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
MST1P9	11223	broad.mit.edu	37	1	17085865	17085865	+	Missense_Mutation	SNP	A	G	G	rs1057378	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17085865A>G	uc010ock.1	-	8	956	c.956T>C	c.(955-957)CTC>CCC	p.L319P	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						TGAGCCGTCGAGGTTCCAGCA	0.667													3	36	---	---	---	---	PASS
RHD	6007	broad.mit.edu	37	1	25617207	25617207	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25617207G>A	uc001bjz.2	+	3	469	c.411G>A	c.(409-411)GCG>GCA	p.A137A	RHD_uc010oep.1_Silent_p.A137A|RHD_uc001bkc.2_Silent_p.A137A|RHD_uc009vrm.2_5'UTR|RHD_uc001bka.2_Silent_p.A137A|RHD_uc001bkb.2_Silent_p.A137A|RHD_uc009vrn.2_Silent_p.A137A|RHD_uc009vro.2_Silent_p.A137A|RHD_uc009vrp.2_Silent_p.A137A	NM_016124	NP_057208	Q02161	RHD_HUMAN	Rh blood group D antigen isoform 1	137	Helical; (Potential).					integral to plasma membrane				breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TCAACTTGGCGCAGTTGGTGG	0.557													4	73	---	---	---	---	PASS
TMEM56	148534	broad.mit.edu	37	1	95616924	95616924	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95616924A>T	uc001drb.2	+	5	639	c.348A>T	c.(346-348)AAA>AAT	p.K116N	RWDD3_uc001drd.3_Missense_Mutation_p.K116N|TMEM56_uc001drc.2_Missense_Mutation_p.K116N	NM_152487	NP_689700	Q96MV1	TMM56_HUMAN	transmembrane protein 56	116	TLC.					integral to membrane					0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		TTGGTGACAAATTTTTTATAA	0.343													7	188	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803746	142803746	+	Intron	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803746A>G	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		actatggattagagctgatta	0.000													4	16	---	---	---	---	PASS
S100A7A	338324	broad.mit.edu	37	1	153391728	153391728	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153391728C>T	uc001fbt.1	+	3	306	c.249C>T	c.(247-249)GCC>GCT	p.A83A		NM_176823	NP_789793	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7-like 1	83	EF-hand 2.					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)			GAGACATAGCCGCAGACTACC	0.522													6	104	---	---	---	---	PASS
ADAM15	8751	broad.mit.edu	37	1	155028577	155028577	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155028577C>T	uc001fgr.1	+	9	867	c.766C>T	c.(766-768)CGA>TGA	p.R256*	ADAM15_uc001fgq.1_Translation_Start_Site|ADAM15_uc009wpc.1_RNA|ADAM15_uc010pet.1_Nonsense_Mutation_p.R240*|ADAM15_uc010peu.1_Nonsense_Mutation_p.R273*|ADAM15_uc001fgt.1_Nonsense_Mutation_p.R256*|ADAM15_uc010pev.1_Nonsense_Mutation_p.R266*|ADAM15_uc001fgs.1_Nonsense_Mutation_p.R256*|ADAM15_uc001fgu.1_Nonsense_Mutation_p.R256*|ADAM15_uc001fgw.1_Nonsense_Mutation_p.R256*|ADAM15_uc001fgv.1_Nonsense_Mutation_p.R256*|ADAM15_uc001fgx.1_Nonsense_Mutation_p.R256*|ADAM15_uc001fgz.1_RNA|ADAM15_uc001fgy.1_RNA|ADAM15_uc001fha.1_RNA|ADAM15_uc001fhb.1_5'Flank	NM_207197	NP_997080	Q13444	ADA15_HUMAN	a disintegrin and metalloproteinase domain 15	256	Peptidase M12B.|Extracellular (Potential).				angiogenesis|cell-matrix adhesion|collagen catabolic process|proteolysis	acrosomal vesicle|adherens junction|endomembrane system|flagellum|integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			central_nervous_system(3)|skin(2)|ovary(1)	6	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CCTGAATGTACGAGTGGCACT	0.627													19	137	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158592860	158592860	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158592860G>A	uc001fst.1	-	43	6232	c.6033C>T	c.(6031-6033)GCC>GCT	p.A2011A		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2011	Spectrin 19.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TCAGCAGAGCGGCATAACGCT	0.478													279	376	---	---	---	---	PASS
OR6N1	128372	broad.mit.edu	37	1	158736387	158736387	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158736387A>T	uc010piq.1	-	1	86	c.86T>A	c.(85-87)CTC>CAC	p.L29H		NM_001005185	NP_001005185	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N,	29	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					AAGCAACAAGAGGAAGAGATA	0.502													4	88	---	---	---	---	PASS
AIM2	9447	broad.mit.edu	37	1	159038445	159038445	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159038445T>G	uc001ftj.1	-	3	554	c.309A>C	c.(307-309)CAA>CAC	p.Q103H		NM_004833	NP_004824	O14862	AIM2_HUMAN	absent in melanoma 2	103					cellular response to drug|immune response|interleukin-1 beta secretion	mitochondrion|nucleus				ovary(2)|pancreas(1)	3	all_hematologic(112;0.0429)					TCATTTCAGCTTGACTTAGTG	0.343													7	266	---	---	---	---	PASS
DTL	51514	broad.mit.edu	37	1	212274088	212274088	+	Silent	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212274088T>C	uc009xdc.2	+	14	2070	c.1756T>C	c.(1756-1758)TTG>CTG	p.L586L	DTL_uc010ptb.1_Silent_p.L544L|DTL_uc001hiz.3_Silent_p.L315L	NM_016448	NP_057532	Q9NZJ0	DTL_HUMAN	denticleless homolog	586					DNA replication|G2/M transition DNA damage checkpoint|protein monoubiquitination|protein polyubiquitination|response to UV|translesion synthesis|ubiquitin-dependent protein catabolic process	centrosome|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|nuclear membrane	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		AAATCTTCATTTGGATCTGTG	0.453													16	169	---	---	---	---	PASS
OR2T33	391195	broad.mit.edu	37	1	248437020	248437020	+	Missense_Mutation	SNP	C	T	T	rs138653777		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248437020C>T	uc010pzi.1	-	1	97	c.97G>A	c.(97-99)GTT>ATT	p.V33I		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GAGGTCAAAACGATACTCAGA	0.478													5	171	---	---	---	---	PASS
OR2T6	254879	broad.mit.edu	37	1	248551359	248551359	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248551359C>T	uc001iei.1	+	1	450	c.450C>T	c.(448-450)TTC>TTT	p.F150F		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	150	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCTCTTGGTTCGGTGGGGCTT	0.557													7	79	---	---	---	---	PASS
MSGN1	343930	broad.mit.edu	37	2	17998361	17998361	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17998361C>A	uc010yjt.1	+	1	576	c.576C>A	c.(574-576)AGC>AGA	p.S192R		NM_001105569	NP_001099039	A6NI15	MSGN1_HUMAN	mesogenin 1	192					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GAGCCCAGAGCGCGTGAGCTC	0.547													6	66	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29296170	29296170	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29296170G>A	uc002rmt.1	-	1	958	c.958C>T	c.(958-960)CGC>TGC	p.R320C		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	320			R -> C.		response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						CTCAGGAGGCGTTCATCCACA	0.597													38	246	---	---	---	---	PASS
LRRTM1	347730	broad.mit.edu	37	2	80530234	80530234	+	Silent	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80530234C>A	uc002sok.1	-	2	981	c.711G>T	c.(709-711)TCG>TCT	p.S237S	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	237	LRR 7.|Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5						GCAGGCAGAGCGAGTGCAGGG	0.577										HNSCC(69;0.2)			4	158	---	---	---	---	PASS
NCAPH	23397	broad.mit.edu	37	2	97024978	97024978	+	Intron	SNP	A	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97024978A>C	uc002svz.1	+						NCAPH_uc010fhu.1_3'UTR|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)				AGTGTAGATGACCAGCCAGTC	0.498													11	34	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109381816	109381816	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109381816G>A	uc002tem.3	+	20	4947	c.4821G>A	c.(4819-4821)GAG>GAA	p.E1607E		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	1607	RanBP2-type 5.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						CTAAGAAGGAGGGACAGTGGG	0.433													5	175	---	---	---	---	PASS
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma 								7	143	---	---	---	---	PASS
MYL1	4632	broad.mit.edu	37	2	211179711	211179711	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211179711G>A	uc002vec.2	-	1	185	c.56C>T	c.(55-57)GCC>GTC	p.A19V		NM_079420	NP_524144	P05976	MYL1_HUMAN	fast skeletal myosin alkali light chain 1	19					muscle filament sliding|muscle organ development	cytosol|muscle myosin complex|sarcomere	calcium ion binding|structural constituent of muscle			ovary(1)	1				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)		cggtgccggggctggggcAGC	0.318													8	91	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215890474	215890474	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215890474G>A	uc002vew.2	-	11	1430	c.1210C>T	c.(1210-1212)CGA>TGA	p.R404*	ABCA12_uc002vev.2_Nonsense_Mutation_p.R86*|ABCA12_uc010zjn.1_Translation_Start_Site	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	404					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TTTTTAAATCGTATTGTGGAC	0.348													14	131	---	---	---	---	PASS
NEU4	129807	broad.mit.edu	37	2	242758176	242758176	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242758176C>A	uc010fzr.2	+	4	1343	c.1257C>A	c.(1255-1257)TAC>TAA	p.Y419*	NEU4_uc002wcl.2_RNA|NEU4_uc002wcm.2_Nonsense_Mutation_p.Y419*|NEU4_uc002wcn.1_Nonsense_Mutation_p.Y431*|NEU4_uc002wco.1_Nonsense_Mutation_p.Y419*|NEU4_uc002wcp.1_Nonsense_Mutation_p.Y431*	NM_080741	NP_542779	Q8WWR8	NEUR4_HUMAN	sialidase 4	419		Nucleophile (By similarity).				lysosomal lumen|organelle inner membrane	exo-alpha-sialidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CCAGCGGCTACTCCGACCTGG	0.657													6	18	---	---	---	---	PASS
ARPP21	10777	broad.mit.edu	37	3	35785388	35785388	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35785388C>T	uc003cgb.2	+	18	2227	c.1963C>T	c.(1963-1965)CGG>TGG	p.R655W	ARPP21_uc003cga.2_Missense_Mutation_p.R636W|ARPP21_uc011axy.1_Missense_Mutation_p.R656W|ARPP21_uc003cgf.2_Missense_Mutation_p.R491W|ARPP21_uc003cgg.2_Missense_Mutation_p.R178W|uc011axz.1_5'Flank|MIR128-2_hsa-mir-128-2|MI0000727_5'Flank	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	655	Gln-rich.					cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						GCAACAGTACCGGCCCATGGC	0.493													5	193	---	---	---	---	PASS
CASR	846	broad.mit.edu	37	3	122003254	122003254	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122003254G>T	uc003eev.3	+	7	2825	c.2453G>T	c.(2452-2454)TGG>TTG	p.W818L	CASR_uc003eew.3_Missense_Mutation_p.W828L	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	818	Helical; Name=6; (Potential).				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	TTCATCGTCTGGATCTCCTTC	0.527													4	156	---	---	---	---	PASS
SDHAP2	727956	broad.mit.edu	37	3	195410627	195410627	+	Missense_Mutation	SNP	A	G	G	rs6583272	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195410627A>G	uc003fuw.2	+	13	1718	c.524A>G	c.(523-525)CAG>CGG	p.Q175R	SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						CCTCAGGTGCAGATTGATGAG	0.473													4	12	---	---	---	---	PASS
HTT	3064	broad.mit.edu	37	4	3148562	3148562	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3148562G>A	uc011bvq.1	+	26	3333	c.3188G>A	c.(3187-3189)AGC>AAC	p.S1063N		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	1061					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TCTAGGAAGAGCTGTACCGTT	0.468													14	637	---	---	---	---	PASS
KLHL5	51088	broad.mit.edu	37	4	39064620	39064620	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39064620T>G	uc003gts.2	+	1	561	c.486T>G	c.(484-486)AGT>AGG	p.S162R	KLHL5_uc003gtp.2_Missense_Mutation_p.S116R|KLHL5_uc003gtq.2_Intron|KLHL5_uc003gtr.1_Missense_Mutation_p.S162R|KLHL5_uc003gtt.2_Missense_Mutation_p.S162R	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1	162						cytoplasm|cytoskeleton	actin binding			ovary(1)	1						ATGGCACTAGTGAAGAAGAAA	0.418													6	168	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46099328	46099328	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46099328G>A	uc003gxb.2	-	2	295	c.143C>T	c.(142-144)ACG>ATG	p.T48M		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	48	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		TTTGTTCACCGTTAAATCCTC	0.343													14	291	---	---	---	---	PASS
SLAIN2	57606	broad.mit.edu	37	4	48422300	48422300	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48422300C>T	uc003gya.3	+	7	1663	c.1519C>T	c.(1519-1521)CAG>TAG	p.Q507*		NM_020846	NP_065897	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	507						centrosome					0						TCCTATGGTTCAGAGCACAGT	0.512													4	173	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69693267	69693267	+	Splice_Site	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69693267G>A	uc003hee.2	+	5	1332	c.1307_splice	c.e5+1	p.S436_splice	UGT2B10_uc011cam.1_Splice_Site_p.S352_splice	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity	p.?(2)		skin(3)|ovary(2)	5						ATGATCCTTCGTGAGTAGAAC	0.383													12	210	---	---	---	---	PASS
DCTD	1635	broad.mit.edu	37	4	183812459	183812459	+	3'UTR	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183812459G>A	uc003ivf.2	-	6					DCTD_uc003ivg.2_3'UTR|DCTD_uc010irw.2_3'UTR|DCTD_uc003ivh.2_3'UTR	NM_001921	NP_001912	P32321	DCTD_HUMAN	dCMP deaminase isoform b						nucleotide biosynthetic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide metabolic process	cytosol	dCMP deaminase activity|zinc ion binding				0		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)		ATACTGGCTAGTAAGAAGTTA	0.368													11	57	---	---	---	---	PASS
LYSMD3	116068	broad.mit.edu	37	5	89815106	89815106	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89815106G>C	uc003kjr.2	-	3	599	c.451C>G	c.(451-453)CTT>GTT	p.L151V	LYSMD3_uc010jaz.1_Intron|LYSMD3_uc003kjs.1_3'UTR	NM_198273	NP_938014	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain	151	Extracellular (Potential).				cell wall macromolecule catabolic process	integral to membrane					0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		CTGTAAGCAAGAGAATCATTA	0.393													4	197	---	---	---	---	PASS
ST8SIA4	7903	broad.mit.edu	37	5	100147519	100147519	+	3'UTR	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100147519A>G	uc003knk.2	-	5						NM_005668	NP_005659	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide						axon guidance|N-glycan processing	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			large_intestine(1)|central_nervous_system(1)	2		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		TCTTCAGAAAAGAAGTGCATA	0.363													4	63	---	---	---	---	PASS
DND1	373863	broad.mit.edu	37	5	140052407	140052407	+	Missense_Mutation	SNP	G	A	A	rs76991427		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140052407G>A	uc003lgt.2	-	3	271	c.227C>T	c.(226-228)CCG>CTG	p.P76L		NM_194249	NP_919225	Q8IYX4	DND1_HUMAN	dead end homolog 1	76	RRM 1.				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGAACAGCGGGATAAGCTG	0.667													3	18	---	---	---	---	PASS
PCDHA10	56139	broad.mit.edu	37	5	140237082	140237082	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140237082G>A	uc003lhx.2	+	1	1449	c.1449G>A	c.(1447-1449)GCG>GCA	p.A483A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Silent_p.A483A|PCDHA10_uc011dad.1_Silent_p.A483A	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	483	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGCGGACGCGCAGGAGAACG	0.662													6	210	---	---	---	---	PASS
PCDHB8	56128	broad.mit.edu	37	5	140559493	140559493	+	Silent	SNP	C	T	T	rs34866056		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559493C>T	uc011dai.1	+	1	2064	c.1878C>T	c.(1876-1878)CGC>CGT	p.R626R	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	626	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGAGGTGCGCACCGCCAGGC	0.701													6	103	---	---	---	---	PASS
PCDHB10	56126	broad.mit.edu	37	5	140574045	140574045	+	Silent	SNP	C	G	G	rs619668	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140574045C>G	uc003lix.2	+	1	2094	c.1920C>G	c.(1918-1920)CTC>CTG	p.L640L		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	640	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGCACAGGCTCGTGGTGCTTG	0.682													9	50	---	---	---	---	PASS
PCDHGA2	56113	broad.mit.edu	37	5	140720422	140720422	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140720422G>A	uc003ljk.1	+	1	2069	c.1884G>A	c.(1882-1884)ACG>ACA	p.T628T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Silent_p.T628T	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	628	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGCGCACGGCGCGAGCCC	0.682													14	154	---	---	---	---	PASS
PCDHGA10	56106	broad.mit.edu	37	5	140794395	140794395	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140794395G>A	uc003lkl.1	+	1	1653	c.1653G>A	c.(1651-1653)TCG>TCA	p.S551S	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_uc011day.1_Silent_p.S551S|PCDHGB7_uc003lkm.2_5'Flank|PCDHGB7_uc003lkn.1_5'Flank	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1	551	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAACGTGTCGTTGAGCCTGT	0.597													10	329	---	---	---	---	PASS
FAT2	2196	broad.mit.edu	37	5	150928993	150928993	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150928993T>C	uc003lue.3	-	8	4665	c.4652A>G	c.(4651-4653)CAC>CGC	p.H1551R	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1551	Extracellular (Potential).|Cadherin 13.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGGGGTGGGTGGAGGTTTCC	0.567													7	94	---	---	---	---	PASS
FOXF2	2295	broad.mit.edu	37	6	1390758	1390758	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1390758G>A	uc003mtm.2	+	1	690	c.576G>A	c.(574-576)CGG>CGA	p.R192R	FOXF2_uc003mtn.2_Silent_p.R192R	NM_001452	NP_001443	Q12947	FOXF2_HUMAN	forkhead box F2	192					epithelial to mesenchymal transition|genitalia development|palate development|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		TCCGCCGCCGGCCGCGCGGCT	0.706													4	135	---	---	---	---	PASS
HLA-C	3107	broad.mit.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	T	T	rs2308538	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31239613C>T	uc003nsy.2	-	2	113	c.106G>A	c.(106-108)GTG>ATG	p.V36M	HLA-C_uc011dnj.1_Missense_Mutation_p.V8M|HLA-C_uc003nsx.2_Translation_Start_Site|HLA-C_uc003nsz.2_Missense_Mutation_p.V36M|HLA-C_uc010jsl.2_Missense_Mutation_p.V36M|HLA-C_uc003nta.2_Missense_Mutation_p.V36M|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-C_uc011dnl.1_Translation_Start_Site|HLA-B_uc003ntf.2_Intron	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C	36	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						GGCCGGGACACGGCGGTGTCG	0.721													4	32	---	---	---	---	PASS
PIM1	5292	broad.mit.edu	37	6	37139130	37139130	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37139130A>C	uc003onk.2	+	4	900	c.470A>C	c.(469-471)CAC>CCC	p.H157P	PIM1_uc011dtw.1_5'Flank	NM_002648	NP_002639	P11309	PIM1_HUMAN	non-specific serine/threonine protein kinase	248	Protein kinase.				cell cycle|cell proliferation|multicellular organismal development|negative regulation of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|protein autophosphorylation	cytoplasm|nucleus|plasma membrane	ATP binding|manganese ion binding|protein binding|protein binding|protein serine/threonine kinase activity|transcription factor binding			large_intestine(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	GCCGTGCGGCACTGCCACAAC	0.617			T	BCL6	NHL								13	86	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66205045	66205045	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66205045T>C	uc011dxu.1	-	4	797	c.259A>G	c.(259-261)ATC>GTC	p.I87V	EYS_uc003peq.2_Missense_Mutation_p.I87V|EYS_uc003per.1_Missense_Mutation_p.I87V|EYS_uc010kaj.1_RNA	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	87					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ATTACAAGGATATCTCCTAAT	0.363													7	228	---	---	---	---	PASS
MAD1L1	8379	broad.mit.edu	37	7	1855777	1855777	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1855777G>A	uc003slh.1	-	19	2352	c.2086C>T	c.(2086-2088)CGC>TGC	p.R696C	MAD1L1_uc003sle.1_Missense_Mutation_p.R425C|MAD1L1_uc003slf.1_Missense_Mutation_p.R696C|MAD1L1_uc003slg.1_Missense_Mutation_p.R696C|MAD1L1_uc010ksh.1_Missense_Mutation_p.R696C|MAD1L1_uc003sli.1_Missense_Mutation_p.R604C|MAD1L1_uc003sld.1_Missense_Mutation_p.R152C	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein	696					cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		CTGTCCTGGCGCCGCAGGTGC	0.672													7	105	---	---	---	---	PASS
MEOX2	4223	broad.mit.edu	37	7	15725595	15725595	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15725595C>T	uc003stc.2	-	1	714	c.433G>A	c.(433-435)GCG>ACG	p.A145T	MEOX2_uc011jxw.1_Missense_Mutation_p.A145T	NM_005924	NP_005915	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	145					blood circulation|multicellular organismal development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		TCCCCCGGCGCGCACGCGGCC	0.711													5	219	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43484982	43484982	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43484982C>T	uc003tid.1	+	11	2816	c.2211C>T	c.(2209-2211)GAC>GAT	p.D737D	HECW1_uc011kbi.1_Silent_p.D737D	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	737					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						CCTCGCAAGACGACGAGGAGG	0.652													76	122	---	---	---	---	PASS
KIAA1549	57670	broad.mit.edu	37	7	138603105	138603105	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138603105C>G	uc011kql.1	-	2	1316	c.1267G>C	c.(1267-1269)GCC>CCC	p.A423P	KIAA1549_uc003vuk.3_Missense_Mutation_p.A373P|KIAA1549_uc011kqj.1_Missense_Mutation_p.A423P	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	423						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						ACAGTGCAGGCCGCACACCAA	0.562			O	BRAF	pilocytic astrocytoma								57	80	---	---	---	---	PASS
OR2A5	393046	broad.mit.edu	37	7	143747902	143747902	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143747902G>A	uc011ktw.1	+	1	408	c.408G>A	c.(406-408)ATG>ATA	p.M136I		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	136	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)					CTGTCATCATGAGATGGGGAG	0.512													7	441	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	148979201	148979201	+	Intron	SNP	T	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148979201T>A	uc003wfr.3	+						uc011kuo.1_5'Flank					Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																		CGCCTGCCCCTACTGCGGCAA	0.706													7	41	---	---	---	---	PASS
KCNB2	9312	broad.mit.edu	37	8	73480433	73480433	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73480433A>T	uc003xzb.2	+	2	1052	c.464A>T	c.(463-465)GAG>GTG	p.E155V		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	155	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)			CTGAGGCGAGAGGCAGAGACT	0.453													9	185	---	---	---	---	PASS
GDF6	392255	broad.mit.edu	37	8	97156855	97156855	+	Missense_Mutation	SNP	G	A	A	rs140782427		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97156855G>A	uc003yhp.2	-	2	1404	c.1304C>T	c.(1303-1305)GCG>GTG	p.A435V		NM_001001557	NP_001001557	Q6KF10	GDF6_HUMAN	growth differentiation factor 6 precursor	435					activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(1)|breast(1)|pancreas(1)	3	Breast(36;2.67e-05)					ATTATTGCCCGCGTCGATGTA	0.602													7	56	---	---	---	---	PASS
SDC2	6383	broad.mit.edu	37	8	97605800	97605800	+	Silent	SNP	C	T	T	rs1126681	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97605800C>T	uc003yhv.1	+	2	771	c.153C>T	c.(151-153)TAC>TAT	p.Y51Y	SDC2_uc011lgu.1_Silent_p.Y22Y	NM_002998	NP_002989	P34741	SDC2_HUMAN	syndecan 2 precursor	51	Extracellular (Potential).					integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)	ACGATGACTACGCTTCTGCGT	0.473													4	168	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142185524	142185524	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142185524G>T	uc003yvy.2	+	14	2539	c.2261G>T	c.(2260-2262)GGC>GTC	p.G754V	DENND3_uc010mep.2_Missense_Mutation_p.G715V|DENND3_uc003yvz.1_Missense_Mutation_p.G438V	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	754										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			GGAAGGCCAGGCTACTTGGAG	0.468											OREG0019025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	160	---	---	---	---	PASS
C9orf93	203238	broad.mit.edu	37	9	15744747	15744747	+	Silent	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15744747A>G	uc003zmd.2	+	17	2841	c.2526A>G	c.(2524-2526)GGA>GGG	p.G842G	C9orf93_uc010mih.1_Silent_p.G850G|C9orf93_uc003zme.2_Silent_p.G757G|C9orf93_uc011lmu.1_Silent_p.G850G|C9orf93_uc003zmf.1_Silent_p.G150G	NM_173550	NP_775821	Q6TFL3	CI093_HUMAN	hypothetical protein LOC203238	842											0				GBM - Glioblastoma multiforme(50;4.84e-07)		TGTGCACAGGAGAGCCCCAAG	0.398													34	57	---	---	---	---	PASS
IFNA10	3446	broad.mit.edu	37	9	21206631	21206631	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21206631C>G	uc003zoq.1	-	1	512	c.466G>C	c.(466-468)GAG>CAG	p.E156Q	IFNA14_uc003zoo.1_Intron	NM_002171	NP_002162	P01566	IFN10_HUMAN	interferon, alpha 10 precursor	156					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TATTTCCTCTCTATTAGATAA	0.448													8	723	---	---	---	---	PASS
KIAA1045	23349	broad.mit.edu	37	9	34971518	34971518	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34971518G>A	uc003zvq.2	+	2	401	c.223G>A	c.(223-225)GGC>AGC	p.G75S	KIAA1045_uc003zvr.2_Missense_Mutation_p.G75S	NM_015297	NP_056112	Q9UPV7	K1045_HUMAN	hypothetical protein LOC23349	75							calcium ion binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00575)			GAGTAGTGCCGGCCGCGCAGC	0.652													67	103	---	---	---	---	PASS
PCSK5	5125	broad.mit.edu	37	9	78790187	78790187	+	Intron	SNP	G	C	C	rs10118321		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78790187G>C	uc004ajz.2	+						PCSK5_uc004ajy.2_Missense_Mutation_p.W681S|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						ggaatggaatggaatcgaatc	0.119													6	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	88430887	88430887	+	RNA	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88430887G>C	uc004aog.1	+	2		c.191G>C			uc004aoh.1_Intron					Homo sapiens cDNA FLJ42532 fis, clone BRACE3003004.																		TGCCAAGGAAGAAATACCAGT	0.348													3	90	---	---	---	---	PASS
C9orf156	51531	broad.mit.edu	37	9	100684719	100684719	+	Silent	SNP	A	C	C	rs3183928	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100684719A>C	uc004axv.1	-	1	134	c.57T>G	c.(55-57)GTT>GTG	p.V19V	C9orf156_uc004axw.1_5'UTR|C9orf156_uc004axx.1_5'UTR|C9orf156_uc010msq.1_5'UTR	NM_016481	NP_057565	Q9BU70	NAP1_HUMAN	Nef associated protein 1	19					interspecies interaction between organisms		hydrolase activity				0		Acute lymphoblastic leukemia(62;0.158)				GAGCCGGCTTAACGCAGCCGC	0.637											OREG0019350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	5	---	---	---	---	PASS
AK1	203	broad.mit.edu	37	9	130630299	130630299	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130630299G>A	uc004bsm.3	-	7	726	c.573C>T	c.(571-573)GAC>GAT	p.D191D		NM_000476	NP_000467	P00568	KAD1_HUMAN	adenylate kinase 1	191					ATP metabolic process|nucleobase, nucleoside and nucleotide interconversion	cytosol	adenylate kinase activity|ATP binding|protein binding				0						ACTTTAGGGCGTCCAGGTGGG	0.667													10	102	---	---	---	---	PASS
GFI1B	8328	broad.mit.edu	37	9	135866396	135866396	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135866396G>A	uc004ccg.2	+	7	1103	c.952G>A	c.(952-954)GAC>AAC	p.D318N	GFI1B_uc010mzy.2_Missense_Mutation_p.D272N	NM_004188	NP_004179	Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription	318	C2H2-type 6.|Mediates interaction with GATA1.|Interaction with ARIH2.				cell proliferation|chromatin modification|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|zinc ion binding	p.D318N(1)		large_intestine(1)|ovary(1)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		GCGCAAGGTGGACCTGCGGCG	0.652													35	128	---	---	---	---	PASS
CHAT	1103	broad.mit.edu	37	10	50835688	50835688	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50835688G>A	uc001jhz.2	+	7	1121	c.968G>A	c.(967-969)CGT>CAT	p.R323H	CHAT_uc001jhv.1_Missense_Mutation_p.R205H|CHAT_uc001jhx.1_Missense_Mutation_p.R205H|CHAT_uc001jhy.1_Missense_Mutation_p.R205H|CHAT_uc001jia.2_Missense_Mutation_p.R205H|CHAT_uc010qgs.1_Missense_Mutation_p.R205H	NM_020549	NP_065574	P28329	CLAT_HUMAN	choline acetyltransferase isoform 2	323					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity	p.R323H(1)		central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)	AATTTCCGCCGTCTCAGTGAG	0.512													10	380	---	---	---	---	PASS
IPMK	253430	broad.mit.edu	37	10	60028894	60028894	+	5'Flank	SNP	C	T	T	rs2251039	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60028894C>T	uc001jkb.2	-						CISD1_uc001jkc.3_5'Flank	NM_152230	NP_689416	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase							nucleus	ATP binding|inositol trisphosphate 6-kinase activity			ovary(1)	1						ACACACGTGCCTACGACCCGC	0.642													10	6	---	---	---	---	PASS
SORBS1	10580	broad.mit.edu	37	10	97192294	97192294	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97192294A>T	uc001kkp.2	-	4	257	c.212T>A	c.(211-213)GTG>GAG	p.V71E	SORBS1_uc001kkn.2_Missense_Mutation_p.V27E|SORBS1_uc001kkm.2_Missense_Mutation_p.V59E|SORBS1_uc001kko.2_Missense_Mutation_p.V71E|SORBS1_uc001kkq.2_Missense_Mutation_p.V71E|SORBS1_uc001kkr.2_Missense_Mutation_p.V39E|SORBS1_uc001kks.2_Missense_Mutation_p.V39E|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_Missense_Mutation_p.V71E|SORBS1_uc001kkv.2_Missense_Mutation_p.V39E|SORBS1_uc001kkw.2_Missense_Mutation_p.V71E|SORBS1_uc010qoe.1_Missense_Mutation_p.V39E|SORBS1_uc010qof.1_Missense_Mutation_p.V39E|SORBS1_uc001kkx.1_Missense_Mutation_p.V39E	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	71					focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		CCGGAGAGTCACCGCTCCCTT	0.517													4	128	---	---	---	---	PASS
COL17A1	1308	broad.mit.edu	37	10	105798243	105798243	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105798243G>A	uc001kxr.2	-	45	3160	c.2991C>T	c.(2989-2991)CCC>CCT	p.P997P		NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	997	Extracellular (Potential).|Triple-helical region.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GGGGCCCAGGGGGCCCTGGCG	0.602													15	340	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	106959827	106959827	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106959827C>T	uc001kyi.1	+	15	2307	c.2080C>T	c.(2080-2082)CGG>TGG	p.R694W	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	694	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity	p.R694R(1)		ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TATCTTCAGCCGGCATTGCAC	0.532													7	214	---	---	---	---	PASS
TDRD1	56165	broad.mit.edu	37	10	115986961	115986961	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115986961A>C	uc001lbg.1	+	23	3459	c.3306A>C	c.(3304-3306)AAA>AAC	p.K1102N	TDRD1_uc001lbf.2_Missense_Mutation_p.K979N|TDRD1_uc001lbh.1_Missense_Mutation_p.K1089N|TDRD1_uc001lbi.1_Missense_Mutation_p.K1093N|TDRD1_uc010qsc.1_Intron|TDRD1_uc001lbj.2_Missense_Mutation_p.K811N	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	1102					DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		CAGTTGAGAAATGTTCTGAGA	0.343													72	130	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093512	1093512	+	Silent	SNP	C	A	A	rs34493663	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093512C>A	uc001lsx.1	+	31	12444	c.12417C>A	c.(12415-12417)ACC>ACA	p.T4139T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4139						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)	ctacgatgaccccaaccccaa	0.129													3	13	---	---	---	---	PASS
KRTAP5-4	387267	broad.mit.edu	37	11	1642976	1642976	+	Silent	SNP	A	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1642976A>C	uc009ycy.1	-	3	573	c.486T>G	c.(484-486)GGT>GGG	p.G162G		NM_001012709	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	176	9 X 4 AA repeats of C-C-X-P.					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)		CCCCCTTGGAACCCCCACAGG	0.662													6	37	---	---	---	---	PASS
PSMA1	5682	broad.mit.edu	37	11	14535392	14535392	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14535392C>A	uc001mlk.2	-	6	531	c.385G>T	c.(385-387)GGT>TGT	p.G129C	PSMA1_uc001mll.2_Missense_Mutation_p.G135C|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Missense_Mutation_p.G104C	NM_002786	NP_002777	P25786	PSA1_HUMAN	proteasome alpha 1 subunit isoform 2	129					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|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	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2						AGACCAACACCATATGGTCTC	0.299													3	69	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587401	55587401	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587401T>C	uc010rin.1	+	1	296	c.296T>C	c.(295-297)GTA>GCA	p.V99A		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	99	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				TTAGGATGCGTAGTACAATTC	0.428													9	502	---	---	---	---	PASS
OR4D6	219983	broad.mit.edu	37	11	59225135	59225135	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59225135C>G	uc010rku.1	+	1	702	c.702C>G	c.(700-702)AAC>AAG	p.N234K		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	234	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						AGGGGCGGAACAAGGCCCTCT	0.587													4	149	---	---	---	---	PASS
MS4A12	54860	broad.mit.edu	37	11	60264884	60264884	+	Missense_Mutation	SNP	A	C	C	rs78557637		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60264884A>C	uc001npr.2	+	2	150	c.93A>C	c.(91-93)CAA>CAC	p.Q31H	MS4A12_uc009ynb.2_Missense_Mutation_p.Q31H	NM_017716	NP_060186	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member	31	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						CTGGATTTCAACAGCCTCTGG	0.488													14	105	---	---	---	---	PASS
TIGD3	220359	broad.mit.edu	37	11	65123520	65123520	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65123520G>C	uc001odo.3	+	2	404	c.241G>C	c.(241-243)GAG>CAG	p.E81Q		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	81	HTH CENPB-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						CGGGATCGACGAGGCTCTGCT	0.627													9	172	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66469126	66469126	+	Silent	SNP	G	A	A	rs144636685		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66469126G>A	uc001ojd.2	-	15	2817	c.2745C>T	c.(2743-2745)GCC>GCT	p.A915A		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	915	Spectrin 6.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						GTAACTGCTCGGCAATGTCAT	0.572													7	260	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92088335	92088335	+	Silent	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92088335C>A	uc001pdj.3	+	1	3074	c.3057C>A	c.(3055-3057)GTC>GTA	p.V1019V		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1019	Cadherin 9.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGCGGCCTGTCTCTCTGTCAT	0.463										TCGA Ovarian(4;0.039)			4	82	---	---	---	---	PASS
CASP1	834	broad.mit.edu	37	11	104899864	104899864	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104899864G>C	uc010rve.1	-	7	1010	c.993C>G	c.(991-993)TGC>TGG	p.C331W	CASP1_uc001pig.2_Missense_Mutation_p.C238W|CASP1_uc001pik.2_Missense_Mutation_p.C294W|CASP1_uc010rvf.1_Missense_Mutation_p.C238W|CASP1_uc010rvg.1_Missense_Mutation_p.C310W|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Missense_Mutation_p.C331W|CASP1_uc009yxi.2_Missense_Mutation_p.C310W|CASP1_uc010rvj.1_Missense_Mutation_p.C331W|CASP1_uc009yxj.2_Missense_Mutation_p.C176W|CASP1_uc010rvk.1_Missense_Mutation_p.C292W	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor	331					cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)	GTGTGGAAGAGCAGAAAGCGA	0.408													13	106	---	---	---	---	PASS
BACE1	23621	broad.mit.edu	37	11	117186309	117186309	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117186309C>G	uc001pqz.2	-	1	664	c.203G>C	c.(202-204)AGG>ACG	p.R68T	BACE1_uc001pqw.2_Missense_Mutation_p.R68T|BACE1_uc001pqx.2_Missense_Mutation_p.R68T|BACE1_uc001pqy.2_Missense_Mutation_p.R68T|BACE1_uc001pra.1_Missense_Mutation_p.R68T	NM_012104	NP_036236	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1 isoform A	68	Extracellular (Potential).				beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		CGACTTGCCCCTCAGGTTGTC	0.711													12	31	---	---	---	---	PASS
ARHGAP32	9743	broad.mit.edu	37	11	128844094	128844094	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128844094C>A	uc009zcp.2	-	20	2956	c.2956G>T	c.(2956-2958)GAA>TAA	p.E986*	ARHGAP32_uc009zcq.1_Nonsense_Mutation_p.E946*|ARHGAP32_uc009zco.2_5'UTR|ARHGAP32_uc001qez.2_Nonsense_Mutation_p.E637*	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	986					cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5						CCTGGCAATTCTACTTCTTCA	0.478													6	215	---	---	---	---	PASS
SPATA19	219938	broad.mit.edu	37	11	133712384	133712384	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133712384G>A	uc001qgv.1	-	5	484	c.433C>T	c.(433-435)CGA>TGA	p.R145*		NM_174927	NP_777587	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19 precursor	145					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrial outer membrane					0	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		GCTTACCTTCGTCTCACCTGC	0.527													8	198	---	---	---	---	PASS
FKBP4	2288	broad.mit.edu	37	12	2910444	2910444	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2910444G>T	uc001qkz.2	+	9	1392	c.1194G>T	c.(1192-1194)CAG>CAT	p.Q398H		NM_002014	NP_002005	Q02790	FKBP4_HUMAN	FK506 binding protein 52	398	Interaction with tubulin (By similarity).				negative regulation of microtubule polymerization or depolymerization|negative regulation of neuron projection development|protein folding	axonal growth cone|cytosol|membrane|microtubule|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity|protein binding, bridging				0			OV - Ovarian serous cystadenocarcinoma(31;0.00105)		Dimethyl sulfoxide(DB01093)	TGTGCCAGCAGCGGATCCGAA	0.567													37	195	---	---	---	---	PASS
TAS2R43	259289	broad.mit.edu	37	12	11244166	11244166	+	Silent	SNP	G	C	C	rs35720106	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11244166G>C	uc001qzq.1	-	1	747	c.663C>G	c.(661-663)ACC>ACG	p.T221T	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176884	NP_795365	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	221	Cytoplasmic (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste	cilium membrane|motile cilium	bitter taste receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TGTGGACCTTGGTGCTGGGAT	0.398													3	13	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546799	11546799	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546799G>A	uc010shk.1	-	3	248	c.213C>T	c.(211-213)CCC>CCT	p.P71P		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GAGGAGGTGGGGGACCTTGAG	0.612													9	439	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13717457	13717457	+	Silent	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13717457G>T	uc001rbt.2	-	13	2894	c.2715C>A	c.(2713-2715)GCC>GCA	p.A905A		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	905	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	CCATGTTCTTGGCCGTGCGCA	0.592													17	326	---	---	---	---	PASS
RACGAP1P	83956	broad.mit.edu	37	12	45457916	45457916	+	RNA	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45457916C>T	uc001rol.2	-	1		c.1279G>A				NR_026583				Homo sapiens FKSG42 (FKSG42) mRNA, complete cds.												0						ATCCACTTTGCTGACGAGGGG	0.433													4	151	---	---	---	---	PASS
C12orf10	60314	broad.mit.edu	37	12	53700067	53700067	+	Missense_Mutation	SNP	G	T	T	rs150319735	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53700067G>T	uc001scp.3	+	5	780	c.728G>T	c.(727-729)CGG>CTG	p.R243L	C12orf10_uc009zmx.2_Missense_Mutation_p.R192L|C12orf10_uc001scq.3_Missense_Mutation_p.R128L	NM_021640	NP_067653	Q86UA3	Q86UA3_HUMAN	MYG1 protein precursor	243										ovary(2)	2						CTGCCAGCCCGGGCCTTGGTG	0.532													6	273	---	---	---	---	PASS
ANKRD52	283373	broad.mit.edu	37	12	56650922	56650922	+	Intron	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56650922G>A	uc001skm.3	-						ANKRD52_uc001skn.1_RNA	NM_173595	NP_775866	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52								protein binding			ovary(2)	2						AGGTATGAAGGAAGCCAGTAA	0.502													7	15	---	---	---	---	PASS
AVPR1A	552	broad.mit.edu	37	12	63543828	63543828	+	Silent	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63543828A>G	uc001sro.1	-	1	2763	c.789T>C	c.(787-789)GGT>GGC	p.G263G		NM_000706	NP_000697	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	263	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)	GGAAGGCCACACCCGCTTGCT	0.587													11	273	---	---	---	---	PASS
RFX4	5992	broad.mit.edu	37	12	107075878	107075878	+	Intron	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107075878G>T	uc001tlr.2	+						RFX4_uc010swv.1_Intron|RFX4_uc001tls.2_Intron|RFX4_uc001tlt.2_Intron|RFX4_uc001tlv.2_5'Flank|uc001tlu.3_RNA	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1						ACATCTATGGGCCTCGAGACA	0.562													9	92	---	---	---	---	PASS
TSC22D1	8848	broad.mit.edu	37	13	45008837	45008837	+	Silent	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45008837A>G	uc001uzn.3	-	3	3638	c.3147T>C	c.(3145-3147)CCT>CCC	p.P1049P	TSC22D1_uc001uzo.1_Intron|TSC22D1_uc001uzm.3_Silent_p.P120P	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1	1049					transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		GGGTGGTGGCAGGGGGGGAGC	0.642													6	32	---	---	---	---	PASS
ATP7B	540	broad.mit.edu	37	13	52513267	52513267	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52513267G>C	uc001vfw.2	-	17	3776	c.3619C>G	c.(3619-3621)CAC>GAC	p.H1207D	ATP7B_uc010adv.2_Missense_Mutation_p.H777D|ATP7B_uc001vfx.2_Missense_Mutation_p.H1000D|ATP7B_uc001vfy.2_Missense_Mutation_p.H1096D|ATP7B_uc010tgt.1_Missense_Mutation_p.H1142D|ATP7B_uc010tgu.1_Missense_Mutation_p.H1159D|ATP7B_uc010tgv.1_Missense_Mutation_p.H1129D|ATP7B_uc001vfv.2_Missense_Mutation_p.H479D|ATP7B_uc010tgs.1_Missense_Mutation_p.H418D	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1207	Cytoplasmic (Potential).				ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)		TGCAGCGTGTGCACAGCCAGG	0.582									Wilson_disease				4	97	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101944634	101944634	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101944634G>A	uc001vox.1	-	8	1072	c.883C>T	c.(883-885)CGT>TGT	p.R295C	NALCN_uc001voy.2_Missense_Mutation_p.R10C|NALCN_uc001voz.2_Missense_Mutation_p.R295C|NALCN_uc001vpa.2_Missense_Mutation_p.R295C	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	295	Extracellular (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GAACGCCAACGGGGAAAGCTG	0.468													8	64	---	---	---	---	PASS
SNAPC1	6617	broad.mit.edu	37	14	62229113	62229113	+	5'UTR	SNP	G	A	A	rs17099207	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62229113G>A	uc001xft.2	+	1						NM_003082	NP_003073	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		TGGTTTCCTGGGCGACCACCG	0.677													3	11	---	---	---	---	PASS
SLC8A3	6547	broad.mit.edu	37	14	70633677	70633677	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70633677C>T	uc001xly.2	-	2	2217	c.1463G>A	c.(1462-1464)CGC>CAC	p.R488H	SLC8A3_uc001xlw.2_Missense_Mutation_p.R488H|SLC8A3_uc001xlx.2_Missense_Mutation_p.R488H|SLC8A3_uc001xlz.2_Missense_Mutation_p.R488H|SLC8A3_uc010ara.2_RNA	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	488	Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CTCCTCTATGCGGACATTGCT	0.527													10	295	---	---	---	---	PASS
GALC	2581	broad.mit.edu	37	14	88459434	88459434	+	Silent	SNP	G	T	T	rs111976362	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88459434G>T	uc001xvt.2	-	1	474	c.75C>A	c.(73-75)GGC>GGA	p.G25G	GALC_uc010tvx.1_Intron|GALC_uc010tvy.1_Silent_p.G25G|GALC_uc010tvz.1_5'Flank|GALC_uc001xvu.1_Silent_p.G25G	NM_000153	NP_000144	P54803	GALC_HUMAN	galactosylceramidase isoform a precursor	25					carbohydrate metabolic process|galactosylceramide catabolic process	lysosome	cation binding|galactosylceramidase activity				0						CCGCGGCGCGGCCCGCCGAAC	0.711													8	8	---	---	---	---	PASS
MIR758	768212	broad.mit.edu	37	14	101492436	101492436	+	RNA	SNP	A	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101492436A>T	hsa-mir-758|MI0003757	+			c.80A>T			MIR329-1_hsa-mir-329-1|MI0001725_5'Flank|MIR329-2_hsa-mir-329-2|MI0001726_5'Flank																	0						AACCCTCAGTATCTAATGCCC	0.507													8	226	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105417068	105417068	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105417068C>G	uc010axc.1	-	7	4840	c.4720G>C	c.(4720-4722)GGG>CGG	p.G1574R	AHNAK2_uc001ypx.2_Missense_Mutation_p.G1474R	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1574						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCAGGTGCCCTTTGAGGCCG	0.607													10	657	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106237878	106237878	+	Intron	SNP	G	A	A	rs28393514	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106237878G>A	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0						TTGGGTGTGCGCCTGGCTGGC	0.692													4	10	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107099378	107099378	+	RNA	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107099378G>A	uc010tyt.1	-	96		c.4385C>T								Parts of antibodies, mostly variable regions.												0						AGAGTCTCAGGGACCCCCCAG	0.567													4	92	---	---	---	---	PASS
ABHD2	11057	broad.mit.edu	37	15	89736470	89736470	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89736470A>G	uc002bnj.2	+	15	1918	c.1001A>G	c.(1000-1002)TAT>TGT	p.Y334C	ABHD2_uc002bnk.2_Missense_Mutation_p.Y334C	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein	334						integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					TTGCAGATTTATGTTCCTCTC	0.408													33	123	---	---	---	---	PASS
POLG	5428	broad.mit.edu	37	15	89871740	89871740	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89871740G>A	uc002bns.3	-	6	1479	c.1197C>T	c.(1195-1197)GAC>GAT	p.D399D	POLG_uc002bnr.3_Silent_p.D399D	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	399					base-excision repair, gap-filling|cell death|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			TGGCCCACACGTCCTGGGCAC	0.607								DNA_polymerases_(catalytic_subunits)					39	45	---	---	---	---	PASS
RUNDC2A	84127	broad.mit.edu	37	16	12136844	12136844	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12136844G>T	uc002dbw.1	+	5	400	c.338G>T	c.(337-339)GGC>GTC	p.G113V		NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A	113	RUN.									ovary(1)	1						TCAGACGTGGGCCGGGGTCGC	0.652			T	CIITA	PMBL|Hodgkin Lymphona|								4	58	---	---	---	---	PASS
ACSM3	6296	broad.mit.edu	37	16	20792044	20792044	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20792044G>C	uc002dhr.2	+	5	834	c.647G>C	c.(646-648)AGT>ACT	p.S216T	ACSM3_uc002dhq.2_Missense_Mutation_p.S216T|ACSM3_uc010vba.1_Missense_Mutation_p.S245T|ERI2_uc002dhs.2_Missense_Mutation_p.L303V	NM_005622	NP_005613	Q53FZ2	ACSM3_HUMAN	SA hypertension-associated homolog isoform 1	216					regulation of blood pressure	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			ovary(1)	1						AGACATGCCAGTGACAGCCAC	0.428													5	219	---	---	---	---	PASS
SCNN1B	6338	broad.mit.edu	37	16	23392149	23392149	+	3'UTR	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23392149T>C	uc002dln.2	+	13						NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CCCGGGCGGCTGAAACTCACT	0.627													16	152	---	---	---	---	PASS
RUNDC2C	440352	broad.mit.edu	37	16	29376056	29376056	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29376056T>A	uc002dsj.1	+	5	795	c.398T>A	c.(397-399)ATC>AAC	p.I133N	uc010vct.1_Intron|RUNDC2C_uc010bys.1_RNA|RUNDC2C_uc010vdo.1_Missense_Mutation_p.I114N	NM_001012391	NP_001012391			RecName: Full=RUN domain-containing protein 2A;												0						ACCAACATTATCTCATTTGAT	0.393													4	134	---	---	---	---	PASS
HERPUD1	9709	broad.mit.edu	37	16	56976046	56976046	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56976046A>G	uc002eke.1	+	7	1317	c.908A>G	c.(907-909)CAT>CGT	p.H303R	HERPUD1_uc002ekf.1_Missense_Mutation_p.H302R|HERPUD1_uc002ekg.1_Missense_Mutation_p.H278R|HERPUD1_uc010cco.1_Missense_Mutation_p.I312V|HERPUD1_uc010ccp.1_Missense_Mutation_p.H205R|HERPUD1_uc002ekh.1_Missense_Mutation_p.H121R	NM_014685	NP_055500	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum	303	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	protein binding				0						CTTTGAAGGCATCACGTTGGG	0.478			T	ERG	prostate								10	263	---	---	---	---	PASS
CDH13	1012	broad.mit.edu	37	16	83704517	83704517	+	Silent	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83704517G>C	uc002fgx.2	+	9	1344	c.1224G>C	c.(1222-1224)GGG>GGC	p.G408G	CDH13_uc010vns.1_Silent_p.G455G|CDH13_uc010vnt.1_Silent_p.G154G|CDH13_uc010vnu.1_Silent_p.G369G	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	408	Cadherin 3.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		GAAACCCCGGGCAGAGCTTTG	0.502													10	221	---	---	---	---	PASS
TNFSF12	8742	broad.mit.edu	37	17	7460486	7460486	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7460486G>C	uc002ghg.2	+	7	665	c.569G>C	c.(568-570)CGC>CCC	p.R190P	TNFSF12_uc002ghh.2_RNA|TNFSF12-TNFSF13_uc002ghi.1_Intron|TNFSF13_uc002ghj.2_5'Flank|TNFSF13_uc002ghk.2_5'Flank|TNFSF13_uc002ghl.2_5'Flank|TNFSF13_uc010cmk.2_5'Flank|TNFSF13_uc010vua.1_5'Flank	NM_003809	NP_003800	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily,	190	Extracellular (Potential).				angiogenesis|apoptosis|cell differentiation|endothelial cell migration|immune response|induction of apoptosis|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|signal transduction	extracellular space|integral to plasma membrane|perinuclear region of cytoplasm	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)				CTGGCCCTGCGCTGCCTGGAG	0.657													28	45	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8052022	8052022	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8052022C>A	uc002gkd.2	-	8	1226	c.988G>T	c.(988-990)GGG>TGG	p.G330W	PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Missense_Mutation_p.G314W	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	330					circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						GCAGGGGCCCCATCTGAGACC	0.642			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					5	203	---	---	---	---	PASS
PIK3R5	23533	broad.mit.edu	37	17	8792523	8792523	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8792523C>T	uc002glt.2	-	9	895	c.828G>A	c.(826-828)GGG>GGA	p.G276G	PIK3R5_uc010vuz.1_Silent_p.G276G|PIK3R5_uc002glu.3_5'UTR|PIK3R5_uc010coa.1_Missense_Mutation_p.G225E|PIK3R5_uc010cob.1_5'UTR	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	276				AKTLAELEDIFTETAEAQELASGIGDAAEARRWLRTKLQAV GEKAGFPGVLDTAKPGKLHTIPIPVARCYTYSWSQDS -> TLQNQGSSIPSPSLSPGATPTAGARTALTSCRKSCSRNRSC SSQGSWEMMKRRKRRRRRWRRTWKLMGTVPREIPCSP (in Ref. 6; AAW63122).	platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						TGTGGAGCTTCCCTGGTTTTG	0.423													17	48	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10405105	10405105	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10405105G>T	uc002gmo.2	-	25	3329	c.3235C>A	c.(3235-3237)CAA>AAA	p.Q1079K	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1079	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						TCATCAAGTTGTTGTTTGTCA	0.343													11	78	---	---	---	---	PASS
SLFN5	162394	broad.mit.edu	37	17	33588030	33588030	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33588030G>C	uc002hjf.3	+	3	1170	c.1053G>C	c.(1051-1053)TTG>TTC	p.L351F	SLFN5_uc010wcg.1_Missense_Mutation_p.L351F	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5	351					cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		AGTTGAGTTTGTCATCTGCCA	0.468													13	281	---	---	---	---	PASS
KRTAP4-12	83755	broad.mit.edu	37	17	39280114	39280114	+	Silent	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39280114T>C	uc002hwa.2	-	1	306	c.261A>G	c.(259-261)AGA>AGG	p.R87R		NM_031854	NP_114060	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	87	15.|31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCACTGGGGTCTGCAGCAGC	0.607													4	98	---	---	---	---	PASS
KRT31	3881	broad.mit.edu	37	17	39551764	39551764	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39551764C>A	uc002hwn.2	-	4	753	c.700G>T	c.(700-702)GCC>TCC	p.A234S	KRT31_uc010cxn.2_Missense_Mutation_p.A234S	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31	234	Coil 2.|Rod.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)				TCCACCAGGGCCTCATACTGA	0.632													4	164	---	---	---	---	PASS
MLX	6945	broad.mit.edu	37	17	40723699	40723699	+	3'UTR	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40723699G>T	uc002iag.2	+	8					MLX_uc002iaf.2_3'UTR|MLX_uc002iah.2_3'UTR	NM_170607	NP_733752	Q9UH92	MLX_HUMAN	transcription factor-like protein 4 isoform						energy reserve metabolic process|negative regulation of transcription, DNA-dependent|positive regulation of cellular metabolic process	cytoplasm|nucleus	DNA binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding				0		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		CTGGGCCCGGGAGACTGGACT	0.507													5	82	---	---	---	---	PASS
RSAD1	55316	broad.mit.edu	37	17	48557076	48557076	+	Silent	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48557076T>C	uc002iqw.1	+	2	278	c.222T>C	c.(220-222)TGT>TGC	p.C74C	RSAD1_uc010wmp.1_Silent_p.C74C|RSAD1_uc010wmq.1_Intron	NM_018346	NP_060816	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing	74					porphyrin biosynthetic process	mitochondrion	4 iron, 4 sulfur cluster binding|coproporphyrinogen oxidase activity|metal ion binding				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TGCAGAAGTGTCTGGTGACCG	0.597											OREG0024566	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	86	---	---	---	---	PASS
GALK1	2584	broad.mit.edu	37	17	73759393	73759393	+	Intron	SNP	G	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73759393G>C	uc010wsi.1	-						GALK1_uc002jpk.2_Intron|GALK1_uc010wsj.1_Missense_Mutation_p.S161R	NM_000154	NP_000145	P51570	GALK1_HUMAN	galactokinase 1						galactose catabolic process	cytosol	ATP binding|galactokinase activity|galactose binding				0	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGGGGCCTAGCTGGTACCTG	0.637													5	97	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	7034620	7034620	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7034620C>T	uc002knm.2	-	14	2003	c.1909G>A	c.(1909-1911)GTG>ATG	p.V637M	LAMA1_uc010wzj.1_Missense_Mutation_p.V113M	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	637	Laminin IV type A 1.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGTCTAACCACGTTTAGGTAC	0.408													5	205	---	---	---	---	PASS
HOOK2	29911	broad.mit.edu	37	19	12878871	12878871	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12878871G>A	uc002muy.2	-	12	1342	c.1171C>T	c.(1171-1173)CGC>TGC	p.R391C	HOOK2_uc010xmq.1_5'Flank|HOOK2_uc002muz.2_Missense_Mutation_p.R391C	NM_013312	NP_037444	Q96ED9	HOOK2_HUMAN	hook homolog 2 isoform 1	391	Sufficient for interaction with microtubules.|Potential.				early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)|skin(1)	3						TCCAGGTTGCGGCATTCAAAT	0.572													5	281	---	---	---	---	PASS
SSBP4	170463	broad.mit.edu	37	19	18545063	18545063	+	3'UTR	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18545063G>A	uc002niy.2	+	18					SSBP4_uc002niz.2_3'UTR	NM_032627	NP_116016	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4 isoform a							nucleus	single-stranded DNA binding				0						GTGATGGGGCGGCAGCCCCGG	0.706													4	76	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38572844	38572844	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38572844G>T	uc002ohk.2	+	3	1148	c.639G>T	c.(637-639)ATG>ATT	p.M213I		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	213					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGCAGGGCATGCCCGAGCAGA	0.721													4	148	---	---	---	---	PASS
LYPD5	284348	broad.mit.edu	37	19	44303066	44303066	+	Missense_Mutation	SNP	C	G	G	rs11547806	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44303066C>G	uc002oxm.3	-	3	349	c.268G>C	c.(268-270)GCG>CCG	p.A90P	LYPD5_uc002oxn.3_Missense_Mutation_p.A47P	NM_001031749	NP_001026919	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5 isoform A	90						anchored to membrane|plasma membrane					0		Prostate(69;0.0352)				AGCGCGTCCGCGTTCGATTGC	0.687													6	10	---	---	---	---	PASS
NKPD1	284353	broad.mit.edu	37	19	45656261	45656261	+	Silent	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45656261C>A	uc010xxi.1	-	4	1434	c.1434G>T	c.(1432-1434)ACG>ACT	p.T478T		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		CGGACAGCAGCGTGTTGATGG	0.672													3	12	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47423299	47423299	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47423299G>A	uc010ekv.2	+	1	1367	c.1367G>A	c.(1366-1368)CGT>CAT	p.R456H		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	456	FF 3.				axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		GAAGAGGCCCGTAGTTTTATT	0.413													4	73	---	---	---	---	PASS
DHX34	9704	broad.mit.edu	37	19	47876082	47876082	+	Missense_Mutation	SNP	G	A	A	rs146830596	byFrequency	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47876082G>A	uc010xyn.1	+	8	2205	c.1864G>A	c.(1864-1866)GCC>ACC	p.A622T	DHX34_uc010elc.1_Missense_Mutation_p.A537T	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	622						intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CACCCGCAGCGCCCAGAGCAG	0.657													10	68	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56369349	56369349	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56369349C>T	uc002qmd.3	+	3	1012	c.590C>T	c.(589-591)CCG>CTG	p.P197L	NLRP4_uc002qmf.2_Missense_Mutation_p.P122L|NLRP4_uc010etf.2_Missense_Mutation_p.P28L	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	197	NACHT.						ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		AGGGAGTTGCCGCCAACGAGT	0.517													89	103	---	---	---	---	PASS
ZNF835	90485	broad.mit.edu	37	19	57175472	57175472	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57175472G>A	uc010ygo.1	-	2	1161	c.1161C>T	c.(1159-1161)CAC>CAT	p.H387H	ZNF835_uc010ygn.1_Silent_p.H365H	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4						TGCCGCAGTCGTGGCAGGGGT	0.701													4	39	---	---	---	---	PASS
C20orf114	92747	broad.mit.edu	37	20	31890815	31890815	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31890815C>A	uc002wyw.1	+	11	1236	c.1075C>A	c.(1075-1077)CAA>AAA	p.Q359K	C20orf114_uc002wyx.1_RNA	NM_033197	NP_149974	Q8TDL5	LPLC1_HUMAN	LPLUNC1 protein precursor	359						extracellular space	lipid binding			central_nervous_system(2)|skin(2)	4						CAAGGTGGCCCAACTGATCGT	0.532													23	76	---	---	---	---	PASS
CD40	958	broad.mit.edu	37	20	44751805	44751805	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44751805C>T	uc002xrg.1	+	5	521	c.444C>T	c.(442-444)GTC>GTT	p.V148V	CD40_uc002xrf.1_3'UTR|CD40_uc002xrh.1_Silent_p.V148V|CD40_uc002xri.1_Silent_p.V148V|CD40_uc002xrj.1_Intron|CD40_uc002xrk.1_Intron	NM_001250	NP_001241	P25942	TNR5_HUMAN	CD40 antigen isoform 1 precursor	148	TNFR-Cys 4.|Extracellular (Potential).				B cell proliferation|cellular response to mechanical stimulus|inflammatory response|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein complex assembly	CD40 receptor complex|extracellular region	enzyme binding|receptor activity			lung(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)			Simvastatin(DB00641)	CCTGCCCAGTCGGCTTCTTCT	0.532									Immune_Deficiency_with_Hyper-IgM				67	153	---	---	---	---	PASS
CDH22	64405	broad.mit.edu	37	20	44869813	44869813	+	Silent	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44869813G>A	uc002xrm.2	-	2	740	c.339C>T	c.(337-339)GAC>GAT	p.D113D	CDH22_uc010ghk.1_Silent_p.D113D	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	113	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				CTGTCAGCTCGTCGATCAGGA	0.627													7	43	---	---	---	---	PASS
POTED	317754	broad.mit.edu	37	21	15011886	15011886	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15011886G>A	uc002yjb.1	+	10	1512	c.1460G>A	c.(1459-1461)GGA>GAA	p.G487E		NM_174981	NP_778146	Q86YR6	POTED_HUMAN	pote protein	487						plasma membrane				ovary(3)|skin(3)	6						CAGAACACTGGAATATCACAA	0.323													3	66	---	---	---	---	PASS
COL6A1	1291	broad.mit.edu	37	21	47423843	47423843	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47423843C>A	uc002zhu.1	+	35	3105	c.3003C>A	c.(3001-3003)AGC>AGA	p.S1001R	COL6A1_uc010gqd.1_Missense_Mutation_p.S332R|COL6A1_uc002zhv.1_Missense_Mutation_p.S332R|COL6A1_uc002zhw.1_Missense_Mutation_p.S95R	NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor	1001	C-terminal globular domain.|VWFA 3.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	ACGGCGAGAGCCACCTGTTCC	0.672													8	157	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23241829	23241829	+	RNA	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23241829G>A	uc011aim.1	+	366		c.15445G>A			uc002zws.2_Intron					Parts of antibodies, mostly variable regions.												0						CAAGCTGACCGTCCTAGGTGA	0.547													7	95	---	---	---	---	PASS
SEZ6L	23544	broad.mit.edu	37	22	26701985	26701985	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26701985C>T	uc003acb.2	+	6	1545	c.1389C>T	c.(1387-1389)CGC>CGT	p.R463R	SEZ6L_uc003acc.2_Silent_p.R463R|SEZ6L_uc011akc.1_Silent_p.R463R|SEZ6L_uc003acd.2_Silent_p.R463R|SEZ6L_uc011akd.1_Silent_p.R463R|SEZ6L_uc003ace.2_Silent_p.R463R|SEZ6L_uc003acf.1_Silent_p.R236R|SEZ6L_uc010gvc.1_Silent_p.R236R	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	463	CUB 2.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						CCATCGGCCGCGTCCTCTCCC	0.483													5	70	---	---	---	---	PASS
C22orf28	51493	broad.mit.edu	37	22	32793937	32793937	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32793937C>A	uc003amm.2	-	7	936	c.805G>T	c.(805-807)GTA>TTA	p.V269L	C22orf28_uc011ama.1_RNA	NM_014306	NP_055121	Q9Y3I0	RTCB_HUMAN	hypothetical protein LOC51493	269					cell-matrix adhesion|substrate adhesion-dependent cell spreading|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|tRNA-splicing ligase complex	ATP binding|metal ion binding|RNA ligase (ATP) activity|vinculin binding				0						CCTGTGGCTACTTGGTGGCCC	0.348													6	67	---	---	---	---	PASS
BRD1	23774	broad.mit.edu	37	22	50217746	50217746	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50217746T>C	uc003biv.2	-	1	707	c.220A>G	c.(220-222)AAC>GAC	p.N74D	BRD1_uc011arf.1_5'UTR|BRD1_uc011arg.1_Missense_Mutation_p.N74D|BRD1_uc011arh.1_Missense_Mutation_p.N74D|BRD1_uc003biu.3_Missense_Mutation_p.N74D	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	74					histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TTGTTGCTGTTGCACTCACTC	0.473													6	200	---	---	---	---	PASS
LMF2	91289	broad.mit.edu	37	22	50941923	50941923	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50941923C>T	uc003blp.2	-	14	2052	c.2021G>A	c.(2020-2022)CGC>CAC	p.R674H	LMF2_uc010hba.2_Missense_Mutation_p.R496H|LMF2_uc003blo.2_Missense_Mutation_p.R649H	NM_033200	NP_149977	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	674						endoplasmic reticulum membrane|integral to membrane				breast(1)	1		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGCTGGCCTGCGCTTCTCCCC	0.662													6	34	---	---	---	---	PASS
PDK3	5165	broad.mit.edu	37	X	24516991	24516991	+	Silent	SNP	C	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24516991C>T	uc004dbg.2	+	3	523	c.294C>T	c.(292-294)AGC>AGT	p.S98S	PDK3_uc004dbh.2_Silent_p.S98S	NM_005391	NP_005382	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase 3 isoform 2	98					glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|protein binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6						AAAATAAGAGCCCTGAGGATC	0.323													31	14	---	---	---	---	PASS
ZCCHC5	203430	broad.mit.edu	37	X	77913571	77913571	+	Missense_Mutation	SNP	G	A	A	rs144237768		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77913571G>A	uc004edc.1	-	2	643	c.347C>T	c.(346-348)GCG>GTG	p.A116V		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	116	Pro-rich.						nucleic acid binding|zinc ion binding			ovary(1)	1						TGCTGGAGGCGCCAGGGACTC	0.627													5	49	---	---	---	---	PASS
PCDH19	57526	broad.mit.edu	37	X	99662413	99662413	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99662413G>A	uc010nmz.2	-	1	2859	c.1183C>T	c.(1183-1185)CGA>TGA	p.R395*	PCDH19_uc004efw.3_Nonsense_Mutation_p.R395*|PCDH19_uc004efx.3_Nonsense_Mutation_p.R395*	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	395	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7						TCCTGCAGTCGAAAGGGCACA	0.607													7	125	---	---	---	---	PASS
PLP1	5354	broad.mit.edu	37	X	103045510	103045510	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103045510G>A	uc010nov.2	+	8	1098	c.818G>A	c.(817-819)CGA>CAA	p.R273Q	RAB9B_uc004eli.1_Intron|PLP1_uc004elk.2_Missense_Mutation_p.R273Q|PLP1_uc004elj.2_Missense_Mutation_p.R238Q|PLP1_uc011msf.1_Missense_Mutation_p.R218Q|PLP1_uc010nox.2_Missense_Mutation_p.R227Q	NM_001128834	NP_001122306	P60201	MYPR_HUMAN	proteolipid protein 1 isoform 1	273	Cytoplasmic (Probable).				cell death|synaptic transmission	integral to membrane				ovary(1)	1						CTCATGGGCCGAGGCACCAAG	0.473													9	153	---	---	---	---	PASS
MCF2	4168	broad.mit.edu	37	X	138713596	138713596	+	Silent	SNP	G	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138713596G>T	uc004fau.2	-	3	540	c.246C>A	c.(244-246)GGC>GGA	p.G82G	MCF2_uc004fav.2_Silent_p.G82G|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Silent_p.G82G|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Silent_p.G227G|MCF2_uc004faw.2_Silent_p.G142G|MCF2_uc011mwo.1_Silent_p.G142G	NM_005369	NP_005360	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	82	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)					ACTGCAAGGTGCCGCCTAACT	0.388													4	163	---	---	---	---	PASS
MAGEA12	4111	broad.mit.edu	37	X	151896701	151896701	+	RNA	SNP	G	T	T	rs139874720	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151896701G>T	uc004fgb.2	-	3		c.276C>A						P43365	MAGAC_HUMAN	Homo sapiens melanoma antigen family A, 12, mRNA (cDNA clone MGC:4914 IMAGE:3450217), complete cds.											skin(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					AGTGaaggcaggccagcaggc	0.269													7	76	---	---	---	---	PASS
SPRY3	10251	broad.mit.edu	37	X	155003970	155003970	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155003970T>A	uc004fnq.1	+	2	891	c.437T>A	c.(436-438)ATC>AAC	p.I146N	SPRY3_uc010nvl.1_Intron	NM_005840	NP_005831	O43610	SPY3_HUMAN	sprouty homolog 3	146					multicellular organismal development|regulation of signal transduction	cytoplasm|membrane					0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CACCTCTTCATCTGTGAGGAA	0.612													7	221	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1580356	1580356	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1580356delA	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|CDK11B_uc010nyr.1_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						ctctgcctccaaaaaaaaaaa	0.299													4	2	---	---	---	---	
MEGF6	1953	broad.mit.edu	37	1	3418615	3418615	+	Intron	DEL	G	-	-	rs111656273		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3418615delG	uc001akl.2	-						MEGF6_uc001akk.2_Intron	NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor							extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GTGCCCCCCCGGCGCCTCCTC	0.711													8	5	---	---	---	---	
PADI4	23569	broad.mit.edu	37	1	17660223	17660223	+	Intron	DEL	G	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17660223delG	uc001baj.2	+						PADI4_uc009vpc.2_Intron	NM_012387	NP_036519	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV						chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	ctccattgctgggcccccata	0.000													4	2	---	---	---	---	
YTHDF2	51441	broad.mit.edu	37	1	29095640	29095640	+	3'UTR	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29095640delA	uc001brc.2	+	5					YTHDF2_uc001brd.2_3'UTR|YTHDF2_uc010ofx.1_3'UTR|YTHDF2_uc001bre.2_3'UTR	NM_016258	NP_057342	Q9Y5A9	YTHD2_HUMAN	high glucose-regulated protein 8						humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGaaaatgaaaaaaaaaag	0.289													5	3	---	---	---	---	
DCDC2B	149069	broad.mit.edu	37	1	32680712	32680712	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32680712delA	uc001bun.2	+						C1orf91_uc001buo.3_Intron|C1orf91_uc001bup.3_Intron	NM_001099434	NP_001092904	A2VCK2	DCD2B_HUMAN	doublecortin domain containing 2B						intracellular signal transduction						0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GACTGCCCGTAAAAAAAAAAA	0.458													9	4	---	---	---	---	
CYP4Z2P	163720	broad.mit.edu	37	1	47325313	47325315	+	RNA	DEL	GTT	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47325313_47325315delGTT	uc001cqo.1	-	9		c.1253_1255delAAC				NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0						AAAAAAAAAAGTTGTTTTAAGAC	0.409													162	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121484513	121484513	+	IGR	DEL	T	-	-	rs74212356		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121484513delT								LOC647121 (170827 upstream) : None (None downstream)																							tatttgcaagtggagatttca	0.000													2050	7	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205036040	205036041	+	Intron	INS	-	G	G	rs151113569	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205036040_205036041insG	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron|CNTN2_uc001hbs.2_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CACACAGCATTGCAGAGGCACC	0.317													7	6	---	---	---	---	
CAPN9	10753	broad.mit.edu	37	1	230916617	230916618	+	Intron	INS	-	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230916617_230916618insT	uc001htz.1	+						CAPN9_uc009xfg.1_Intron|CAPN9_uc001hua.1_Intron	NM_006615	NP_006606	O14815	CAN9_HUMAN	calpain 9 isoform 1						digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				tttattattaattttttttttt	0.198													3	3	---	---	---	---	
RASGRP3	25780	broad.mit.edu	37	2	33746842	33746843	+	Intron	INS	-	C	C	rs11676264	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33746842_33746843insC	uc002rox.2	+						RASGRP3_uc010ync.1_Intron|RASGRP3_uc002roy.2_Intron	NM_170672	NP_733772	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and						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)					aaaaacaactgcaagtttatgt	0.109													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	39723084	39723085	+	Intron	INS	-	CTTC	CTTC	rs145006304	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39723084_39723085insCTTC	uc002rrq.2	+						uc002rrr.1_Intron					Homo sapiens cDNA FLJ33477 fis, clone BRAMY2002604.																		tctttctttttcttccttcctt	0.064													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49509859	49509860	+	IGR	INS	-	T	T	rs142578046	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49509859_49509860insT								FSHR (128229 upstream) : NRXN1 (635784 downstream)																							AAATTCCTTTCTTTTTATCCTC	0.431													1	5	---	---	---	---	
ZNF638	27332	broad.mit.edu	37	2	71582900	71582900	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71582900delT	uc002shx.2	+	3	1688	c.1369delT	c.(1369-1371)TTAfs	p.L457fs	ZNF638_uc010fec.2_Frame_Shift_Del_p.L563fs|ZNF638_uc010yqw.1_Intron|ZNF638_uc002shw.2_Frame_Shift_Del_p.L457fs|ZNF638_uc002shy.2_Frame_Shift_Del_p.L457fs|ZNF638_uc002shz.2_Frame_Shift_Del_p.L457fs|ZNF638_uc002sia.2_Frame_Shift_Del_p.L457fs|ZNF638_uc002sib.1_Frame_Shift_Del_p.L457fs	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	457					RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						CTGTCGACAGTTACGTCAACA	0.289													74	7	---	---	---	---	
SMYD1	150572	broad.mit.edu	37	2	88409719	88409720	+	Intron	INS	-	GTGT	GTGT	rs139694354	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88409719_88409720insGTGT	uc002ssr.2	+						SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_Intron	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						TTGATGAATGAgtgtgtgtgtg	0.411													4	2	---	---	---	---	
REV1	51455	broad.mit.edu	37	2	100052594	100052595	+	Intron	INS	-	GTTT	GTTT	rs145209140	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100052594_100052595insGTTT	uc002tad.2	-						REV1_uc002tac.2_Intron	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						GTCTCTAATTAGTCAAAAAGTG	0.292								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					3	3	---	---	---	---	
RANBP2	5903	broad.mit.edu	37	2	109369249	109369249	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109369249delA	uc002tem.3	+							NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						actctgtctcaaaaaaaaaaa	0.144													9	5	---	---	---	---	
UNC80	285175	broad.mit.edu	37	2	210640560	210640561	+	Intron	INS	-	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210640560_210640561insA	uc010zjc.1	+						UNC80_uc002vdj.1_Intron	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1							integral to membrane					0						TTTCTTAGTTTACGTGgttttg	0.322													68	10	---	---	---	---	
SEPT2	4735	broad.mit.edu	37	2	242282913	242282913	+	Intron	DEL	A	-	-	rs71967730		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242282913delA	uc002wbc.2	+						SEPT2_uc002wbd.2_Intron|SEPT2_uc002wbf.2_Intron|SEPT2_uc002wbg.2_Intron|SEPT2_uc002wbh.2_Intron|SEPT2_uc010zop.1_Intron	NM_001008491	NP_001008491	Q15019	SEPT2_HUMAN	septin 2						cell division|mitosis	actin cytoskeleton|cleavage furrow|condensed chromosome kinetochore|midbody|nucleolus|septin complex|spindle	GTP binding			central_nervous_system(1)	1		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		actctgtctcaaaaaaaaaaa	0.129													29	7	---	---	---	---	
HEG1	57493	broad.mit.edu	37	3	124738635	124738635	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124738635delA	uc003ehs.3	-						HEG1_uc011bke.1_Intron	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor							extracellular region|integral to membrane	calcium ion binding			ovary(2)	2						AGAGTAATACAAAAAAATATA	0.333													6	4	---	---	---	---	
GPR125	166647	broad.mit.edu	37	4	22449283	22449283	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22449283delA	uc003gqm.1	-						GPR125_uc010ieo.1_Intron|GPR125_uc003gqo.2_Intron	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				GAGCGATTAGAAAACACTTCC	0.284													5	7	---	---	---	---	
LIMCH1	22998	broad.mit.edu	37	4	41689701	41689701	+	Intron	DEL	A	-	-	rs5857811		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41689701delA	uc003gvu.3	+						LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron|LIMCH1_uc011byu.1_Intron|LIMCH1_uc003gwc.3_Intron|LIMCH1_uc003gwd.3_Intron|LIMCH1_uc011byv.1_Intron|LIMCH1_uc011byw.1_Intron	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						TTTGTTCATTAAAAAAAAAAA	0.289													4	2	---	---	---	---	
TBC1D9	23158	broad.mit.edu	37	4	141545161	141545162	+	Intron	INS	-	AA	AA	rs151003995	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141545161_141545162insAA	uc010ioj.2	-							NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GTAAAGGCCCCAGTTATTATTT	0.347													2	4	---	---	---	---	
FGB	2244	broad.mit.edu	37	4	155489853	155489856	+	Intron	DEL	AAAA	-	-	rs140754470		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155489853_155489856delAAAA	uc003ioa.3	+						FGB_uc003iob.3_Intron|FGB_uc010ipv.2_Intron|FGB_uc010ipw.2_Intron|FGB_uc003ioc.3_Intron	NM_005141	NP_005132	P02675	FIBB_HUMAN	fibrinogen, beta chain preproprotein						platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen|soluble fraction	chaperone binding|eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	aaaaaataccaaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SLC22A5	6584	broad.mit.edu	37	5	131726325	131726325	+	Intron	DEL	C	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131726325delC	uc003kww.3	+						SLC22A5_uc003kwx.3_Intron|SLC22A5_uc010jdr.1_Intron	NM_003060	NP_003051	O76082	S22A5_HUMAN	solute carrier family 22 member 5						positive regulation of intestinal epithelial structure maintenance|quorum sensing involved in interaction with host|sodium ion transport|sodium-dependent organic cation transport	apical plasma membrane|brush border membrane|integral to membrane	ATP binding|carnitine transporter activity|PDZ domain binding|symporter activity				0		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)	AAAAGTTGTACAGGTTGGGAA	0.408													127	14	---	---	---	---	
ZCCHC10	54819	broad.mit.edu	37	5	132334285	132334287	+	In_Frame_Del	DEL	TTC	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132334285_132334287delTTC	uc003kyh.2	-	5	578_580	c.567_569delGAA	c.(565-570)AAGAAA>AAA	p.189_190KK>K	ZCCHC10_uc003kyg.2_In_Frame_Del_p.167_168KK>K|ZCCHC10_uc011cxl.1_In_Frame_Del_p.153_154KK>K	NM_017665	NP_060135	Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	189_190	Poly-Lys.						nucleic acid binding|zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTATTTCTTTTTCTTCTTCTTTG	0.369													109	7	---	---	---	---	
TXNDC15	79770	broad.mit.edu	37	5	134232341	134232342	+	Intron	INS	-	T	T	rs11438328		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134232341_134232342insT	uc003lac.1	+						TXNDC15_uc010jdy.1_Intron|TXNDC15_uc011cxv.1_Intron	NM_024715	NP_078991	Q96J42	TXD15_HUMAN	disulfide isomerase precursor						cell redox homeostasis	integral to membrane				ovary(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ttttttttcccttttttttttt	0.114													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58776848	58776848	+	IGR	DEL	T	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58776848delT								GUSBL2 (489124 upstream) : None (None downstream)																							tgagacaccgtttttgtagaa	0.000													525	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58778432	58778451	+	IGR	DEL	AAAAGGGAATATCTTTCCAT	-	-	rs4428530		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58778432_58778451delAAAAGGGAATATCTTTCCAT								GUSBL2 (490708 upstream) : None (None downstream)																							cctatggtagaaaagggaatatctttccataaaaggtaga	0.000													477	9	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	151126074	151126075	+	Intron	INS	-	T	T	rs67930452		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151126074_151126075insT	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GATATTATAACttttttttttt	0.178													4	2	---	---	---	---	
SLC22A2	6582	broad.mit.edu	37	6	160677932	160677934	+	Intron	DEL	CTC	-	-	rs58095836		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160677932_160677934delCTC	uc003qtf.2	-						SLC22A2_uc003qte.1_Intron|SLC22A2_uc003qth.1_Intron	NM_003058	NP_003049	O15244	S22A2_HUMAN	solute carrier family 22 member 2						body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)		CTCTCTCTCTCtctttttttttt	0.172													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30970255	30970256	+	IGR	DEL	GT	-	-	rs71557476		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30970255_30970256delGT								AQP1 (5124 upstream) : GHRHR (33380 downstream)																							ATCACTTTGGgtgtgtgtgtgt	0.371													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61970367	61970367	+	IGR	DEL	C	-	-	rs4718027		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61970367delC								None (None upstream) : LOC643955 (781305 downstream)																							aacgggatttcttcattgaat	0.000													1220	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61970472	61970472	+	IGR	DEL	C	-	-	rs4302722		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61970472delC								None (None upstream) : LOC643955 (781200 downstream)																							ttgaaacactctttttgcgga	0.000													591	8	---	---	---	---	
STAG3L4	64940	broad.mit.edu	37	7	66772495	66772495	+	Intron	DEL	T	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66772495delT	uc003tvt.3	+						STAG3L4_uc010laj.2_Intron	NM_022906	NP_075057	Q8TBR4	STG34_HUMAN	stromal antigen 3-like 4												0		Lung NSC(55;0.0839)|all_lung(88;0.181)				GCTTGATTCCTTTTTTTTTTT	0.274													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	71145845	71145848	+	Intron	DEL	TTCC	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71145845_71145848delTTCC	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ccttttttctttccttccttcctt	0.000													4	2	---	---	---	---	
ING3	54556	broad.mit.edu	37	7	120608900	120608900	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120608900delA	uc003vjn.2	+						ING3_uc003vjo.2_Intron|ING3_uc003vjp.2_Intron|ING3_uc011kns.1_Intron	NM_019071	NP_061944	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3 isoform 1						histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex	zinc ion binding			ovary(1)	1	all_neural(327;0.117)					actccacctcaaaaaaaaaaa	0.075													4	2	---	---	---	---	
ABCF2	10061	broad.mit.edu	37	7	150919382	150919383	+	Intron	INS	-	A	A	rs112640220	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150919382_150919383insA	uc003wjp.2	-						ABCF2_uc003wjo.1_Intron	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2							ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGGATTTTTTTTAAAAAAAAAA	0.282													4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113505142	113505143	+	Intron	INS	-	A	A	rs149084982	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113505142_113505143insA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						tagtaatctagaatgatttaat	0.000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			3	3	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121823372	121823372	+	Intron	DEL	C	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121823372delC	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			CGCCACCCTTCCCCCCCCCCC	0.622													8	4	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	125034095	125034096	+	Intron	INS	-	T	T	rs138450142	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125034095_125034096insT	uc003yqw.2	+						uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGCTTTATTCATTTTTTTTTCA	0.386													10	5	---	---	---	---	
EPPK1	83481	broad.mit.edu	37	8	144940081	144940081	+	Intron	DEL	C	-	-	rs60421625		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940081delC	uc003zaa.1	-							NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1							cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			aaaaaaaaaacaaaaaaaaaa	0.338													4	2	---	---	---	---	
SPTAN1	6709	broad.mit.edu	37	9	131343989	131343989	+	Intron	DEL	C	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131343989delC	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						GGCCAAAATACCCTTTGCTTC	0.358													136	76	---	---	---	---	
ADAMTS13	11093	broad.mit.edu	37	9	136288055	136288055	+	Intron	DEL	T	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136288055delT	uc004cdv.3	+						ADAMTS13_uc004cdp.3_Intron|ADAMTS13_uc004cdt.1_Intron|ADAMTS13_uc004cdu.1_Intron|ADAMTS13_uc004cdw.3_Intron|ADAMTS13_uc004cdx.3_Intron|ADAMTS13_uc004cdq.1_Intron|ADAMTS13_uc004cds.1_Intron|ADAMTS13_uc004cdr.1_Intron	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1						cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		tctctctctcttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2561172	2561173	+	IGR	INS	-	C	C	rs72507108	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2561172_2561173insC								ADARB2 (781454 upstream) : PFKP (548579 downstream)																							aagaagaagGGGGGGGGAGGAG	0.307													4	3	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18827911	18827911	+	Intron	DEL	T	-	-	rs35948042		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18827911delT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	CTGCTGCTGCTTTTTTTTTTT	0.353													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31435689	31435694	+	IGR	DEL	CACACG	-	-	rs151268729	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31435689_31435694delCACACG								ZNF438 (114823 upstream) : LOC220930 (169764 downstream)																							TGCGCGTacacacacgcacacacaca	0.437													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38981874	38981875	+	IGR	DEL	AC	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38981874_38981875delAC								LOC399744 (240794 upstream) : None (None downstream)																							AAGGATCTGTACACACACACAC	0.267													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42384716	42384716	+	IGR	DEL	G	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42384716delG								None (None upstream) : LOC441666 (442599 downstream)																							ggaatcgaatggaatcatcat	0.000													625	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42385235	42385235	+	IGR	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42385235delA								None (None upstream) : LOC441666 (442080 downstream)																							aatggtctcgaatggaatcat	0.000													2955	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42597159	42597159	+	IGR	DEL	T	-	-	rs149908177		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42597159delT								None (None upstream) : LOC441666 (230156 downstream)																							ttgaacggaatcgaatggaat	0.035													1337	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42597165	42597165	+	IGR	DEL	G	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42597165delG								None (None upstream) : LOC441666 (230150 downstream)																							ggaatcgaatggaatcatcat	0.020													1262	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42599753	42599753	+	IGR	DEL	A	-	-	rs144849414		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42599753delA								None (None upstream) : LOC441666 (227562 downstream)																							tggaatcgtcatcgaatgaat	0.000													1447	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42599763	42599763	+	IGR	DEL	T	-	-	rs141771710		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42599763delT								None (None upstream) : LOC441666 (227552 downstream)																							atcgaatgaattgaatgcaat	0.000													1732	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42599788	42599791	+	IGR	DEL	GAAT	-	-	rs139251831		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42599788_42599791delGAAT								None (None upstream) : LOC441666 (227524 downstream)																							gaatggtctcgaatggaatcatct	0.000													1846	7	---	---	---	---	
LZTS2	84445	broad.mit.edu	37	10	102765511	102765512	+	Intron	DEL	AG	-	-	rs34809526		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102765511_102765512delAG	uc001ksj.2	+						LZTS2_uc010qpw.1_Intron|LZTS2_uc001ksk.2_Intron|LZTS2_uc001ksl.2_Intron|LZTS2_uc001ksm.2_Intron	NM_032429	NP_115805	Q9BRK4	LZTS2_HUMAN	leucine zipper, putative tumor suppressor 2						cell division|mitosis|Wnt receptor signaling pathway	membrane|microtubule|microtubule organizing center				ovary(2)|large_intestine(1)|breast(1)	4				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		AGGGTCACACAGGGAGAAACCC	0.673													6	3	---	---	---	---	
RNH1	6050	broad.mit.edu	37	11	497746	497749	+	Intron	DEL	CTCA	-	-	rs71462088		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:497746_497749delCTCA	uc001lpk.1	-						RNH1_uc001lpl.1_Intron|RNH1_uc001lpm.1_Intron|RNH1_uc001lpn.1_Intron|RNH1_uc001lpo.1_Intron|RNH1_uc009ybw.1_Intron|RNH1_uc001lpp.1_Intron|RNH1_uc001lpt.1_Intron|RNH1_uc001lpq.1_Intron|RNH1_uc001lpr.1_Intron|RNH1_uc001lps.1_Intron	NM_203389	NP_976323	P13489	RINI_HUMAN	ribonuclease/angiogenin inhibitor						mRNA catabolic process|regulation of angiogenesis	angiogenin-PRI complex|cytoplasm	protein binding|ribonuclease inhibitor activity				0		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		gaccctcgtgctcactcacgtgct	0.064													6	3	---	---	---	---	
BRSK2	9024	broad.mit.edu	37	11	1467277	1467291	+	Intron	DEL	GCTGGGCTGGGCTGG	-	-	rs141282726		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1467277_1467291delGCTGGGCTGGGCTGG	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron|BRSK2_uc001ltn.2_Intron|BRSK2_uc010qwx.1_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		actgggcttagctgggctgggctgggctgggcttg	0.265													10	7	---	---	---	---	
MRE11A	4361	broad.mit.edu	37	11	94203462	94203462	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94203462delA	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582	P49959	MRE11_HUMAN	meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				TCAATGACTTAAAAAAAAAAA	0.318								Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				6	3	---	---	---	---	
CDON	50937	broad.mit.edu	37	11	125893045	125893045	+	Intron	DEL	T	-	-	rs5795474		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125893045delT	uc009zbw.2	-						CDON_uc001qdc.3_Intron|CDON_uc001qdd.3_5'Flank|CDON_uc009zbx.2_Intron	NM_016952	NP_058648	Q4KMG0	CDON_HUMAN	surface glycoprotein, Ig superfamily member						cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|skin(2)|breast(1)	6	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		AAAATATGTATTTTTTTTTAA	0.323													5	3	---	---	---	---	
PPFIBP1	8496	broad.mit.edu	37	12	27751472	27751483	+	Intron	DEL	TGTGTGTGTGTG	-	-	rs72133993		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27751472_27751483delTGTGTGTGTGTG	uc001ric.1	+						PPFIBP1_uc001rhy.1_Intron|PPFIBP1_uc001rhz.1_Intron|PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					CTCTATAATCtgtgtgtgtgtgtgtgtgtgtg	0.123													4	2	---	---	---	---	
LOC283392	283392	broad.mit.edu	37	12	72666481	72666483	+	Intron	DEL	AAG	-	-	rs111457826		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72666481_72666483delAAG	uc010stv.1	-						TRHDE_uc001sxa.2_5'Flank	NR_026836				Homo sapiens thyrotropin-releasing hormone degrading enzyme, mRNA (cDNA clone IMAGE:4992272).												0						gaagaagaaaaagaagaggaaga	0.488													9	4	---	---	---	---	
VPS29	51699	broad.mit.edu	37	12	110937446	110937446	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110937446delA	uc001tqy.2	-						VPS29_uc001tqw.2_5'Flank|VPS29_uc001tqx.2_Intron|VPS29_uc001tqz.2_Intron|RAD9B_uc001trc.1_5'Flank|RAD9B_uc001trf.3_5'Flank|RAD9B_uc001trg.3_5'Flank|RAD9B_uc010sya.1_5'Flank|RAD9B_uc001tre.3_5'Flank|RAD9B_uc001trd.3_5'Flank	NM_016226	NP_057310	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 isoform 1						protein transport	endosome membrane	metal ion binding|phosphoserine phosphatase activity				0						aaaagaaaccaaaaaaaaaaa	0.289													6	3	---	---	---	---	
PRKAB1	5564	broad.mit.edu	37	12	120110460	120110461	+	Intron	DEL	AG	-	-	rs150497180		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120110460_120110461delAG	uc009zwu.2	+						PRKAB1_uc001txg.2_Intron	NM_006253	NP_006244	Q9Y478	AAKB1_HUMAN	AMP-activated protein kinase beta 1						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol					0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Adenosine monophosphate(DB00131)|Metformin(DB00331)	TACAGAAGAAAGAGAATATTTC	0.342													2	7	---	---	---	---	
PLEKHH1	57475	broad.mit.edu	37	14	68008873	68008873	+	Intron	DEL	T	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68008873delT	uc001xjl.1	+							NM_020715	NP_065766	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H							cytoskeleton	binding				0				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GTCCGAGCAGTTTACTAAGCT	0.468													4	2	---	---	---	---	
UPF0639	400224	broad.mit.edu	37	14	69965943	69965944	+	Intron	DEL	CA	-	-	rs10551303		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69965943_69965944delCA	uc010ttf.1	+						UPF0639_uc001xli.2_Intron	NM_001161498	NP_001154970	B9EJC2	B9EJC2_HUMAN	similar to pleckstrin homology domain protein												0						CTCATACGTGcacacacacaca	0.213													0	6	---	---	---	---	
MTA1	9112	broad.mit.edu	37	14	105905492	105905493	+	Intron	INS	-	T	T	rs140601392	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105905492_105905493insT	uc001yqx.2	+						MTA1_uc001yqy.2_Intron|MTA1_uc001yqz.1_Intron|MTA1_uc001yra.1_Intron	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein						signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		GAGCTCTGCCCCCACCCCTGAG	0.644													4	3	---	---	---	---	
GABRB3	2562	broad.mit.edu	37	15	26831544	26831545	+	Intron	INS	-	ACACACAC	ACACACAC	rs149254517	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26831544_26831545insACACACAC	uc001zaz.2	-						GABRB3_uc010uae.1_Intron|GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	AACCACCCCTAacacacacaca	0.282													4	2	---	---	---	---	
SCAMP2	10066	broad.mit.edu	37	15	75158292	75158319	+	Intron	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAG	-	-	rs67717107		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75158292_75158319delGAAGGAAGGAAGGAAGGAAGGAAGGAAG	uc002azb.1	-						SCAMP2_uc010bkg.1_Intron	NM_005697	NP_005688	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2						post-Golgi vesicle-mediated transport|protein transport	integral to membrane|nucleus|recycling endosome membrane|trans-Golgi network membrane	protein binding			ovary(1)	1						actctgtctcgaaggaaggaaggaaggaaggaaggaaggaaggaagga	0.009													3	3	---	---	---	---	
ZNF263	10127	broad.mit.edu	37	16	3338252	3338252	+	Intron	DEL	A	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3338252delA	uc002cuq.2	+						ZNF263_uc010uww.1_Intron|ZNF263_uc002cur.2_5'Flank	NM_005741	NP_005732	O14978	ZN263_HUMAN	zinc finger protein 263						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4						actctgtctcaaaaaaaaaaa	0.179													5	3	---	---	---	---	
CORO7	79585	broad.mit.edu	37	16	4407754	4407755	+	Intron	DEL	GT	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4407754_4407755delGT	uc002cwh.3	-						CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron|CORO7_uc002cwi.1_3'UTR	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7							cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0						CAGTGTGTGCGTGTGTGTGtgt	0.342													4	2	---	---	---	---	
GDPD3	79153	broad.mit.edu	37	16	30119308	30119309	+	Intron	DEL	AC	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30119308_30119309delAC	uc002dwp.2	-						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|GDPD3_uc002dwq.2_Intron	NM_024307	NP_077283	Q7L5L3	GDPD3_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process	integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding				0						gagactcTTGacacacacacac	0.020													5	3	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74526721	74526722	+	Intron	INS	-	A	A			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74526721_74526722insA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						tccgtctcaagaaaaaaaaaaa	0.124													5	5	---	---	---	---	
DYNLL2	140735	broad.mit.edu	37	17	56164787	56164788	+	Intron	DEL	GT	-	-	rs72193116		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56164787_56164788delGT	uc010wnn.1	+							NM_080677	NP_542408	Q96FJ2	DYL2_HUMAN	dynein, light chain, LC8-type 2						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|microtubule-based process|transport	centrosome|cytosol|dynein complex|microtubule|myosin complex|plasma membrane	motor activity				0						GCTCTGCCAGgtgtgtgtgtgt	0.356													2	4	---	---	---	---	
ANKRD30B	374860	broad.mit.edu	37	18	14779833	14779834	+	Intron	INS	-	CCA	CCA			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14779833_14779834insCCA	uc010dlo.2	+						ANKRD30B_uc010xak.1_Intron	NM_001145029	NP_001138501	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B											ovary(1)|skin(1)	2						GTGGTTGTTATTCAATAGAATA	0.257													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37956482	37956483	+	IGR	INS	-	CA	CA	rs55796434		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37956482_37956483insCA								LOC647946 (576200 upstream) : None (None downstream)																							TATATATacaccacacacacac	0.262													5	3	---	---	---	---	
ATP5A1	498	broad.mit.edu	37	18	43668136	43668137	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43668136_43668137insT	uc002lbr.1	-	6	827_828	c.737_738insA	c.(736-738)TATfs	p.Y246fs	ATP5A1_uc010dnl.1_Frame_Shift_Ins_p.Y196fs|ATP5A1_uc002lbs.1_Frame_Shift_Ins_p.Y196fs|ATP5A1_uc002lbt.1_Frame_Shift_Ins_p.Y246fs	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	246					ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						CAATAGCAACATAAATACAGTA	0.347													229	43	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27732215	27732216	+	IGR	INS	-	C	C	rs74197760		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27732215_27732216insC								None (None upstream) : LOC148189 (549186 downstream)																							agaaaaggaaatatcttcgtat	0.000													2086	43	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27736453	27736453	+	IGR	DEL	T	-	-	rs4567863		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27736453delT								None (None upstream) : LOC148189 (544949 downstream)																							tggaaacgggtttttttcttg	0.000													548	14	---	---	---	---	
COX7A1	1346	broad.mit.edu	37	19	36642561	36642562	+	Intron	DEL	GA	-	-	rs150771533	by1000genomes	TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36642561_36642562delGA	uc002odm.1	-							NM_001864	NP_001855	P24310	CX7A1_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 1						generation of precursor metabolites and energy	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CACCCCCCCCGACCCCCCACCT	0.698													23	9	---	---	---	---	
LSM14B	149986	broad.mit.edu	37	20	60699938	60699939	+	Intron	INS	-	T	T	rs142325994		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60699938_60699939insT	uc010gjy.1	+						LSM14B_uc002ybt.2_Intron|LSM14B_uc010gjx.1_Intron|LSM14B_uc002ybv.2_Intron|LSM14B_uc010gjz.1_Intron|LSM14B_uc010zzz.1_Intron	NM_144703	NP_653304	Q9BX40	LS14B_HUMAN	LSM14 homolog B						multicellular organismal development|regulation of translation	ribonucleoprotein complex					0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			GAGGAATAACCttttttttttt	0.248													11	5	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43257865	43257882	+	Intron	DEL	TCCTGAGCTCCAGAACAT	-	-	rs71969131		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43257865_43257882delTCCTGAGCTCCAGAACAT	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACCATTAAACTCCTGAGCTCCAGAACATTCCTGAGCTC	0.381													14	11	---	---	---	---	
TXNRD2	10587	broad.mit.edu	37	22	19882492	19882493	+	Intron	INS	-	A	A	rs35599379		TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19882492_19882493insA	uc011ahc.1	-						TXNRD2_uc002zql.1_Intron|TXNRD2_uc002zqm.1_Intron|TXNRD2_uc002zqn.1_Intron|TXNRD2_uc002zqo.1_Intron|TXNRD2_uc002zqp.1_Intron|TXNRD2_uc002zqr.1_Intron|TXNRD2_uc010grv.1_3'UTR|TXNRD2_uc002zqj.1_Intron|TXNRD2_uc002zqs.2_3'UTR	NM_006440	NP_006431	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2 precursor						cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)					gactccatctcaaaaaaaaaaa	0.149													3	3	---	---	---	---	
ZMYM3	9203	broad.mit.edu	37	X	70463721	70463722	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-CH-5772-01	TCGA-CH-5772-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70463721_70463722delAT	uc004dzh.1	-	21	3476_3477	c.3389_3390delAT	c.(3388-3390)TATfs	p.Y1130fs	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Frame_Shift_Del_p.Y1130fs|ZMYM3_uc004dzj.1_Frame_Shift_Del_p.Y1118fs	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	1130					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)					TGTCAGGTTCATATCGTTCACC	0.495													26	53	---	---	---	---	
