGT>TGC	p.C66C	ADAL_uc001zrh.2_Silent_p.C66C	NM_001159280	NP_001152752	Q6DHV7	ADAL_HUMAN	adenosine deaminase-like isoform 1	66					adenosine catabolic process|inosine biosynthetic process|purine ribonucleoside monophosphate biosynthetic process		adenosine deaminase activity|metal ion binding				0		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		GTTGCAGATGTTTCCAGATGT	0.269													5	185	---	---	---	---	PASS
MAP1A	4130	broad.mit.edu	37	15	43821515	43821515	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43821515C>A	uc001zrt.2	+	4	8311	c.7844C>A	c.(7843-7845)CCA>CAA	p.P2615Q		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2615						cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(3)|breast(3)|pancreas(2)|skin(1)	9		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AAGGCCAAGCCAGCGTCCCCT	0.662													18	27	---	---	---	---	PASS
SNX22	79856	broad.mit.edu	37	15	64446114	64446114	+	Intron	SNP	A	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64446114A>C	uc002anc.1	+						SNX22_uc002amz.1_Intron|SNX22_uc002ana.1_3'UTR|SNX22_uc002anb.1_Intron	NM_024798	NP_079074	Q96L94	SNX22_HUMAN	sorting nexin 22						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0						CCCATGGTTCATGACCCTGTT	0.612											OREG0023180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	35	55	---	---	---	---	PASS
ASB7	140460	broad.mit.edu	37	15	101169838	101169838	+	Silent	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101169838C>T	uc002bwk.2	+	5	1177	c.408C>T	c.(406-408)CTC>CTT	p.L136L	ASB7_uc002bwj.2_Silent_p.L136L	NM_198243	NP_937886	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box-containing protein 7	136	ANK 4.				intracellular signal transduction					skin(1)	1	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			TCCGGCTCCTCCTGGAGTTCA	0.532													3	55	---	---	---	---	PASS
RUNDC2A	84127	broad.mit.edu	37	16	12136831	12136831	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12136831G>T	uc002dbw.1	+	5	387	c.325G>T	c.(325-327)GCC>TCC	p.A109S		NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A	109	RUN.									ovary(1)	1						GCGCCACATCGCCTCAGACGT	0.657			T	CIITA	PMBL|Hodgkin Lymphona|								6	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	21902089	21902089	+	RNA	SNP	A	G	G	rs56214519	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902089A>G	uc002djs.3	-	2		c.156T>C			uc010vbo.1_RNA|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																		TCTTACTGTCAGCTAAAAGGC	0.373													2	2	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51173118	51173118	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51173118A>C	uc010vgs.1	-	2	3046	c.3015T>G	c.(3013-3015)ATT>ATG	p.I1005M	SALL1_uc010vgr.1_Missense_Mutation_p.I908M|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	1005	C2H2-type 6.				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TTTTGCCACAAATGTCACAAG	0.398													17	36	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51173119	51173119	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51173119A>T	uc010vgs.1	-	2	3045	c.3014T>A	c.(3013-3015)ATT>AAT	p.I1005N	SALL1_uc010vgr.1_Missense_Mutation_p.I908N|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	1005	C2H2-type 6.				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TTTGCCACAAATGTCACAAGC	0.398													17	36	---	---	---	---	PASS
CTCF	10664	broad.mit.edu	37	16	67660544	67660544	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67660544C>A	uc002etl.2	+	8	1734	c.1444C>A	c.(1444-1446)CTC>ATC	p.L482I	CTCF_uc010cek.2_Missense_Mutation_p.L154I|CTCF_uc002etm.1_5'Flank	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	482	C2H2-type 8.				chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		GCGCTATGCCCTCATCCAGCA	0.453													43	46	---	---	---	---	PASS
GEMIN4	50628	broad.mit.edu	37	17	649272	649272	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:649272G>C	uc002frs.1	-	2	2130	c.2011C>G	c.(2011-2013)CTG>GTG	p.L671V		NM_015721	NP_056536	P57678	GEMI4_HUMAN	gemin 4	671					rRNA processing|spliceosomal snRNP assembly	Cajal body|cytosol|nucleolus|small nuclear ribonucleoprotein complex|spliceosomal complex	protein binding			ovary(2)|kidney(1)|skin(1)	4		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		AAGATCCTCAGACTGAGGTCT	0.532													18	37	---	---	---	---	PASS
LHX1	3975	broad.mit.edu	37	17	35297675	35297675	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35297675A>C	uc002hnh.1	+	2	1255	c.259A>C	c.(259-261)AAC>CAC	p.N87H	LHX1_uc010cux.1_5'UTR	NM_005568	NP_005559	P48742	LHX1_HUMAN	LIM homeobox protein 1	87	LIM zinc-binding 2.				cerebellar Purkinje cell differentiation|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation|cervix development|comma-shaped body morphogenesis|dorsal/ventral pattern formation|ectoderm formation|embryonic pattern specification|embryonic retina morphogenesis in camera-type eye|embryonic viscerocranium morphogenesis|endoderm formation|forebrain regionalization|head development|motor axon guidance|negative regulation of transcription, DNA-dependent|nephric duct morphogenesis|nephron tubule epithelial cell differentiation|neuron migration|oviduct epithelium development|paramesonephric duct development|positive regulation of anterior head development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of embryonic development|positive regulation of gastrulation|positive regulation of transcription, DNA-dependent|post-embryonic development|primitive streak formation|renal vesicle morphogenesis|retina layer formation|S-shaped body morphogenesis|spinal cord association neuron differentiation|transcription from RNA polymerase II promoter|ureteric bud development|uterine epithelium development|vagina development	nucleus|protein complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(25;0.00607)				GTTTCACCTGAACTGCTTCAC	0.527													22	25	---	---	---	---	PASS
CWC25	54883	broad.mit.edu	37	17	36963045	36963045	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36963045C>T	uc002hqu.2	-	7	1028	c.875G>A	c.(874-876)AGG>AAG	p.R292K	CWC25_uc010wdv.1_Missense_Mutation_p.R229K|CWC25_uc010wdw.1_RNA|CWC25_uc010wdx.1_RNA	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49	292											0						GGACCGTGACCTTCTGCCCAG	0.577													32	46	---	---	---	---	PASS
TOP2A	7153	broad.mit.edu	37	17	38545828	38545828	+	Silent	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38545828T>C	uc002huq.2	-	35	4665	c.4539A>G	c.(4537-4539)GTA>GTG	p.V1513V		NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme	1513					apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TCTTTGCCCGTACAGATTTTG	0.413													3	92	---	---	---	---	PASS
PCTP	58488	broad.mit.edu	37	17	53853436	53853436	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53853436G>C	uc002iul.3	+	6	729	c.620G>C	c.(619-621)TGT>TCT	p.C207S	PCTP_uc002ium.3_Missense_Mutation_p.C135S|PCTP_uc010dcg.2_3'UTR|PCTP_uc010dch.2_RNA	NM_021213	NP_067036	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein isoform 1	207	START.					cytosol	phosphatidylcholine binding|phosphatidylcholine transmembrane transporter activity			lung(1)	1			BRCA - Breast invasive adenocarcinoma(1;0.00207)			GCAAGAGCCTGTCAGAACTAC	0.438													40	52	---	---	---	---	PASS
APOH	350	broad.mit.edu	37	17	64213023	64213023	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64213023T>G	uc002jfn.3	-	6	726	c.667A>C	c.(667-669)ACA>CCA	p.T223P		NM_000042	NP_000033	P02749	APOH_HUMAN	apolipoprotein H precursor	223	Sushi 4.				blood coagulation, intrinsic pathway|negative regulation of angiogenesis|negative regulation of blood coagulation|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of myeloid cell apoptosis|negative regulation of smooth muscle cell apoptosis|plasminogen activation|positive regulation of lipoprotein lipase activity|triglyceride metabolic process|triglyceride transport	cell surface|chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	eukaryotic cell surface binding|glycoprotein binding|heparin binding|lipoprotein lipase activator activity|phospholipid binding				0			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TAATAAAGTGTTGGTTTTGCA	0.373													42	147	---	---	---	---	PASS
MRO	83876	broad.mit.edu	37	18	48325675	48325675	+	3'UTR	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48325675T>C	uc002lew.3	-	8					MRO_uc010xdn.1_3'UTR|MRO_uc010dpa.2_3'UTR|MRO_uc010dpb.2_3'UTR|MRO_uc010dpc.2_3'UTR|MRO_uc002lex.3_3'UTR	NM_031939	NP_114145	Q9BYG7	MSTRO_HUMAN	maestro isoform a							nucleolus	binding				0		Colorectal(6;0.0596)		Colorectal(21;0.082)		AGCAATGCACTCATACAGAAC	0.468													4	91	---	---	---	---	PASS
MRO	83876	broad.mit.edu	37	18	48345981	48345981	+	5'UTR	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48345981T>C	uc002lew.3	-	2					MRO_uc010xdn.1_5'UTR|MRO_uc010dpa.2_Silent_p.S37S|MRO_uc010dpb.2_Silent_p.S37S|MRO_uc010dpc.2_Intron|MRO_uc002lex.3_5'UTR	NM_031939	NP_114145	Q9BYG7	MSTRO_HUMAN	maestro isoform a							nucleolus	binding				0		Colorectal(6;0.0596)		Colorectal(21;0.082)		TGCCACGTGATGAACCGGAGC	0.602											OREG0024982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	36	---	---	---	---	PASS
DCC	1630	broad.mit.edu	37	18	49867049	49867049	+	5'UTR	SNP	C	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49867049C>A	uc002lfe.1	+	1						NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		gaggaggaAGCCGAAGGGGCT	0.358													7	67	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22154068	22154068	+	Silent	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22154068T>C	uc002nqp.2	-	6	3533	c.3384A>G	c.(3382-3384)GAA>GAG	p.E1128E	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				TGCCACATTCTTCACATTTGT	0.383													2	0	---	---	---	---	PASS
PAK4	10298	broad.mit.edu	37	19	39668357	39668357	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39668357G>A	uc002okj.1	+	10	1989	c.1528G>A	c.(1528-1530)GAC>AAC	p.D510N	PAK4_uc002okl.1_Missense_Mutation_p.D510N|PAK4_uc002okn.1_Missense_Mutation_p.D510N|PAK4_uc002okm.1_Missense_Mutation_p.D357N|PAK4_uc002oko.1_Missense_Mutation_p.D357N|PAK4_uc002okp.1_Missense_Mutation_p.D420N	NM_001014831	NP_001014831	O96013	PAK4_HUMAN	p21-activated kinase 4 isoform 1	510	Protein kinase.				cellular component movement|signal transduction	Golgi apparatus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			TGAGATGGTGGACGGAGAGCC	0.602													50	82	---	---	---	---	PASS
ZNF841	284371	broad.mit.edu	37	19	52568835	52568835	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52568835C>T	uc002pyl.1	-	5	2504	c.1952G>A	c.(1951-1953)TGT>TAT	p.C651Y	ZNF841_uc010ydh.1_Missense_Mutation_p.C767Y|ZNF841_uc010epk.1_Intron	NM_001136499	NP_001129971	Q6ZN19	ZN841_HUMAN	zinc finger protein 841	651	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACATTCATTACATTTGTAAGG	0.428													12	25	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56539267	56539267	+	Silent	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56539267C>T	uc002qmj.2	+	7	1668	c.1668C>T	c.(1666-1668)CTC>CTT	p.L556L	NLRP5_uc002qmi.2_Silent_p.L537L	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	556	NACHT.					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)		TTCAAGGACTCGGGGAGTCTG	0.532													4	79	---	---	---	---	PASS
LIME1	54923	broad.mit.edu	37	20	62370185	62370185	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62370185A>G	uc002ygp.3	+	6	924	c.820A>G	c.(820-822)ACG>GCG	p.T274A	ZGPAT_uc002ygn.3_RNA|LIME1_uc011abi.1_3'UTR|SLC2A4RG_uc002ygq.2_5'Flank|SLC2A4RG_uc002ygr.2_5'Flank|SLC2A4RG_uc011abj.1_5'Flank|SLC2A4RG_uc002ygs.2_5'Flank	NM_017806	NP_060276	Q9H400	LIME1_HUMAN	Lck interacting transmembrane adaptor 1	274	Cytoplasmic (Potential).					integral to membrane|plasma membrane					0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CGGGGCTGGGACGCCCCCTGC	0.682													5	9	---	---	---	---	PASS
ADORA2A	135	broad.mit.edu	37	22	24836844	24836844	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24836844A>G	uc002zzx.2	+	5	1389	c.626A>G	c.(625-627)AAG>AGG	p.K209R	ADORA2A_uc002zzy.3_Missense_Mutation_p.K209R|ADORA2A_uc011ajs.1_Missense_Mutation_p.K70R|ADORA2A_uc010gup.2_Missense_Mutation_p.K209R|ADORA2A_uc010guq.2_Missense_Mutation_p.K209R|ADORA2A_uc003aab.2_Missense_Mutation_p.K209R|ADORA2A_uc003aac.2_Missense_Mutation_p.K70R|C22orf45_uc003aad.1_Intron	NM_000675	NP_000666	P29274	AA2AR_HUMAN	adenosine A2a receptor	209	Cytoplasmic.				apoptosis|blood coagulation|cAMP biosynthetic process|cellular defense response|inflammatory response|nerve growth factor receptor signaling pathway|phagocytosis|sensory perception	integral to plasma membrane|membrane fraction	enzyme binding				0	Colorectal(2;0.196)				Caffeine(DB00201)|Defibrotide(DB04932)|Pegademase bovine(DB00061)|Theophylline(DB00277)	CGACAGCTGAAGCAGATGGAG	0.592													4	59	---	---	---	---	PASS
TUBGCP6	85378	broad.mit.edu	37	22	50657163	50657163	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50657163T>C	uc003bkb.1	-	21	5302	c.4790A>G	c.(4789-4791)GAT>GGT	p.D1597G	TUBGCP6_uc003bka.1_Missense_Mutation_p.D684G|TUBGCP6_uc010har.1_Missense_Mutation_p.D1589G|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1597					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GCTCAGCACATCCGGGGCGTT	0.677													32	52	---	---	---	---	PASS
P2RY8	286530	broad.mit.edu	37	X	1585028	1585028	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1585028C>A	uc004cpz.2	-	2	672	c.424G>T	c.(424-426)GCC>TCC	p.A142S		NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8	142	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GCACACGCGGCCACCGCGTAA	0.682			T	CRLF2	B-ALL|Downs associated ALL								8	51	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34961299	34961299	+	Silent	SNP	C	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34961299C>T	uc004ddi.1	+	1	369	c.351C>T	c.(349-351)TTC>TTT	p.F117F		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	117										ovary(3)|breast(1)	4						GGAAGGCGTTCGTAGAGGAAG	0.542													3	87	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76890185	76890185	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76890185A>C	uc004ecp.3	-	17	4941	c.4709T>G	c.(4708-4710)TTT>TGT	p.F1570C	ATRX_uc004ecq.3_Missense_Mutation_p.F1532C|ATRX_uc004eco.3_Missense_Mutation_p.F1355C	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1570					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATCCCACATAAACTGAACACC	0.353			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						42	87	---	---	---	---	PASS
SLC6A8	6535	broad.mit.edu	37	X	152956789	152956789	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152956789T>A	uc004fib.3	+	3	703	c.425T>A	c.(424-426)TTC>TAC	p.F142Y	SLC6A8_uc004fic.3_Missense_Mutation_p.F142Y|SLC6A8_uc011myx.1_Missense_Mutation_p.F27Y|SLC6A8_uc010nuj.2_5'Flank|SLC6A8_uc010nui.1_Missense_Mutation_p.F27Y	NM_005629	NP_005620	P48029	SC6A8_HUMAN	solute carrier family 6 member 8 isoform 1	142	Helical; (Potential).				creatine metabolic process|muscle contraction	integral to plasma membrane	creatine:sodium symporter activity|neurotransmitter:sodium symporter activity			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	GTGATCGTCTTCTACTGCAAC	0.597													25	92	---	---	---	---	PASS
DVL1	1855	broad.mit.edu	37	1	1276931	1276932	+	Intron	DEL	CA	-	-	rs75244934		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1276931_1276932delCA	uc001aer.3	-						DVL1_uc002quu.2_5'Flank|DVL1_uc009vka.2_5'Flank|DVL1_uc001aeu.1_Intron	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1						canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		cacacacatgcacacacacgca	0.386													4	3	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21268983	21268983	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21268983delT	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GTCTCTTTTCTTTTTTTACTT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	80961985	80961986	+	IGR	DEL	CG	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80961985_80961986delCG								None (None upstream) : LPHN2 (809859 downstream)																							GCTTTGCGCACGGACCAGAAAA	0.490													4	2	---	---	---	---	
CTBS	1486	broad.mit.edu	37	1	85039999	85040007	+	In_Frame_Del	DEL	GCAGCGCCA	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85039999_85040007delGCAGCGCCA	uc001dka.2	-	1	157_165	c.92_100delTGGCGCTGC	c.(91-102)CTGGCGCTGCGG>CGG	p.LAL31del	CTBS_uc001dkc.2_5'UTR|CTBS_uc001dkd.2_5'UTR|CTBS_uc001dkb.2_5'UTR	NM_004388	NP_004379	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl- precursor	31_33						lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		GCCGCGAGCCgcagcgccagcagcgccag	0.589													4	7	---	---	---	---	
SORT1	6272	broad.mit.edu	37	1	109898267	109898268	+	Intron	INS	-	C	C	rs12027996	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109898267_109898268insC	uc001dxm.1	-						SORT1_uc010ovi.1_Intron|SORT1_uc009wfb.2_Intron	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein						endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		CATTCCACCCGCCCCCCCCCCC	0.564													4	3	---	---	---	---	
DENND2C	163259	broad.mit.edu	37	1	115165425	115165425	+	Intron	DEL	A	-	-	rs78541550		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115165425delA	uc001efd.1	-						DENND2C_uc001eez.2_Intron|DENND2C_uc001efc.1_Intron	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AACAACAACCAAAAAAAAAAA	0.179													5	5	---	---	---	---	
SPAG17	200162	broad.mit.edu	37	1	118658193	118658193	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118658193delA	uc001ehk.2	-							NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTGCTGGCTGAAAAAAAAAAG	0.333													5	3	---	---	---	---	
S100A7A	338324	broad.mit.edu	37	1	153387649	153387650	+	5'Flank	DEL	TG	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153387649_153387650delTG	uc001fbt.1	+							NM_176823	NP_789793	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7-like 1							cytoplasm	calcium ion binding			skin(1)	1	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			tgtgtgtgtttgtgtgtgtgtg	0.178													4	2	---	---	---	---	
CENPL	91687	broad.mit.edu	37	1	173772753	173772753	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173772753delA	uc001gje.3	-						CENPL_uc009wwg.2_Intron|CENPL_uc001gjg.3_Intron|CENPL_uc001gjf.3_Intron	NM_033319	NP_201576	Q8N0S6	CENPL_HUMAN	centromere protein L isoform 2						mitotic prometaphase	chromosome, centromeric region|cytosol|nucleus					0						TAATACTTGCAAAAAAAAACA	0.249													4	2	---	---	---	---	
CDK18	5129	broad.mit.edu	37	1	205494569	205494569	+	Intron	DEL	T	-	-	rs80154131		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205494569delT	uc001hcr.2	+						CDK18_uc010pri.1_Intron|CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron|CDK18_uc001hcs.2_Intron|CDK18_uc009xbm.1_Intron	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a								ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2						GAATCCAGTCTTTTTTTTTTC	0.328													5	4	---	---	---	---	
MTR	4548	broad.mit.edu	37	1	237057959	237057959	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237057959delT	uc001hyi.3	+						MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine						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)	AACCAGTGTCTTTTTTTTTTT	0.463													4	3	---	---	---	---	
C1orf100	200159	broad.mit.edu	37	1	244527742	244527743	+	Intron	INS	-	T	T			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244527742_244527743insT	uc001iah.2	+						C1orf100_uc001iai.2_Intron	NM_001012970	NP_001012988	Q5SVJ3	CA100_HUMAN	hypothetical protein LOC200159												0	all_cancers(71;3.94e-05)|all_epithelial(71;0.000138)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|all_lung(81;0.0736)|Ovarian(71;0.0761)|Lung NSC(105;0.103)		all cancers(7;8.19e-08)|GBM - Glioblastoma multiforme(7;2.05e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.000984)			tacttatttaatttttttttaC	0.168													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72968233	72968233	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72968233delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						actccgcctcaaaaaaaaaaG	0.154													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133066592	133066592	+	Intron	DEL	G	-	-	rs78544491		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133066592delG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AAAAGGAAAAGAATGTGCAGG	0.433													3	3	---	---	---	---	
ACVR2A	92	broad.mit.edu	37	2	148602536	148602536	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148602536delT	uc002twg.2	+						ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_5'Flank	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor						activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		cgttgtgctcttttttttctt	0.303													4	2	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159992543	159992562	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGC	-	-	rs70994268	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159992543_159992562delGTGTGTGTGTGTGTGTGTGC	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uah.1_5'Flank	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						gtgtgtgtgtgtgtgtgtgtgtgtgtgtgCGCGCGCGCGC	0.400													6	3	---	---	---	---	
INO80D	54891	broad.mit.edu	37	2	206874082	206874083	+	Intron	INS	-	A	A	rs144079921	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206874082_206874083insA	uc002vaz.3	-							NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						AAGTCAGTTTCGCGTCTGTTCT	0.203													3	3	---	---	---	---	
UQCRC1	7384	broad.mit.edu	37	3	48640912	48640912	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48640912delC	uc003cub.1	-						UQCRC1_uc003cua.1_Intron|UQCRC1_uc003cuc.1_Intron|UQCRC1_uc003cud.1_Intron	NM_003365	NP_003356	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I						aerobic respiration|proteolysis		metalloendopeptidase activity|ubiquinol-cytochrome-c reductase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	Atovaquone(DB01117)	GGTGAAAGGTCCCCTATGGTG	0.587													9	17	---	---	---	---	
BAP1	8314	broad.mit.edu	37	3	52436345	52436345	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52436345delG	uc003ddx.2	-	17	2264	c.2149delC	c.(2149-2151)CGGfs	p.R717fs	BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_RNA	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	717	Nuclear localization signal.|Interaction with BRCA1.			RRKRSR->AAAAAA: Abolishes nuclear localization.	monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CGTTTCCGCCGGTCAGGCTTC	0.662			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								10	14	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52712605	52712605	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52712605delC	uc003des.2	-	2	159	c.147delG	c.(145-147)GTGfs	p.V49fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.V49fs|PBRM1_uc003der.2_Frame_Shift_Del_p.V49fs|PBRM1_uc003det.2_Frame_Shift_Del_p.V49fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.V49fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.V49fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.V49fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.V49fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.V49fs|PBRM1_uc003dfb.1_5'UTR	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	49			V -> L (found in a lung cancer cell line).		chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTTCATGGCACACGGCAATCT	0.393			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								15	34	---	---	---	---	
DNAH12	201625	broad.mit.edu	37	3	57400934	57400934	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57400934delA	uc003dit.2	-							NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						TCTCAGGCTTAAAAAAAAAAC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90306703	90306703	+	IGR	DEL	A	-	-	rs79990547		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90306703delA								EPHA3 (775421 upstream) : None (None downstream)																							TCGAACTGAGAAAAAAACGCA	0.308													4	2	---	---	---	---	
MYH15	22989	broad.mit.edu	37	3	108195085	108195085	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108195085delA	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CATCACAAGTAAAAACATTTG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	125903901	125903901	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125903901delA	uc003eiq.2	+											Homo sapiens cDNA FLJ40189 fis, clone TESTI2018974.																		TTCCCCCTTTAAAGGGCCTGC	0.493													4	2	---	---	---	---	
ZNF639	51193	broad.mit.edu	37	3	179052260	179052260	+	3'UTR	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179052260delT	uc003fjq.1	+	6					ZNF639_uc003fjr.1_3'UTR	NM_016331	NP_057415	Q9UID6	ZN639_HUMAN	zinc finger protein 639						initiation of viral infection|negative regulation by host of viral transcription|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of cell growth|positive regulation of transcription, DNA-dependent	nucleus	protein self-association|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding				0	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			AAATTCATCCTTTTTTTGGAG	0.274													4	2	---	---	---	---	
CCDC39	339829	broad.mit.edu	37	3	180381458	180381458	+	Intron	DEL	A	-	-	rs113125291		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180381458delA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			acttcatctcaaaaaaaaaaa	0.139													2	4	---	---	---	---	
MUC20	200958	broad.mit.edu	37	3	195447642	195447642	+	5'Flank	DEL	G	-	-	rs11185521		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195447642delG	uc010hzo.2	+							NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		aaaaaaaaaagaaGCTAGTGA	0.254													3	8	---	---	---	---	
TFRC	7037	broad.mit.edu	37	3	195792148	195792148	+	Intron	DEL	G	-	-	rs79124655		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195792148delG	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		aaaaaaaaaagaaaCTAACAC	0.204			T	BCL6	NHL								4	2	---	---	---	---	
KIAA1109	84162	broad.mit.edu	37	4	123108773	123108773	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123108773delT	uc003ieh.2	+						KIAA1109_uc003iei.1_Intron	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TTTTGTGGAGTTTTTTTTAGT	0.224													4	2	---	---	---	---	
DCLK2	166614	broad.mit.edu	37	4	151160754	151160754	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151160754delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					ccgtgtcttcaaaaaaaaaaa	0.169													4	5	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112824048	112824049	+	In_Frame_Ins	INS	-	GCC	GCC			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112824048_112824049insGCC	uc003kql.3	-	1	479_480	c.63_64insGGC	c.(61-66)insGGC	p.21_22insG		NM_001085377	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ctgctgccgctgccgccgccgc	0.391													5	3	---	---	---	---	
P4HA2	8974	broad.mit.edu	37	5	131543137	131543138	+	Intron	INS	-	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131543137_131543138insA	uc003kwh.2	-						P4HA2_uc003kwg.2_Intron|P4HA2_uc003kwi.2_Intron|P4HA2_uc003kwk.2_Intron|P4HA2_uc003kwl.2_Intron|P4HA2_uc003kwj.2_Intron	NM_004199	NP_004190	O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha II subunit isoform 1							endoplasmic reticulum lumen	electron carrier activity|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity|protein binding				0		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	AACTGACACACCAGTGTAGACC	0.356													3	4	---	---	---	---	
PCDHGA12	26025	broad.mit.edu	37	5	140812776	140812776	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140812776delT	uc003lkt.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc011dba.1_Frame_Shift_Del_p.L817fs	NM_003735	NP_003726	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCttctttcttttttttttt	0.179													9	5	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167671782	167671782	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167671782delT	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TTCCGGCttcttttttttttt	0.249													9	4	---	---	---	---	
MAPK13	5603	broad.mit.edu	37	6	36098497	36098498	+	Intron	INS	-	GGGGGGC	GGGGGGC	rs146539855	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36098497_36098498insGGGGGGC	uc003ols.2	+						MAPK13_uc003olt.2_Intron	NM_002754	NP_002745	O15264	MK13_HUMAN	mitogen-activated protein kinase 13						cell cycle|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|positive regulation of interleukin-6 production|Ras protein signal transduction|response to stress		ATP binding|MAP kinase activity|protein binding			breast(2)|central_nervous_system(1)	3						CCTgggccgctggggggcgggg	0.599													2	7	---	---	---	---	
SYTL3	94120	broad.mit.edu	37	6	159146359	159146360	+	Intron	DEL	GT	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159146359_159146360delGT	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		gtgtgtgtgcgtgtgtgtgtgt	0.386													7	5	---	---	---	---	
ACAT2	39	broad.mit.edu	37	6	160187987	160187987	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160187987delT	uc010kjy.2	+						ACAT2_uc011efw.1_Intron	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2							mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CACTGTGACATTTTGTCTTTC	0.483													74	37	---	---	---	---	
PSMB1	5689	broad.mit.edu	37	6	170852899	170852899	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170852899delA	uc011ehe.1	-						PSMB1_uc003qxq.2_Intron|PSMB1_uc003qxr.2_Intron	NM_002793	NP_002784	P20618	PSB1_HUMAN	proteasome beta 1 subunit precursor						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cell junction|cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)	TAAAGTGAATAAATAAATGCA	0.353													19	17	---	---	---	---	
CYTH3	9265	broad.mit.edu	37	7	6229955	6229956	+	Intron	INS	-	TTGTTA	TTGTTA	rs138333025	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6229955_6229956insTTGTTA	uc003spt.2	-							NM_004227	NP_004218	O43739	CYH3_HUMAN	cytohesin 3						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|membrane fraction|plasma membrane	1-phosphatidylinositol binding|ARF guanyl-nucleotide exchange factor activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity				0						CATCttttttttttgttatttt	0.282													5	5	---	---	---	---	
ZNF12	7559	broad.mit.edu	37	7	6731954	6731954	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6731954delA	uc003sqt.1	-	5	1173	c.619delT	c.(619-621)TATfs	p.Y207fs	ZNF12_uc011jxa.1_Frame_Shift_Del_p.Y45fs|ZNF12_uc003sqs.1_Frame_Shift_Del_p.Y169fs	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	207					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		ATTTTCTGATAAAGACTTTCT	0.338													19	19	---	---	---	---	
PMS2CL	441194	broad.mit.edu	37	7	6763490	6763491	+	Intron	DEL	CT	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6763490_6763491delCT	uc003squ.2	+											Homo sapiens PMS2CL mRNA for PMS2-C terminal -like, complete cds.												0						aaacagtttgctctctctctcc	0.000													4	2	---	---	---	---	
TARP	445347	broad.mit.edu	37	7	38316139	38316140	+	Intron	INS	-	A	A			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38316139_38316140insA	uc003tge.1	-						uc003tfz.1_Intron|TARP_uc003tgb.2_5'Flank|TARP_uc003tgc.1_5'Flank|TARP_uc003tgd.1_5'Flank|TARP_uc010kxi.1_Intron|TARP_uc003tgf.1_Intron|TARP_uc003tgj.1_Intron|TARP_uc003tgh.1_Intron|TARP_uc003tgi.1_Intron|TARP_uc003tgg.1_Intron			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.												0						AAGGGAAATGGAAAAAAAAAAG	0.337													4	2	---	---	---	---	
PTPRZ1	5803	broad.mit.edu	37	7	121513383	121513384	+	5'UTR	DEL	CA	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121513383_121513384delCA	uc003vjy.2	+	1					PTPRZ1_uc003vjz.2_5'UTR	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						ctctctctctcacacacacaca	0.243													5	3	---	---	---	---	
BRAF	673	broad.mit.edu	37	7	140476994	140476994	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140476994delT	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)	CAGAAAAAGCTTTTTTTTTTT	0.199		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				7	4	---	---	---	---	
ZNF212	7988	broad.mit.edu	37	7	148936762	148936763	+	5'Flank	INS	-	CGG	CGG	rs141414617	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148936762_148936763insCGG	uc003wfp.2	+							NM_012256	NP_036388	Q9UDV6	ZN212_HUMAN	zinc finger protein 212						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			TGGCATCAACACGGCGGCGGCG	0.703											OREG0018424	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	17	---	---	---	---	
KCNH2	3757	broad.mit.edu	37	7	150649386	150649387	+	Intron	INS	-	TCTTTCTC	TCTTTCTC	rs142675575	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150649386_150649387insTCTTTCTC	uc003wic.2	-						KCNH2_uc003wib.2_Intron|KCNH2_uc011kux.1_Intron|KCNH2_uc003wid.2_Intron|KCNH2_uc003wie.2_Intron	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,						blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			skin(3)|ovary(1)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)	ctctcccactgtctttctctct	0.465													10	5	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48848624	48848624	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48848624delA	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				TGATTGCCTTAAAAAAAAAAC	0.303								NHEJ					3	4	---	---	---	---	
SLC25A32	81034	broad.mit.edu	37	8	104426905	104426905	+	Intron	DEL	A	-	-	rs10709873		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104426905delA	uc003yll.2	-						SLC25A32_uc011lhr.1_Intron|DCAF13_uc003ylm.1_5'Flank|DCAF13_uc003yln.2_5'Flank|DCAF13_uc003ylo.2_5'Flank	NM_030780	NP_110407	Q9H2D1	MFTC_HUMAN	solute carrier family 25, member 32						folic acid metabolic process|mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding|folic acid transporter activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	CGCGGACAGCAACGCTCCCTT	0.602													9	6	---	---	---	---	
SLC25A32	81034	broad.mit.edu	37	8	104426908	104426908	+	Intron	DEL	G	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104426908delG	uc003yll.2	-						SLC25A32_uc011lhr.1_Intron|DCAF13_uc003ylm.1_5'Flank|DCAF13_uc003yln.2_5'Flank|DCAF13_uc003ylo.2_5'Flank	NM_030780	NP_110407	Q9H2D1	MFTC_HUMAN	solute carrier family 25, member 32						folic acid metabolic process|mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding|folic acid transporter activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	GGACAGCAACGCTCCCTTCAA	0.592													10	6	---	---	---	---	
ACO1	48	broad.mit.edu	37	9	32423511	32423513	+	Intron	DEL	ATT	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32423511_32423513delATT	uc003zqw.3	+						ACO1_uc010mjh.1_Intron|ACO1_uc003zqx.3_Intron|ACO1_uc003zqy.3_Intron	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1						citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		CTAGTAGGAAATTAGTCACTGCC	0.409													18	13	---	---	---	---	
CNTNAP3	79937	broad.mit.edu	37	9	39154059	39154059	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39154059delA	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron|CNTNAP3_uc011lqs.1_Intron|CNTNAP3_uc004abl.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CATTAAATAGAAAAAAAAAAA	0.428													2	4	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124074857delA	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						GAATTTGAGGAAAAAAAAAAA	0.333													5	4	---	---	---	---	
NCS1	23413	broad.mit.edu	37	9	132985664	132985664	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132985664delT	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101	P62166	NCS1_HUMAN	frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0						gtccttagccttttttttttg	0.214													4	3	---	---	---	---	
ABL1	25	broad.mit.edu	37	9	133711046	133711050	+	Intron	DEL	CTCTT	-	-	rs113276697		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133711046_133711050delCTCTT	uc004bzw.2	+						ABL1_uc004bzv.2_Intron	NM_005157	NP_005148	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	tctttcttccctcttctcttctctt	0.312			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								6	5	---	---	---	---	
INPP5E	56623	broad.mit.edu	37	9	139325759	139325760	+	Intron	INS	-	C	C	rs67885688		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139325759_139325760insC	uc004cho.2	-						INPP5E_uc010nbm.2_Intron	NM_019892	NP_063945	Q9NRR6	INP5E_HUMAN	inositol polyphosphate-5-phosphatase E							cilium axoneme|cytoskeleton|Golgi cisterna membrane	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity			skin(1)	1		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		ctccacgcccgccccccaggcc	0.000													2	5	---	---	---	---	
PAPSS2	9060	broad.mit.edu	37	10	89419638	89419639	+	5'UTR	INS	-	GCT	GCT			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89419638_89419639insGCT	uc001kex.2	+	1					PAPSS2_uc001kew.2_5'UTR|PAPSS2_uc009xtg.1_5'Flank	NM_004670	NP_004661	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		GTCCGGCAgccgctgctgctgc	0.530													8	5	---	---	---	---	
EXOSC1	51013	broad.mit.edu	37	10	99197683	99197683	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99197683delT	uc001kni.2	-						EXOSC1_uc009xvp.1_Intron	NM_016046	NP_057130	Q9Y3B2	EXOS1_HUMAN	exosomal core protein CSL4						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	protein binding|RNA binding				0		Renal(717;0.000147)|Colorectal(252;0.00205)|Ovarian(717;0.00965)		all cancers(201;8.29e-42)|Epithelial(162;5.7e-33)|BRCA - Breast invasive adenocarcinoma(275;0.000315)|Kidney(138;0.000832)|KIRC - Kidney renal clear cell carcinoma(50;0.00269)|STAD - Stomach adenocarcinoma(243;0.202)		CAAATGAAAAttttttttttt	0.159													4	2	---	---	---	---	
COX15	1355	broad.mit.edu	37	10	101487560	101487560	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101487560delT	uc001kqb.3	-						COX15_uc001kqc.3_Intron|COX15_uc010qpj.1_Intron	NM_078470	NP_510870	Q7KZN9	COX15_HUMAN	COX15 homolog isoform 1						heme a biosynthetic process|respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		TCCCCAATTCTTTTTTTTTTC	0.358													2	4	---	---	---	---	
HIF1AN	55662	broad.mit.edu	37	10	102305592	102305592	+	Intron	DEL	T	-	-	rs11817143	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102305592delT	uc001krj.3	+							NM_017902	NP_060372	Q9NWT6	HIF1N_HUMAN	hypoxia-inducible factor 1, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|protein binding				0		Colorectal(252;0.234)		Epithelial(162;6.75e-10)|all cancers(201;4.88e-08)		TAAGGCATCGTTTTTTTTTTG	0.303													6	3	---	---	---	---	
CUZD1	50624	broad.mit.edu	37	10	124596659	124596659	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124596659delT	uc001lgq.2	-						CUZD1_uc001lgp.2_Intron|CUZD1_uc009yad.2_Intron|CUZD1_uc009yaf.2_Intron|CUZD1_uc001lgr.2_Intron|CUZD1_uc010qty.1_Intron|CUZD1_uc009yae.2_Intron|CUZD1_uc001lgs.2_Intron|CUZD1_uc010qtz.1_Intron	NM_022034	NP_071317	Q86UP6	CUZD1_HUMAN	CUB and zona pellucida-like domains 1 precursor						cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		TGATTATGGATTTTTTTTTTC	0.368													7	4	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126714531	126714532	+	Intron	DEL	GT	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126714531_126714532delGT	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron|CTBP2_uc001lie.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TTGTTTGGTGGTGTGTGTGTGT	0.574													4	2	---	---	---	---	
EBF3	253738	broad.mit.edu	37	10	131760659	131760659	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131760659delT	uc001lki.1	-						EBF3_uc010qur.1_3'UTR	NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		TCTCGCTTAATTTTTTTTTTC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134290812	134290812	+	IGR	DEL	G	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134290812delG								C10orf91 (28988 upstream) : INPP5A (60541 downstream)																							ACTCATCCCAGGGCCCTCCGC	0.647													4	2	---	---	---	---	
INPP5A	3632	broad.mit.edu	37	10	134464159	134464161	+	Intron	DEL	TGG	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134464159_134464161delTGG	uc001llp.2	+						INPP5A_uc001llo.1_Intron|INPP5A_uc001llq.2_Intron	NM_005539	NP_005530	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		GCAGCCTGCTTGGTGGTCTGCTC	0.645													8	6	---	---	---	---	
SLC22A18	5002	broad.mit.edu	37	11	2940338	2940360	+	Intron	DEL	GGCACTTTCCACACCAGGGATAC	-	-	rs143592360		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2940338_2940360delGGCACTTTCCACACCAGGGATAC	uc001lwx.2	+						SLC22A18_uc001lwy.2_Intron|SLC22A18_uc001lwz.2_Intron	NM_183233	NP_899056	Q96BI1	S22AI_HUMAN	tumor suppressing subtransferable candidate 5						excretion|organic cation transport	apical plasma membrane|cytoplasmic part|integral to membrane|nuclear envelope	drug:hydrogen antiporter activity|symporter activity|ubiquitin protein ligase binding			central_nervous_system(2)|ovary(1)	3		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		ccacacgagaggcactttccacaccagggatacggcagaatcc	0.157													4	5	---	---	---	---	
HPS5	11234	broad.mit.edu	37	11	18314724	18314724	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18314724delT	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3						ttcttttttcttttttttttg	0.030									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
SCGB2A1	4246	broad.mit.edu	37	11	61978225	61978225	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61978225delC	uc001nta.2	+							NM_002407	NP_002398	O75556	SG2A1_HUMAN	secretoglobin, family 2A, member 1 precursor							extracellular region	androgen binding				0						TTTGCCACTTCACATTGAGAA	0.418													3	3	---	---	---	---	
BTG4	54766	broad.mit.edu	37	11	111384419	111384419	+	5'Flank	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111384419delT	uc001plj.2	-						BTG4_uc001plk.2_5'Flank|uc001pll.2_RNA|C11orf88_uc009yyd.2_5'Flank|C11orf88_uc001pln.3_5'Flank|C11orf88_uc001plo.1_5'Flank	NM_017589	NP_060059	Q9NY30	BTG4_HUMAN	B-cell translocation gene 4						cell cycle arrest|negative regulation of cell proliferation|neuron differentiation						0		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)		TTTTGTTTTGTTTTTTTTTCA	0.294													4	2	---	---	---	---	
USP2	9099	broad.mit.edu	37	11	119231138	119231138	+	Intron	DEL	T	-	-	rs11339666		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119231138delT	uc001pwm.3	-						USP2_uc001pwl.3_Intron|USP2_uc001pwn.3_Intron	NM_004205	NP_004196	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2 isoform a						cell cycle|muscle organ development|negative regulation of transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|protein deubiquitination|protein stabilization|ubiquitin-dependent protein catabolic process	nucleus|perinuclear region of cytoplasm	cyclin binding|cysteine-type endopeptidase activity|metal ion binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity			ovary(2)|urinary_tract(1)|skin(1)	4		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		ttttcttttcttttttttttt	0.174													4	3	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81741691	81741691	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81741691delT	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						TTTTTTCATCTTTTTTTTTTC	0.299													4	2	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100774908	100774915	+	Intron	DEL	CATCTCAG	-	-	rs68046331		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100774908_100774915delCATCTCAG	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						TAGCTCCTCCcatctcagcatctcagca	0.221													9	6	---	---	---	---	
STAB2	55576	broad.mit.edu	37	12	104086376	104086377	+	Intron	DEL	TG	-	-	rs36051361		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104086376_104086377delTG	uc001tjw.2	+							NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						tctctgtctctgtgtgtgtgtg	0.084													9	4	---	---	---	---	
TMEM120B	144404	broad.mit.edu	37	12	122181462	122181462	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122181462delA	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294	A0PK00	T120B_HUMAN	transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		agactctctcaaaaaaaaaaa	0.224													6	4	---	---	---	---	
TMED2	10959	broad.mit.edu	37	12	124069112	124069114	+	5'UTR	DEL	GGC	-	-	rs63022462		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124069112_124069114delGGC	uc001ufg.2	+	1						NM_006815	NP_006806	Q15363	TMED2_HUMAN	coated vesicle membrane protein precursor						protein transport|vesicle-mediated transport	COPI coated vesicle membrane|ER-Golgi intermediate compartment|integral to membrane|microsome|zymogen granule membrane	protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		aaggcagcggggcggcggcggcg	0.512													10	5	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131490750	131490750	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131490750delA	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		AAGCGTTTTGAAGGCCACTTG	0.607													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	49034111	49034111	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49034111delC	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ttctctctttctttctttttt	0.020		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			4	2	---	---	---	---	
CLN5	1203	broad.mit.edu	37	13	77574532	77574533	+	Intron	INS	-	G	G			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77574532_77574533insG	uc001vkc.2	+							NM_006493	NP_006484	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5						brain development|cell death|lysosomal lumen acidification|neuron maturation|protein catabolic process	endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		aaaaaaaaaaaaaaaaaTTAAC	0.163													4	2	---	---	---	---	
ERCC5	2073	broad.mit.edu	37	13	103508647	103508648	+	Intron	INS	-	TA	TA	rs148306316	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103508647_103508648insTA	uc001vpw.2	+						ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjb.1_Intron|ERCC5_uc010tjc.1_Intron|ERCC5_uc010tjd.1_Intron	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein						negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					ctacacacgtgtatatatatat	0.223			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				2	4	---	---	---	---	
SPTLC2	9517	broad.mit.edu	37	14	78021964	78021964	+	Intron	DEL	T	-	-	rs151267420	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78021964delT	uc001xub.2	-							NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	TTACTGCttcttttttttttc	0.134													5	4	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100126463	100126482	+	Intron	DEL	CACGCCAGCCCTGCTGTGGG	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100126463_100126482delCACGCCAGCCCTGCTGTGGG	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				CGCTTTCCACCACGCCAGCCCTGCTGTGGGCACGCCAGCC	0.700													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20086470	20086470	+	IGR	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20086470delT								None (None upstream) : GOLGA6L6 (650624 downstream)																							CACACACCACTTTTACTGGCC	0.318													4	2	---	---	---	---	
EXD1	161829	broad.mit.edu	37	15	41501976	41501977	+	Intron	INS	-	T	T	rs138974872	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41501976_41501977insT	uc001znk.2	-						EXD1_uc010ucv.1_Intron	NM_152596	NP_689809	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding			ovary(1)	1						ACTTCTGATTCTTTTTTTTTGT	0.322													3	3	---	---	---	---	
CCDC33	80125	broad.mit.edu	37	15	74628156	74628156	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74628156delC	uc002axo.2	+						CCDC33_uc002axp.2_Intron|CCDC33_uc002axq.2_3'UTR|CCDC33_uc002axr.2_3'UTR	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5						CAGGTCATGGCCCACTGGATT	0.557													4	2	---	---	---	---	
SEC14L5	9717	broad.mit.edu	37	16	5037498	5037499	+	Intron	INS	-	GGA	GGA			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5037498_5037499insGGA	uc002cye.2	+							NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5							integral to membrane|intracellular	transporter activity				0						GAGGTCGCGCTGGGGGGGGGGG	0.644													5	4	---	---	---	---	
CPPED1	55313	broad.mit.edu	37	16	12897744	12897745	+	5'UTR	INS	-	GGGGCGGGACT	GGGGCGGGACT	rs3833561		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12897744_12897745insGGGGCGGGACT	uc002dca.3	-	1					CPPED1_uc002dcb.3_5'UTR	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0						CCTTTGATCTcggggcgggact	0.485													5	6	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14711737	14711737	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14711737delT	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						TGTTTCACAAtttttttttta	0.164													4	2	---	---	---	---	
NLRC5	84166	broad.mit.edu	37	16	57104775	57104776	+	Intron	INS	-	GT	GT			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57104775_57104776insGT	uc002ekk.1	+						NLRC5_uc010ccr.1_Intron|NLRC5_uc010ccs.1_Intron|NLRC5_uc002eko.1_Intron|NLRC5_uc002ekq.1_Intron|NLRC5_uc002ekr.1_Intron	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)				gaagggtgtgagagtggtgatg	0.069													2	6	---	---	---	---	
SLC7A6	9057	broad.mit.edu	37	16	68325918	68325918	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68325918delC	uc002evt.1	+						SLC7A6_uc002evu.1_Intron|SLC7A6_uc002evv.1_Intron|SLC7A6_uc010cfc.1_Intron	NM_001076785	NP_001070253	Q92536	YLAT2_HUMAN	solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity|antiporter activity			central_nervous_system(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.0948)		GCTCATGTTTCCATCTGAGAT	0.463													3	3	---	---	---	---	
MNT	4335	broad.mit.edu	37	17	2290068	2290068	+	3'UTR	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2290068delA	uc002fur.2	-	6						NM_020310	NP_064706	Q99583	MNT_HUMAN	MAX binding protein						multicellular organismal development|negative regulation of cell proliferation|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			skin(1)	1				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		CCCTTCCCCTAGGAGGCCTGG	0.632													4	2	---	---	---	---	
RABEP1	9135	broad.mit.edu	37	17	5266498	5266498	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5266498delT	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_Intron	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						AGGACTCTGCTTttttttttt	0.199													4	3	---	---	---	---	
FXR2	9513	broad.mit.edu	37	17	7505004	7505005	+	Intron	DEL	TG	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7505004_7505005delTG	uc002gia.1	-						FXR2_uc010vud.1_Intron	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related							cytosolic large ribosomal subunit	protein binding|RNA binding	p.?(1)			0				READ - Rectum adenocarcinoma(115;0.17)		cccaggactttgggaggccaag	0.144													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22066949	22066949	+	IGR	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22066949delT								FLJ36000 (153879 upstream) : None (None downstream)																							CCAGAAAAAATATGTGAGAGA	0.323													4	2	---	---	---	---	
CCR7	1236	broad.mit.edu	37	17	38712161	38712161	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38712161delT	uc002huw.2	-							NM_001838	NP_001829	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7 precursor						cell maturation|immunological synapse formation|inflammatory response|interleukin-12 secretion|lymphocyte migration into lymph node|positive regulation of dendritic cell antigen processing and presentation|positive regulation of glycoprotein biosynthetic process|positive regulation of humoral immune response|positive regulation of hypersensitivity|positive regulation of interleukin-12 production|positive regulation of neutrophil chemotaxis|regulation of interferon-gamma production|regulation of interleukin-1 beta secretion|T cell costimulation	integral to membrane|intracellular	C-C chemokine receptor activity|chemokine (C-C motif) ligand 19 binding|chemokine (C-C motif) ligand 21 binding			breast(1)	1		Breast(137;0.000496)				GGtttctttcttttttttttt	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39216302	39216303	+	Translation_Start_Site	INS	-	G	G	rs113441706		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39216302_39216303insG	uc002hvx.2	-	1						NM_033184	NP_149440			keratin associated protein 2-4																		GAGCCGGTCATGGTGGTGTCTG	0.634													9	4	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55729771	55729771	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55729771delA	uc002iuz.1	+						MSI2_uc010wnm.1_Intron	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		TCTCTCCTTGAAAAAAAAAAC	0.502			T	HOXA9	CML								6	3	---	---	---	---	
AFMID	125061	broad.mit.edu	37	17	76202718	76202720	+	Intron	DEL	CTT	-	-	rs146402456		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76202718_76202720delCTT	uc002jva.3	+						AFMID_uc002jvb.3_Intron|AFMID_uc002juz.3_Intron	NM_001010982	NP_001010982	Q63HM1	AFMID_HUMAN	arylformamidase isoform 1							cytosol|nucleus	arylformamidase activity			large_intestine(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)			CGTCGTCTTCcttcttcttcttc	0.079													7	6	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80151419	80151419	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80151419delA	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			agaccctgtcaaaaaaaaaaa	0.080													6	3	---	---	---	---	
SERPINB8	5271	broad.mit.edu	37	18	61652122	61652123	+	Intron	INS	-	C	C			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61652122_61652123insC	uc002ljv.2	+						SERPINB8_uc002ljt.2_Intron|SERPINB8_uc002lju.2_Intron|SERPINB8_uc010xex.1_Intron	NM_198833	NP_942130	P50452	SPB8_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)				CTGTTTTTTTTTTCTCACCTGG	0.327													4	2	---	---	---	---	
C18orf62	284274	broad.mit.edu	37	18	73130584	73130584	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73130584delA	uc002lma.1	-						C18orf62_uc010dqw.1_Intron|C18orf62_uc002lmb.1_Intron	NM_001037331	NP_001032408	Q3B7S5	CR062_HUMAN	hypothetical protein LOC284274							integral to membrane					0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		OV - Ovarian serous cystadenocarcinoma(15;6.21e-06)		tttacaaagtaatttgatagc	0.075													6	4	---	---	---	---	
CALR	811	broad.mit.edu	37	19	13050676	13050676	+	Intron	DEL	T	-	-	rs111588637		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13050676delT	uc002mvu.2	+							NM_004343	NP_004334	P27797	CALR_HUMAN	calreticulin precursor						cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGAGCACTGATTTTTTTTTTT	0.393													2	4	---	---	---	---	
PLAUR	5329	broad.mit.edu	37	19	44159013	44159013	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44159013delC	uc002oxf.1	-						PLAUR_uc002oxd.1_Intron|PLAUR_uc002oxe.1_Intron|PLAUR_uc002oxg.1_Intron	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor						attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)	cgtggctcagcccaggtggtg	0.119													4	2	---	---	---	---	
PPFIA3	8541	broad.mit.edu	37	19	49644858	49644859	+	Intron	INS	-	GT	GT	rs147872140		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49644858_49644859insGT	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron|PPFIA3_uc002pmt.2_5'Flank	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		tgtgtgtatgagtgtgtgtgtg	0.198													4	4	---	---	---	---	
CPT1C	126129	broad.mit.edu	37	19	50204395	50204396	+	Intron	INS	-	CT	CT	rs67721255		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50204395_50204396insCT	uc002ppj.2	+						CPT1C_uc002ppl.3_Intron|CPT1C_uc002ppi.2_Intron|CPT1C_uc002ppk.2_Intron|CPT1C_uc010eng.2_Intron|CPT1C_uc010enh.2_Intron|CPT1C_uc010ybc.1_Intron	NM_152359	NP_689572	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C isoform 2						fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		tctctgtccccctctctctggg	0.129													5	3	---	---	---	---	
PPP1R12C	54776	broad.mit.edu	37	19	55603502	55603502	+	Intron	DEL	C	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55603502delC	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		CCCGCCGGCACCCCCAGGCCA	0.741													4	2	---	---	---	---	
PDYN	5173	broad.mit.edu	37	20	1963508	1963526	+	Intron	DEL	GCACACAGCTGCCCAGGCC	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1963508_1963526delGCACACAGCTGCCCAGGCC	uc010gaj.2	-						uc002wfu.1_Intron|PDYN_uc002wfv.2_Intron|PDYN_uc010zpt.1_Intron	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein						cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2						CTACAAGACAGCACACAGCTGCCCAGGCCTGCAACCTCC	0.607													16	7	---	---	---	---	
C20orf152	140894	broad.mit.edu	37	20	34583248	34583248	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34583248delT	uc002xes.1	+						C20orf152_uc002xer.1_Intron|C20orf152_uc010gfp.1_Intron			Q96M20	CT152_HUMAN	SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)					CTTTCCAGCCTTTTTTTTTTA	0.498											OREG0025897	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	6	---	---	---	---	
C20orf132	140699	broad.mit.edu	37	20	35748023	35748025	+	Intron	DEL	GGG	-	-	rs1780670	by1000genomes	TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35748023_35748025delGGG	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron	NM_152503	NP_689716	Q9H579	CT132_HUMAN	hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)				aagaaagagagggacagaaagaa	0.143													8	4	---	---	---	---	
SIK1	150094	broad.mit.edu	37	21	44842069	44842069	+	Intron	DEL	A	-	-	rs111590464		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44842069delA	uc002zdf.2	-							NM_173354	NP_775490	P57059	SIK1_HUMAN	salt-inducible kinase 1						anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7						TTTCTCAAATAAAAAAAAAAT	0.358													4	3	---	---	---	---	
IL17RA	23765	broad.mit.edu	37	22	17584678	17584679	+	Intron	DEL	GT	-	-	rs72290119		TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17584678_17584679delGT	uc002zly.2	+						IL17RA_uc010gqt.2_Intron	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor						fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		caggtggagagtggtgtggacg	0.040													2	5	---	---	---	---	
C22orf43	51233	broad.mit.edu	37	22	23959567	23959567	+	Intron	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23959567delA	uc002zxf.2	-							NM_016449	NP_057533	Q6PGQ1	CV043_HUMAN	hypothetical protein LOC51233											skin(1)	1						ctaggtcagcaaaaaaaccag	0.065													4	2	---	---	---	---	
SUSD2	56241	broad.mit.edu	37	22	24582452	24582452	+	Intron	DEL	G	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24582452delG	uc002zzn.1	+							NM_019601	NP_062547	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2 precursor						immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						GGGAGACTGAGGGGAAGCCCT	0.662													4	2	---	---	---	---	
CXorf59	286464	broad.mit.edu	37	X	36089798	36089798	+	Intron	DEL	T	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36089798delT	uc004ddk.1	+							NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464							integral to membrane				central_nervous_system(1)	1						GTGTTTAGACTTTTTTTTTAC	0.189													4	2	---	---	---	---	
MECP2	4204	broad.mit.edu	37	X	153295696	153295696	+	3'UTR	DEL	A	-	-			TCGA-B8-4151-01A-01D-1806-10	TCGA-B8-4151-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153295696delA	uc004fjv.2	-	4					MECP2_uc004fjw.2_3'UTR	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TTACTGAAAGaaaaaaaaata	0.408													4	2	---	---	---	---	
