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
ZMYM6	9204	broad.mit.edu	37	1	35457966	35457966	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35457966A>T	uc001byh.2	-	15	2243	c.2015T>A	c.(2014-2016)ATG>AAG	p.M672K	ZMYM6_uc001byf.1_Missense_Mutation_p.M672K|ZMYM6_uc010oht.1_Missense_Mutation_p.M575K|ZMYM6_uc009vup.2_Missense_Mutation_p.M478K|ZMYM6_uc009vuq.1_Missense_Mutation_p.M672K	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258	672					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				TGGAAATTTCATAGCATCTTC	0.373													44	124	---	---	---	---	PASS
C1orf103	55791	broad.mit.edu	37	1	111494480	111494480	+	Silent	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111494480A>T	uc001eaa.2	-	2	1282	c.1026T>A	c.(1024-1026)CCT>CCA	p.P342P	C1orf103_uc001dzz.2_Intron|C1orf103_uc001eab.2_Intron|C1orf103_uc001eac.1_Intron	NM_018372	NP_060842	Q5T3J3	LRIF1_HUMAN	receptor-interacting factor 1 isoform 1	342					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix	protein binding				0		all_cancers(81;1.02e-05)|all_epithelial(167;1.87e-05)|all_lung(203;0.000234)|Lung NSC(277;0.000451)		Lung(183;0.0155)|Colorectal(144;0.0314)|all cancers(265;0.082)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0891)|COAD - Colon adenocarcinoma(174;0.134)		GCGTCCCACTAGGATCGATGG	0.348													55	194	---	---	---	---	PASS
C1orf114	57821	broad.mit.edu	37	1	169388196	169388196	+	Intron	SNP	A	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169388196A>G	uc001gga.1	-						C1orf114_uc001gfz.1_Intron|C1orf114_uc009wvq.1_Intron|C1orf114_uc001ggb.2_3'UTR	NM_021179	NP_067002	Q5TID7	CA114_HUMAN	hypothetical protein LOC57821												0	all_hematologic(923;0.208)					CCTTCTATAAATAAGTTCAGC	0.358													17	85	---	---	---	---	PASS
IGFN1	91156	broad.mit.edu	37	1	201190737	201190737	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201190737C>A	uc001gwc.2	+	8	2316	c.1544C>A	c.(1543-1545)ACC>AAC	p.T515N	IGFN1_uc001gwb.2_RNA	NM_178275	NP_840059			RecName: Full=Immunoglobulin-like and fibronectin type III domain-containing protein 1; AltName: Full=EEF1A2-binding protein 1; AltName: Full=KY-interacting protein 1;											ovary(2)|pancreas(1)	3						CATGTGGGCACCGTGCCAGTC	0.637													9	42	---	---	---	---	PASS
C1orf131	128061	broad.mit.edu	37	1	231360348	231360348	+	3'UTR	SNP	C	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231360348C>G	uc001hun.1	-	6					C1orf131_uc001hul.2_Intron|C1orf131_uc001hum.2_Intron	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)				agggcccttgcactggtttct	0.075													2	5	---	---	---	---	PASS
PARD3B	117583	broad.mit.edu	37	2	206305276	206305276	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206305276C>G	uc002var.1	+	20	3131	c.2924C>G	c.(2923-2925)CCT>CGT	p.P975R	PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Missense_Mutation_p.P913R|PARD3B_uc002vaq.1_Missense_Mutation_p.P906R	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	975					cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CCATCTCCCCCTCGAGCTGGA	0.483													5	171	---	---	---	---	PASS
TSEN2	80746	broad.mit.edu	37	3	12544895	12544895	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12544895A>C	uc003bxc.2	+	5	830	c.443A>C	c.(442-444)CAA>CCA	p.Q148P	TSEN2_uc003bwy.2_Missense_Mutation_p.Q148P|TSEN2_uc003bwz.2_Missense_Mutation_p.Q148P|TSEN2_uc003bxa.2_Missense_Mutation_p.Q148P|TSEN2_uc011auq.1_Missense_Mutation_p.Q148P|TSEN2_uc003bxb.2_Missense_Mutation_p.Q148P|TSEN2_uc011aur.1_Missense_Mutation_p.Q57P	NM_025265	NP_079541	Q8NCE0	SEN2_HUMAN	tRNA-intron nuclease 2 isoform 1	148					mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1						GAAGAGGCTCAAGTGCATGAC	0.507													8	83	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52661377	52661377	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52661377T>A	uc003des.2	-	13	1465	c.1453A>T	c.(1453-1455)AAA>TAA	p.K485*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.K485*|PBRM1_uc003der.2_Nonsense_Mutation_p.K453*|PBRM1_uc003det.2_Nonsense_Mutation_p.K485*|PBRM1_uc003deu.2_Nonsense_Mutation_p.K485*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.K485*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.K485*|PBRM1_uc003dey.2_Nonsense_Mutation_p.K485*|PBRM1_uc003dez.1_Nonsense_Mutation_p.K485*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.K383*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	485					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)		GCAAGCTCTTTCTTCTTTGCC	0.428			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								32	84	---	---	---	---	PASS
ARHGEF3	50650	broad.mit.edu	37	3	56779390	56779390	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56779390A>G	uc003dig.2	-	7	882	c.713T>C	c.(712-714)CTA>CCA	p.L238P	ARHGEF3_uc011bew.1_Missense_Mutation_p.L238P|ARHGEF3_uc003dih.2_Missense_Mutation_p.L270P|ARHGEF3_uc011bev.1_Missense_Mutation_p.L209P|ARHGEF3_uc003dif.2_Missense_Mutation_p.L244P|ARHGEF3_uc010hmy.1_Missense_Mutation_p.L36P|ARHGEF3_uc003dii.2_Missense_Mutation_p.L238P	NM_019555	NP_062455	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform	238	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		ACATCGCTGTAGGAAATCCTG	0.493													69	175	---	---	---	---	PASS
IL17RD	54756	broad.mit.edu	37	3	57139906	57139906	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57139906G>T	uc003dil.2	-	7	815	c.726C>A	c.(724-726)TTC>TTA	p.F242L	IL17RD_uc003dik.2_Missense_Mutation_p.F218L|IL17RD_uc010hna.2_Missense_Mutation_p.F98L|IL17RD_uc011bex.1_Missense_Mutation_p.F98L	NM_017563	NP_060033	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D precursor	242	Extracellular (Potential).					Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TCTTTCGCTTGAAAGGTCCTT	0.512													3	40	---	---	---	---	PASS
FGFR3	2261	broad.mit.edu	37	4	1807850	1807850	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1807850G>T	uc003gdr.3	+	14	2165	c.1909G>T	c.(1909-1911)GGG>TGG	p.G637W	FGFR3_uc003gdu.2_Missense_Mutation_p.G639W|FGFR3_uc003gds.3_Missense_Mutation_p.G525W|FGFR3_uc003gdq.3_Missense_Mutation_p.G638W	NM_000142	NP_000133	P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3 isoform 1	637	Protein kinase.|Cytoplasmic (Potential).				bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding			urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1)	2600		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)	CGCAGACTTCGGGCTGGCCCG	0.652		1	Mis|T	IGH@|ETV6	bladder|MM|T-cell lymphoma		Hypochondroplasia|Thanatophoric dysplasia		Muenke_syndrome|Saethre-Chotzen_syndrome				7	23	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151392858	151392858	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151392858A>T	uc010ipj.2	-	44	7092	c.6618T>A	c.(6616-6618)TTT>TTA	p.F2206L	LRBA_uc003ils.3_Missense_Mutation_p.F96L|LRBA_uc003ilt.3_Missense_Mutation_p.F854L|LRBA_uc003ilu.3_Missense_Mutation_p.F2195L	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	2206	BEACH.					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TAGAAGCCTTAAAAAGCTGAC	0.333													6	202	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21751733	21751733	+	3'UTR	SNP	G	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21751733G>T	uc010iuc.2	-	12					CDH12_uc011cno.1_3'UTR|CDH12_uc003jgk.2_3'UTR|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						gtgtgtgtgtgtgtgtgtttg	0.244										HNSCC(59;0.17)			3	40	---	---	---	---	PASS
ACTBL2	345651	broad.mit.edu	37	5	56778275	56778275	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56778275C>A	uc003jrm.2	-	1	362	c.260G>T	c.(259-261)TGG>TTG	p.W87L		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	87						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		TGTGTGGTACCAGATCTTTTC	0.537													14	53	---	---	---	---	PASS
PCDHGB7	56099	broad.mit.edu	37	5	140798416	140798416	+	Silent	SNP	G	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140798416G>A	uc003lkn.1	+	1	1135	c.990G>A	c.(988-990)CGG>CGA	p.R330R	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkm.2_Silent_p.R330R|PCDHGA11_uc003lko.1_5'Flank|PCDHGA11_uc003lkp.1_5'Flank|PCDHGA11_uc003lkq.1_5'Flank	NM_018927	NP_061750	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7 isoform 1	330	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCAACACGGTGTAAAGTAA	0.408													3	72	---	---	---	---	PASS
RDBP	7936	broad.mit.edu	37	6	31922556	31922556	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31922556C>G	uc003nyk.2	-	7	722	c.518G>C	c.(517-519)CGC>CCC	p.R173P	RDBP_uc011dot.1_Missense_Mutation_p.R143P|RDBP_uc003nyl.1_Missense_Mutation_p.R113P|RDBP_uc003nym.1_Missense_Mutation_p.R168P	NM_002904	NP_002895	P18615	NELFE_HUMAN	RD RNA-binding protein	173					positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	mitochondrion|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						GGCACCACTGCGTTCTTCATA	0.498													38	105	---	---	---	---	PASS
SLC35A1	10559	broad.mit.edu	37	6	88210968	88210968	+	Silent	SNP	T	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88210968T>C	uc011dzj.1	+	4	526	c.447T>C	c.(445-447)TTT>TTC	p.F149F	SLC35A1_uc003plx.2_RNA|SLC35A1_uc010kbw.2_Missense_Mutation_p.Y20H|SLC35A1_uc003plz.2_RNA|SLC35A1_uc011dzi.1_Silent_p.F15F|SLC35A1_uc003ply.2_RNA|SLC35A1_uc010kbx.2_Silent_p.F149F|SLC35A1_uc010kby.2_RNA	NM_006416	NP_006407	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid	149	Helical; (Potential).				carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TTTCAGTTTTTATGCTGTGTG	0.403													34	93	---	---	---	---	PASS
PMPCB	9512	broad.mit.edu	37	7	102949606	102949606	+	Intron	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102949606A>T	uc003vbl.2	+						PMPCB_uc010liu.1_3'UTR|PMPCB_uc003vbk.1_Intron|PMPCB_uc003vbm.2_Intron|PMPCB_uc010liv.2_Intron|PMPCB_uc010liw.2_Intron|PMPCB_uc011kll.1_Intron|PMPCB_uc011klm.1_Intron	NM_004279	NP_004270	O75439	MPPB_HUMAN	mitochondrial processing peptidase beta subunit						proteolysis	mitochondrial matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)	4						CTTAAATATAAGTTCTTTGTA	0.279													14	30	---	---	---	---	PASS
REXO1L1	254958	broad.mit.edu	37	8	86573410	86573410	+	3'UTR	SNP	G	A	A	rs79376271	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86573410G>A	uc011lfw.1	-	1						NM_172239	NP_758439	Q8IX06	GOR_HUMAN	exonuclease GOR							cytoplasm|nucleus	exonuclease activity|nucleic acid binding				0						TGGGCAGAGGGATGTGAACAG	0.667													4	19	---	---	---	---	PASS
VPS28	51160	broad.mit.edu	37	8	145649316	145649316	+	Intron	SNP	A	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145649316A>C	uc003zcr.1	-						VPS28_uc003zcs.1_Intron|VPS28_uc003zct.1_Missense_Mutation_p.L219R	NM_016208	NP_057292	Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 isoform 1						cellular membrane organization|endosome transport|negative regulation of protein ubiquitination|protein transport	cytosol|late endosome membrane|plasma membrane	protein binding				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CTGGGAGTGCAGCACAGGGCA	0.677													26	108	---	---	---	---	PASS
SEMA4D	10507	broad.mit.edu	37	9	92008488	92008488	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92008488G>A	uc004aqo.1	-	9	1069	c.497C>T	c.(496-498)TCC>TTC	p.S166F	SEMA4D_uc011ltm.1_Missense_Mutation_p.S166F|SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aqp.1_Missense_Mutation_p.S164F	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	166	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						AACCATGACGGATGTGTAGCT	0.428													20	79	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	119568087	119568087	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119568087C>G	uc004bjs.1	-	13	2321	c.2220G>C	c.(2218-2220)GAG>GAC	p.E740D	ASTN2_uc004bjr.1_Missense_Mutation_p.E736D|ASTN2_uc004bjt.1_Missense_Mutation_p.E689D	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	740	Extracellular (Potential).|EGF-like 3.					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						CCAGTTTGTACTCCTCCACGC	0.493													6	181	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16882524	16882524	+	Silent	SNP	A	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16882524A>G	uc001ioo.2	-	62	9889	c.9837T>C	c.(9835-9837)GGT>GGC	p.G3279G		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3279	CUB 25.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGTATGTTCCACCACAAGGCA	0.453													6	17	---	---	---	---	PASS
C10orf79	80217	broad.mit.edu	37	10	105942200	105942200	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105942200G>T	uc001kxw.2	-	17	2329	c.2213C>A	c.(2212-2214)GCC>GAC	p.A738D	C10orf79_uc009xxq.2_Missense_Mutation_p.A46D|C10orf79_uc001kxx.3_Missense_Mutation_p.A739D	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	738											0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)		CTTGTCCATGGCGCTGCTCAG	0.393													39	155	---	---	---	---	PASS
NHLRC2	374354	broad.mit.edu	37	10	115618352	115618352	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115618352G>A	uc001lax.1	+	2	456	c.244G>A	c.(244-246)GTC>ATC	p.V82I		NM_198514	NP_940916	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	82	Thioredoxin.				cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)		AAAAATAGTCGTCCTTGATTT	0.343													8	267	---	---	---	---	PASS
CNGA4	1262	broad.mit.edu	37	11	6262833	6262833	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6262833C>A	uc001mco.2	+	5	1197	c.1090C>A	c.(1090-1092)CTG>ATG	p.L364M	CNGA4_uc010raa.1_Missense_Mutation_p.L133M|CNGA4_uc001mcn.2_Missense_Mutation_p.L324M	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	364	cNMP.|Cytoplasmic (Potential).				response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTGCTGAAGCTGCAGCCCCA	0.582													42	198	---	---	---	---	PASS
MRVI1	10335	broad.mit.edu	37	11	10647673	10647673	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10647673C>A	uc010rcc.1	-	9	1594	c.1208G>T	c.(1207-1209)GGC>GTC	p.G403V	MRVI1_uc001miw.2_Missense_Mutation_p.G394V|MRVI1_uc010rcb.1_Missense_Mutation_p.G395V|MRVI1_uc009ygb.1_Missense_Mutation_p.G88V|MRVI1_uc001mix.2_Missense_Mutation_p.G88V|MRVI1_uc001miz.2_Missense_Mutation_p.G312V|MRVI1_uc009ygc.1_Missense_Mutation_p.G312V|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_Missense_Mutation_p.G88V|MRVI1_uc010rce.1_Intron	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c	376					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)		CAGCCGGGGGCCAGGTTCTTC	0.662													3	27	---	---	---	---	PASS
ACP2	53	broad.mit.edu	37	11	47264856	47264856	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47264856C>G	uc001nei.2	-	8	906	c.789G>C	c.(787-789)CAG>CAC	p.Q263H	ACP2_uc010rhe.1_Missense_Mutation_p.Q235H|ACP2_uc009ylj.2_Missense_Mutation_p.Q191H|ACP2_uc010rhf.1_Missense_Mutation_p.Q231H|ACP2_uc010rhg.1_Missense_Mutation_p.Q200H|ACP2_uc010rhh.1_Missense_Mutation_p.Q76H|ACP2_uc010rhi.1_Missense_Mutation_p.Q76H|ACP2_uc009ylk.2_Missense_Mutation_p.Q230H	NM_001610	NP_001601	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal isoform 1	263	Lumenal (Potential).					integral to membrane|lysosomal lumen|lysosomal membrane	acid phosphatase activity			ovary(1)	1						TCTTCCTTATCTGAGCCAGCA	0.567													5	77	---	---	---	---	PASS
ADRBK1	156	broad.mit.edu	37	11	67050628	67050628	+	Silent	SNP	T	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67050628T>C	uc009yrn.1	+	15	1523	c.1257T>C	c.(1255-1257)CCT>CCC	p.P419P	ADRBK1_uc009yrm.1_Intron	NM_001619	NP_001610	P25098	ARBK1_HUMAN	beta-adrenergic receptor kinase 1	419	Protein kinase.				activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway	cytosol|soluble fraction	alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity			large_intestine(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCTTCTCCCCTGAACTACGCT	0.632													65	191	---	---	---	---	PASS
DDX10	1662	broad.mit.edu	37	11	108810996	108810996	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108810996T>C	uc001pkm.2	+	18	2539	c.2474T>C	c.(2473-2475)ATG>ACG	p.M825T		NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	825							ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		AAGCAGGGGATGAAGAAGAGG	0.418			T	NUP98	AML*								8	71	---	---	---	---	PASS
ARHGAP20	57569	broad.mit.edu	37	11	110462785	110462785	+	Silent	SNP	C	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110462785C>T	uc001pkz.1	-	11	1344	c.1059G>A	c.(1057-1059)TCG>TCA	p.S353S	ARHGAP20_uc001pky.1_Silent_p.S330S|ARHGAP20_uc009yyb.1_Silent_p.S317S|ARHGAP20_uc001pla.1_Silent_p.S317S|ARHGAP20_uc001plb.2_5'Flank	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	353					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GTGATGTTGGCGATGAGGGCA	0.448													17	259	---	---	---	---	PASS
HDAC7	51564	broad.mit.edu	37	12	48179316	48179316	+	3'UTR	SNP	A	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48179316A>C	uc010slp.1	-	3					HDAC7_uc009zku.2_Intron|HDAC7_uc001rqe.2_Intron|HDAC7_uc010slo.1_Intron|HDAC7_uc001rqj.3_Intron|HDAC7_uc001rqk.3_Intron			Q8WUI4	HDAC7_HUMAN	Synthetic construct DNA, clone: pF1KB0470, Homo sapiens HDAC7 gene for histone deacetylase 7, without stop codon, in Flexi system.						negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)		GCTCACTCCCACCCCAGGGGC	0.572													4	25	---	---	---	---	PASS
C12orf41	54934	broad.mit.edu	37	12	49047945	49047945	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49047945A>C	uc001rrx.2	-	10	1436	c.1361T>G	c.(1360-1362)ATG>AGG	p.M454R	C12orf41_uc001rrw.2_Missense_Mutation_p.M225R|C12orf41_uc001rrz.2_Missense_Mutation_p.M637R|C12orf41_uc001rry.2_RNA|C12orf41_uc001rru.2_Missense_Mutation_p.D84E|C12orf41_uc001rrv.2_Missense_Mutation_p.D137E	NM_017822	NP_060292	Q9H9L4	CL041_HUMAN	hypothetical protein LOC54934	454										ovary(2)	2						ATCTCCAGCCATCTGCATCTG	0.453													7	44	---	---	---	---	PASS
PPP1R14D	54866	broad.mit.edu	37	15	41107825	41107825	+	3'UTR	SNP	C	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41107825C>A	uc001zmy.2	-	4					PPP1R14D_uc001zmz.2_3'UTR	NM_017726	NP_060196	Q9NXH3	PP14D_HUMAN	protein phosphatase 1, regulatory subunit 14D						regulation of phosphorylation	cytoplasm	protein phosphatase inhibitor activity				0		all_cancers(109;6.29e-14)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.88e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CTATTTCCCTCTTAGCCAGGA	0.517													6	18	---	---	---	---	PASS
ABCA3	21	broad.mit.edu	37	16	2328063	2328063	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2328063C>T	uc002cpy.1	-	31	5438	c.4726G>A	c.(4726-4728)GAG>AAG	p.E1576K	ABCA3_uc010bsk.1_Missense_Mutation_p.E1518K	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	1576	ABC transporter 2.				response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				GCCTCACACTCCTCCATGCTG	0.622													5	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	29110458	29110458	+	Intron	SNP	T	C	C	rs151074589	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29110458T>C	uc010vct.1	-						RRN3P2_uc002dsf.3_RNA|RRN3P2_uc002dsg.3_RNA|RRN3P2_uc010vdn.1_RNA					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		GAATTTTGAGTGGATAGTGAT	0.328													7	131	---	---	---	---	PASS
SUPT6H	6830	broad.mit.edu	37	17	27023953	27023953	+	Silent	SNP	T	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27023953T>C	uc002hby.2	+	30	4152	c.4062T>C	c.(4060-4062)GAT>GAC	p.D1354D	SUPT6H_uc010crt.2_Silent_p.D1354D	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog	1354	SH2.				chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)					ACCAGGGTGATGTGATTATCC	0.498													38	109	---	---	---	---	PASS
TLCD1	116238	broad.mit.edu	37	17	27051889	27051889	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27051889C>T	uc002hco.2	-	4	498	c.383G>A	c.(382-384)GGC>GAC	p.G128D	TLCD1_uc010waw.1_Missense_Mutation_p.G81D	NM_138463	NP_612472	Q96CP7	TLCD1_HUMAN	TLC domain containing 1 isoform 1	128	TLC.|Helical; (Potential).					integral to membrane					0	Lung NSC(42;0.00431)					CCAAAAGATGCCGGAGAAGAA	0.498													4	113	---	---	---	---	PASS
ACACA	31	broad.mit.edu	37	17	35581913	35581913	+	Silent	SNP	C	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35581913C>T	uc002hnm.2	-	27	3554	c.3363G>A	c.(3361-3363)CAG>CAA	p.Q1121Q	ACACA_uc002hnk.2_Silent_p.Q1043Q|ACACA_uc002hnl.2_Silent_p.Q1063Q|ACACA_uc002hnn.2_Silent_p.Q1121Q|ACACA_uc002hno.2_Silent_p.Q1158Q|ACACA_uc010cuz.2_Silent_p.Q1121Q	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2	1121					acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	atatatataCCTGCAGGTTCT	0.343													13	41	---	---	---	---	PASS
KIAA1267	284058	broad.mit.edu	37	17	44248412	44248412	+	Silent	SNP	T	C	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44248412T>C	uc002ikb.2	-	1	1183	c.1098A>G	c.(1096-1098)GGA>GGG	p.G366G	KIAA1267_uc002ikc.2_Silent_p.G366G|KIAA1267_uc002ikd.2_Silent_p.G366G|KIAA1267_uc010dav.2_Silent_p.G366G	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	366						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				AGTTGCTAAGTCCCTCTGAAG	0.458													30	190	---	---	---	---	PASS
SCRN2	90507	broad.mit.edu	37	17	45918176	45918176	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45918176A>T	uc002imd.2	-	2	160	c.34T>A	c.(34-36)TGC>AGC	p.C12S	SCRN2_uc002imc.2_Missense_Mutation_p.C20S|SCRN2_uc002imf.2_Missense_Mutation_p.C12S|SCRN2_uc002ime.2_RNA	NM_138355	NP_612364	Q96FV2	SCRN2_HUMAN	secernin 2 isoform 1	12		Potential.			proteolysis		dipeptidase activity			ovary(1)	1						AAGCAGTCGCAGGAACATGGG	0.667													4	17	---	---	---	---	PASS
ABI3	51225	broad.mit.edu	37	17	47299454	47299454	+	Silent	SNP	C	T	T	rs146244763	byFrequency	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47299454C>T	uc002iop.1	+	7	1302	c.804C>T	c.(802-804)GAC>GAT	p.D268D	ABI3_uc002ioq.1_Silent_p.D262D	NM_016428	NP_057512	Q9P2A4	ABI3_HUMAN	NESH protein isoform 1	268	Pro-rich.				cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			TCCCCCAAGACGAAGAGCTGC	0.592										HNSCC(55;0.14)			7	182	---	---	---	---	PASS
LOC651250	651250	broad.mit.edu	37	17	66123962	66123962	+	RNA	SNP	C	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66123962C>T	uc002jgq.2	+	6		c.3085C>T			LOC651250_uc002kit.2_RNA|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0						GGCTGGACTGCATAAGCATGG	0.343													4	10	---	---	---	---	PASS
MXRA7	439921	broad.mit.edu	37	17	74673741	74673741	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74673741C>G	uc002jsk.1	-	4	572	c.544G>C	c.(544-546)GAC>CAC	p.D182H		NM_001008528	NP_001008528	P84157	MXRA7_HUMAN	transmembrane anchor protein 1 isoform 1	182						integral to membrane					0						TCCTTGTTGTCTTTCATGAGC	0.567													42	158	---	---	---	---	PASS
MLLT1	4298	broad.mit.edu	37	19	6270745	6270745	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6270745A>T	uc002mek.2	-	2	202	c.38T>A	c.(37-39)CTG>CAG	p.L13Q		NM_005934	NP_005925	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	13	YEATS.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1						GCGATGCCCCAGCTCTAACCT	0.617			T	MLL	AL						OREG0025198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	65	---	---	---	---	PASS
GMIP	51291	broad.mit.edu	37	19	19746368	19746368	+	Silent	SNP	G	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19746368G>A	uc002nnd.2	-	15	1533	c.1416C>T	c.(1414-1416)GAC>GAT	p.D472D	GMIP_uc010xrb.1_Silent_p.D446D|GMIP_uc010xrc.1_Silent_p.D443D	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	472					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1						TCTCCAGCCCGTCTCCCAGGT	0.572													5	103	---	---	---	---	PASS
ACSS2	55902	broad.mit.edu	37	20	33500951	33500951	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33500951G>T	uc002xbd.2	+	3	548	c.427G>T	c.(427-429)GTC>TTC	p.V143F	ACSS2_uc002xbc.2_Missense_Mutation_p.V48F|ACSS2_uc010zum.1_Intron|ACSS2_uc010gey.2_Missense_Mutation_p.V143F|ACSS2_uc002xbe.2_Intron|ACSS2_uc002xbf.2_Intron	NM_018677	NP_061147	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	143					ethanol oxidation|lipid biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	acetate-CoA ligase activity|ATP binding|protein binding				0					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCAGCTTCTGGTCCAAGTGTG	0.522													48	189	---	---	---	---	PASS
COL18A1	80781	broad.mit.edu	37	21	46912469	46912469	+	Silent	SNP	G	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46912469G>A	uc011afs.1	+	22	3444	c.3423G>A	c.(3421-3423)CCG>CCA	p.P1141P	COL18A1_uc002zhg.2_Silent_p.P726P|COL18A1_uc002zhi.2_Silent_p.P906P	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1141	Nonhelical region 5 (NC5).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TGAGCGTGCCGGGACCTGAGG	0.587													60	293	---	---	---	---	PASS
VSIG1	340547	broad.mit.edu	37	X	107319363	107319363	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107319363A>T	uc004eno.2	+	6	906	c.745A>T	c.(745-747)ATC>TTC	p.I249F	VSIG1_uc011msk.1_Missense_Mutation_p.I285F	NM_182607	NP_872413	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	249	Helical; (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						AGGTGCCGCCATCATCATCTC	0.428													67	92	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5761932	5761933	+	IGR	INS	-	AGGAAGGA	AGGAAGGA	rs76080214	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5761932_5761933insAGGAAGGA								AJAP1 (918082 upstream) : NPHP4 (160937 downstream)																							agaagggagggaggaaggaagg	0.000													3	4	---	---	---	---	
EXOSC10	5394	broad.mit.edu	37	1	11131924	11131926	+	Intron	DEL	CAA	-	-	rs146511139		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11131924_11131926delCAA	uc001asa.2	-						EXOSC10_uc001asb.2_Intron	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1						CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CTCCAACCACCAACGAGACAGCT	0.429													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18427841	18427848	+	IGR	DEL	CTTCCTTT	-	-	rs72072517		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18427841_18427848delCTTCCTTT								ACTL8 (274285 upstream) : IGSF21 (6392 downstream)																							tctttccttccttcctttcttcctttct	0.168													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149689670	149689671	+	IGR	DEL	CA	-	-	rs146375699		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149689670_149689671delCA								HIST2H2BF (290441 upstream) : FCGR1A (64579 downstream)																							ttaaaatagccacacacacaca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152952984	152952985	+	IGR	INS	-	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152952984_152952985insT								SPRR4 (7915 upstream) : SPRR1A (3572 downstream)																							CTGCACCCACATTTGCAAACTT	0.356													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175712100	175712101	+	Intron	DEL	AC	-	-	rs140284213		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175712100_175712101delAC	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					ATGCAACAGTacacacacacac	0.396													4	2	---	---	---	---	
RFWD2	64326	broad.mit.edu	37	1	176015104	176015105	+	Intron	INS	-	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176015104_176015105insA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						TTGGCAACCAGAAAAAAAAAAA	0.297													4	3	---	---	---	---	
KCNG3	170850	broad.mit.edu	37	2	42698325	42698328	+	Intron	DEL	TATA	-	-	rs111230198	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42698325_42698328delTATA	uc002rsn.2	-						KCNG3_uc002rsm.2_Intron	NM_133329	NP_579875	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G,							endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1						tgtgtgtgtgtATATATATatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45224046	45224046	+	IGR	DEL	A	-	-	rs34239087		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45224046delA								SIX3 (51656 upstream) : SIX2 (8279 downstream)																							TTATTTGTTTAAAAAAAAAAA	0.224													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90447339	90447342	+	Intron	DEL	TCTA	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90447339_90447342delTCTA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		GTTTGTTACCTCTATCTACTGTCT	0.353													4	3	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223512162	223512163	+	Intron	INS	-	A	A	rs147059558	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223512162_223512163insA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron|FARSB_uc002vng.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GACCAGCTTTCAGTTTTACTGA	0.450													3	3	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10089935	10089936	+	Intron	DEL	TC	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10089935_10089936delTC	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_5'Flank	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GCTCTAAAATTCTCTGTCTGAA	0.322			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				5	5	---	---	---	---	
CNOT10	25904	broad.mit.edu	37	3	32758896	32758896	+	Intron	DEL	T	-	-	rs75168073		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32758896delT	uc003cfc.1	+						CNOT10_uc011axi.1_Intron|CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						tatagtttaattttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141439773	141439776	+	IGR	DEL	TGTG	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141439773_141439776delTGTG								RASA2 (108576 upstream) : RNF7 (17275 downstream)																							ACACGATGCCtgtgtgtgtgtgtg	0.324													3	3	---	---	---	---	
TBL1XR1	79718	broad.mit.edu	37	3	176744032	176744032	+	Intron	DEL	A	-	-	rs112275760		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176744032delA	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			CAGCCTCAGGAAAAAAAAAAA	0.318													6	5	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164449736	164449737	+	3'UTR	INS	-	TGTT	TGTT	rs144407064	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164449736_164449737insTGTT	uc003iqs.1	-	8					MARCH1_uc003iqr.1_3'UTR	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGCATTTGGTCTGTTTGTTTTT	0.371													3	3	---	---	---	---	
CCDC111	201973	broad.mit.edu	37	4	185613052	185613052	+	Intron	DEL	T	-	-	rs10567357		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185613052delT	uc003iwk.2	+						CCDC111_uc003iwj.2_Intron|CCDC111_uc003iwl.2_Intron|CCDC111_uc003iwm.2_Intron|CCDC111_uc003iwn.2_Intron	NM_152683	NP_689896	Q96LW4	CC111_HUMAN	coiled-coil domain containing 111						DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)		aatacaaaccttttttttttt	0.025													2	4	---	---	---	---	
CLPTM1L	81037	broad.mit.edu	37	5	1342154	1342155	+	Intron	INS	-	GTGC	GTGC	rs55901723	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1342154_1342155insGTGC	uc003jch.2	-						CLPTM1L_uc003jcg.2_5'Flank	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like						apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		tgtgtgtgtgtgCACGCGCACG	0.470													4	3	---	---	---	---	
PAM	5066	broad.mit.edu	37	5	102347082	102347083	+	Intron	INS	-	CACA	CACA	rs143730875	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102347082_102347083insCACA	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron|PAM_uc003knz.2_Intron	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	aaacacacactcacacacacac	0.050													7	6	---	---	---	---	
FAM65B	9750	broad.mit.edu	37	6	24898248	24898251	+	Intron	DEL	AAGA	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24898248_24898251delAAGA	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron	NM_014722	NP_055537	Q9Y4F9	FA65B_HUMAN	hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1						ccagaccctgaagaaagaaagaaa	0.064													4	2	---	---	---	---	
TNFRSF21	27242	broad.mit.edu	37	6	47220840	47220841	+	Intron	DEL	GT	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47220840_47220841delGT	uc003oyv.2	-							NM_014452	NP_055267	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily,						cellular lipid metabolic process	cytoplasm|integral to membrane	protein binding|receptor activity				0			Lung(136;0.189)			AGAAGGTAGGgtgtgtgtgtgt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58159479	58159480	+	IGR	INS	-	GAAGGAAG	GAAGGAAG			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58159479_58159480insGAAGGAAG								PRIM2 (646104 upstream) : GUSBL2 (86679 downstream)																							aggaaaggaaagaaggaaggaa	0.173													4	3	---	---	---	---	
GRIK2	2898	broad.mit.edu	37	6	102370016	102370017	+	Intron	INS	-	TCCCTTCCT	TCCCTTCCT	rs145647959	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102370016_102370017insTCCCTTCCT	uc003pqp.3	+						GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)	ccttccttccctcccttcctcc	0.084													5	4	---	---	---	---	
RBM16	22828	broad.mit.edu	37	6	155129526	155129526	+	Intron	DEL	C	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155129526delC	uc003qqa.2	+						RBM16_uc011efj.1_Intron|RBM16_uc011efk.1_Intron|RBM16_uc003qpz.2_Intron|RBM16_uc010kji.2_Intron	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16						mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)		tggcccagaactgctttgaat	0.090													2	5	---	---	---	---	
KIAA1324L	222223	broad.mit.edu	37	7	86547640	86547646	+	Intron	DEL	AAAAAAA	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86547640_86547646delAAAAAAA	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron|KIAA1324L_uc003uie.2_Intron	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					TAAGAATAGCaaaaaaaaaaaaaaaaa	0.314													4	3	---	---	---	---	
PEX1	5189	broad.mit.edu	37	7	92136560	92136560	+	Intron	DEL	T	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92136560delT	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_Intron	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			Attttttatcttttttttttt	0.114													6	3	---	---	---	---	
TAF6	6878	broad.mit.edu	37	7	99708603	99708603	+	Intron	DEL	A	-	-	rs112139162		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99708603delA	uc003uti.2	-						TAF6_uc003utg.2_Intron|TAF6_uc003uth.2_Intron|TAF6_uc003utk.2_Intron|TAF6_uc011kji.1_Intron|TAF6_uc003utj.2_Intron|TAF6_uc003utl.2_Intron|TAF6_uc003utm.2_Intron|TAF6_uc003utn.1_Intron	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha						negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					actccatctcaaaaaaaaaaa	0.224													1	5	---	---	---	---	
DPY19L2P2	349152	broad.mit.edu	37	7	102815704	102815705	+	3'UTR	DEL	TG	-	-	rs7796853		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102815704_102815705delTG	uc003vbh.3	-	21					DPY19L2P2_uc003vbg.3_RNA|DPY19L2P2_uc010lit.2_RNA	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						AATCAAGttttgtttttttttt	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153152396	153152397	+	IGR	INS	-	CG	CG			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153152396_153152397insCG								ACTR3B (599933 upstream) : DPP6 (432022 downstream)																							acacacacacacGGGTTGGGGA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153441308	153441309	+	IGR	DEL	CA	-	-	rs145664732		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153441308_153441309delCA								ACTR3B (888845 upstream) : DPP6 (143110 downstream)																							cgtgcaggcgcacacacacaca	0.000													4	2	---	---	---	---	
WHSC1L1	54904	broad.mit.edu	37	8	38194673	38194673	+	Intron	DEL	A	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38194673delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron|WHSC1L1_uc003xlj.2_Intron	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			aaaaaaaaagaaaaaaaaaaa	0.124			T	NUP98	AML								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125850042	125850043	+	IGR	INS	-	T	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125850042_125850043insT								MTSS1 (109312 upstream) : LOC157381 (101841 downstream)																							tccttccttccttccttccttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	24676942	24676943	+	IGR	INS	-	AC	AC	rs146279037	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24676942_24676943insAC								ELAVL2 (850879 upstream) : TUSC1 (999451 downstream)																							AATGTGTGTTTacacacacaca	0.144													3	4	---	---	---	---	
OLFML2A	169611	broad.mit.edu	37	9	127549029	127549032	+	Intron	DEL	ACAC	-	-	rs149733353		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127549029_127549032delACAC	uc004bov.2	+						OLFML2A_uc010mwr.1_Intron	NM_182487	NP_872293	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A precursor												0						AGAGACGTAGacacacacacacac	0.157													3	3	---	---	---	---	
SPTAN1	6709	broad.mit.edu	37	9	131337249	131337256	+	Intron	DEL	GTGTATGT	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131337249_131337256delGTGTATGT	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						TGCTCTCTAGGTGTATGTGCTATTCTGT	0.471													6	7	---	---	---	---	
ANKRD1	27063	broad.mit.edu	37	10	92676188	92676189	+	Intron	DEL	TG	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92676188_92676189delTG	uc001khe.1	-							NM_014391	NP_055206	Q15327	ANKR1_HUMAN	cardiac ankyrin repeat protein						cellular lipid metabolic process|defense response|signal transduction		DNA binding				0		Colorectal(252;0.0475)				CTAAATTACAtgtgtgtgtgtg	0.248													5	3	---	---	---	---	
MMP21	118856	broad.mit.edu	37	10	127455708	127455709	+	Intron	INS	-	T	T	rs149560680	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127455708_127455709insT	uc001liu.2	-							NM_147191	NP_671724	Q8N119	MMP21_HUMAN	matrix metalloproteinase 21 preproprotein						proteolysis	extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				CACGttttttgttttttttttg	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	24207169	24207169	+	IGR	DEL	A	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24207169delA								None (None upstream) : LUZP2 (311387 downstream)																							gaaggaagggaagggaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33455651	33455651	+	IGR	DEL	T	-	-	rs35746278		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33455651delT								HIPK3 (79712 upstream) : C11orf41 (108226 downstream)																							AAGAATATGGTATTCTTAGAA	0.209													4	3	---	---	---	---	
ARHGEF17	9828	broad.mit.edu	37	11	73077186	73077187	+	Intron	DEL	GC	-	-	rs55848894		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73077186_73077187delGC	uc001otu.2	+							NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						gtgtgtgtgtgCGCACCTGCAT	0.366													4	2	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40153653	40153654	+	3'UTR	INS	-	A	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40153653_40153654insA	uc010skm.1	-	10					C12orf40_uc009zjv.1_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				GTTCCTTGTGGAAAAAAAAAGT	0.297										HNSCC(50;0.14)			4	2	---	---	---	---	
ADAMTS20	80070	broad.mit.edu	37	12	43837404	43837404	+	Intron	DEL	T	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43837404delT	uc010skx.1	-							NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTTCATTAAGTTTTTTTTTTT	0.274													5	6	---	---	---	---	
LASS5	91012	broad.mit.edu	37	12	50535722	50535723	+	Intron	INS	-	A	A	rs35739493		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50535722_50535723insA	uc001rwd.3	-						LASS5_uc001rwc.2_Intron|LASS5_uc001rwe.3_Intron|LASS5_uc001rwf.3_Intron|LASS5_uc010smq.1_Intron	NM_147190	NP_671723	Q8N5B7	CERS5_HUMAN	LAG1 homolog, ceramide synthase 5						ceramide biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0						gactccgtctcaaaaaaaaaaa	0.124													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	60816040	60816040	+	IGR	DEL	T	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60816040delT								SLC16A7 (640633 upstream) : None (None downstream)																							tctttcttccttttttttttg	0.000													4	2	---	---	---	---	
PARP4	143	broad.mit.edu	37	13	25069017	25069018	+	Intron	INS	-	TTTTTT	TTTTTT	rs139965809	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25069017_25069018insTTTTTT	uc001upl.2	-						PARP4_uc010tdc.1_Intron	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4						cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ttttctttttcttttttttttg	0.099													6	4	---	---	---	---	
LGMN	5641	broad.mit.edu	37	14	93184931	93184931	+	Intron	DEL	A	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93184931delA	uc001yav.2	-						LGMN_uc001yat.2_Intron|LGMN_uc001yau.2_Intron|LGMN_uc001yaw.2_Intron|LGMN_uc010aul.2_Intron|LGMN_uc001yax.2_Intron|LGMN_uc001yay.2_Intron	NM_001008530	NP_001008530	Q99538	LGMN_HUMAN	legumain preproprotein						hormone biosynthetic process|negative regulation of neuron apoptosis|vitamin D metabolic process	lysosome	cysteine-type endopeptidase activity|protein serine/threonine kinase activity			skin(1)	1		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		aaataataataaaaaaaaaaa	0.184													3	3	---	---	---	---	
RTF1	23168	broad.mit.edu	37	15	41762847	41762848	+	Intron	DEL	TC	-	-	rs147077484		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41762847_41762848delTC	uc001zny.2	+							NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		TCATTCAttttctttttttttt	0.238													5	3	---	---	---	---	
TEX9	374618	broad.mit.edu	37	15	56704371	56704372	+	Intron	INS	-	GT	GT	rs137938599	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56704371_56704372insGT	uc002adp.2	+						TEX9_uc010ugl.1_Intron	NM_198524	NP_940926	Q8N6V9	TEX9_HUMAN	testis expressed 9												0				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TACCCCCAAGCgtgtgtgtgtg	0.312													9	4	---	---	---	---	
ITGAX	3687	broad.mit.edu	37	16	31383487	31383487	+	Intron	DEL	G	-	-	rs67981265		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31383487delG	uc002ebu.1	+						ITGAX_uc002ebt.2_Intron	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						cgggaggtctgggggggggga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46417207	46417216	+	IGR	DEL	TTCGAATGGA	-	-	rs60768439		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46417207_46417216delTTCGAATGGA								None (None upstream) : ANKRD26P1 (86033 downstream)																							tggAATCATCTtcgaatggaattgaatgga	0.052													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518737	21518737	+	IGR	DEL	A	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518737delA								C17orf51 (41006 upstream) : FAM27L (306633 downstream)																							TATTGGTAGCAAAACAGCCAT	0.259													3	4	---	---	---	---	
SUZ12	23512	broad.mit.edu	37	17	30322882	30322882	+	Intron	DEL	A	-	-	rs35646011		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30322882delA	uc002hgs.2	+						SUZ12_uc002hgt.2_Intron	NM_015355	NP_056170	Q15022	SUZ12_HUMAN	joined to JAZF1						negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				AACTTTTTTTAAAAAAAAAAA	0.189			T	JAZF1	endometrial stromal tumours								6	3	---	---	---	---	
KRT39	390792	broad.mit.edu	37	17	39122320	39122321	+	Intron	DEL	TG	-	-	rs34892583		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39122320_39122321delTG	uc002hvo.1	-						KRT39_uc010wfm.1_Intron	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35							intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)				tgtgtgtgtatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43908477	43908477	+	Intron	DEL	T	-	-	rs56396707		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43908477delT	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		tccctgcctgtgctctgCCTG	0.199													7	8	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43912267	43912268	+	3'UTR	INS	-	G	G	rs140399885	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43912267_43912268insG	uc010dap.2	+	14					CRHR1_uc010wjx.1_3'UTR|CRHR1_uc002ijp.2_3'UTR|CRHR1_uc002ijm.2_3'UTR|CRHR1_uc002ijn.2_3'UTR|CRHR1_uc010dar.2_3'UTR|CRHR1_uc010dao.2_3'UTR|CRHR1_uc010daq.2_3'UTR	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		ACTGACAGCCTGGGGGGGCCGC	0.678													5	4	---	---	---	---	
RECQL5	9400	broad.mit.edu	37	17	73626934	73626934	+	Intron	DEL	T	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73626934delT	uc010dgl.2	-						RECQL5_uc010dgk.2_Intron|RECQL5_uc002jot.3_5'Flank|LOC643008_uc002jow.2_5'Flank	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			GGGGGGGGGGTGGTCCTTGGT	0.627								Other_identified_genes_with_known_or_suspected_DNA_repair_function					4	2	---	---	---	---	
FAM38B	63895	broad.mit.edu	37	18	10788504	10788505	+	Intron	INS	-	T	T	rs143297013	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10788504_10788505insT	uc002kou.1	-									Q9H5I5	PIEZ2_HUMAN	RecName: Full=Transmembrane protein C18orf30;							integral to membrane	ion channel activity			ovary(1)	1						AATTTTACAGATTTTTTTTGAT	0.104													4	3	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32408818	32408819	+	Intron	INS	-	T	T	rs71962398		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32408818_32408819insT	uc010dmn.1	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						AAATGCAACCATTTTTTTTTTC	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41181654	41181657	+	IGR	DEL	GAAG	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41181654_41181657delGAAG								SYT4 (324039 upstream) : None (None downstream)																							ggaaaggaaagaaggaaggaagga	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	64559997	64559998	+	IGR	INS	-	AAGGAAGGAAGA	AAGGAAGGAAGA	rs62094026	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64559997_64559998insAAGGAAGGAAGA								CDH19 (288781 upstream) : DSEL (613821 downstream)																							aggaagagagggagggagggag	0.000													4	2	---	---	---	---	
GNG7	2788	broad.mit.edu	37	19	2632473	2632476	+	Intron	DEL	CACA	-	-	rs112371743		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2632473_2632476delCACA	uc002lwd.2	-							NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAACAAAACTcacacacacacaca	0.167													3	3	---	---	---	---	
SAFB	6294	broad.mit.edu	37	19	5668445	5668445	+	3'UTR	DEL	T	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5668445delT	uc002mcf.2	+	21					SAFB_uc002mcg.2_3'UTR|SAFB_uc002mce.3_3'UTR|SAFB_uc010xir.1_3'UTR|SAFB_uc010xis.1_3'UTR|SAFB_uc010xit.1_3'UTR|SAFB_uc010xiu.1_3'UTR	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		CGTTTTGGGGTTTTTTTTTTT	0.279													9	5	---	---	---	---	
HAUS8	93323	broad.mit.edu	37	19	17171036	17171039	+	Intron	DEL	AAAA	-	-	rs66825337		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17171036_17171039delAAAA	uc002nfe.2	-						HAUS8_uc002nff.2_Intron|HAUS8_uc002nfg.1_Intron|HAUS8_uc002nfh.1_Intron	NM_033417	NP_219485	Q9BT25	HAUS8_HUMAN	sarcoma antigen NY-SAR-48 isoform a						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole					0						TGGAAAGGCTaaaaaaaaaaaaaa	0.392													4	2	---	---	---	---	
GPATCH1	55094	broad.mit.edu	37	19	33586469	33586469	+	Intron	DEL	T	-	-	rs79024536		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33586469delT	uc002nug.1	+							NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					gcgcccagccTTTTTTttttt	0.000													4	3	---	---	---	---	
RPS19	6223	broad.mit.edu	37	19	42372919	42372922	+	Intron	DEL	TGTC	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42372919_42372922delTGTC	uc002ort.2	+							NM_001022	NP_001013	P39019	RS19_HUMAN	ribosomal protein S19						endocrine pancreas development|erythrocyte differentiation|gas transport|positive regulation of cellular component movement|response to extracellular stimulus|ribosomal small subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						CAGGGCTGTTTGTCAAGGAAGAGC	0.525									Diamond-Blackfan_Anemia				4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15918375	15918376	+	Intron	DEL	TA	-	-	rs76061067		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15918375_15918376delTA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ATAGAAAATTtatatatatata	0.243													5	3	---	---	---	---	
WISP2	8839	broad.mit.edu	37	20	43343894	43343905	+	Intron	DEL	GTGTGTGTGAGC	-	-	rs5841567	by1000genomes	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43343894_43343905delGTGTGTGTGAGC	uc002xmn.2	+						uc002xml.1_Intron|uc002xmm.1_Intron|WISP2_uc002xmo.1_5'UTR|WISP2_uc002xmp.2_5'UTR|WISP2_uc002xmq.2_5'UTR	NM_003881	NP_003872	O76076	WISP2_HUMAN	WNT1 inducible signaling pathway protein 2						cell adhesion|cell-cell signaling|signal transduction	extracellular region|soluble fraction	insulin-like growth factor binding			skin(1)	1		Myeloproliferative disorder(115;0.0122)				gtgtgtgtgtgtgtgtgtgagcgcgcgcgcgc	0.311													4	2	---	---	---	---	
IL10RB	3588	broad.mit.edu	37	21	34660708	34660711	+	Intron	DEL	ACAG	-	-	rs67118950		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660708_34660711delACAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						acacacacacacagacacGCCTCT	0.407													7	4	---	---	---	---	
TOM1	10043	broad.mit.edu	37	22	35726117	35726117	+	Intron	DEL	A	-	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35726117delA	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						ctaaaactacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
