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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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
AADACL4	343066	broad.mit.edu	37	1	12726317	12726317	+	Silent	SNP	C	T	T	rs58218425	byFrequency	TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr1:12726317C>T	uc001auf.2	+	4	795	c.795C>T	c.(793-795)GAC>GAT	p.D265D		NM_001013630	NP_001013652	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	265	Lumenal (Potential).					integral to membrane	carboxylesterase activity				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		CCTGGCGTGACGCCATCTTGA	0.502													12	279	---	---	---	---	PASS
FAM189B	10712	broad.mit.edu	37	1	155218031	155218031	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr1:155218031G>A	uc001fjm.2	-	11	2249	c.1643C>T	c.(1642-1644)GCC>GTC	p.A548V	RAG1AP1_uc010pey.1_Intron|FAM189B_uc009wql.2_Missense_Mutation_p.A350V|FAM189B_uc001fjn.2_Missense_Mutation_p.A452V|FAM189B_uc001fjo.2_Missense_Mutation_p.A530V|FAM189B_uc001fjp.2_RNA	NM_006589	NP_006580	P81408	F189B_HUMAN	hypothetical protein LOC10712 isoform a	548						integral to membrane	WW domain binding			ovary(1)|breast(1)	2						GGCTGACCGGGCACGTAGCAA	0.627													3	48	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176762740	176762740	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr1:176762740G>A	uc001gkz.2	+	20	6229	c.5065G>A	c.(5065-5067)GTG>ATG	p.V1689M	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1689	Sushi 5.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						CAGTGACCCCGTGATGCTACC	0.473													4	133	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181725167	181725167	+	Silent	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr1:181725167C>T	uc001gow.2	+	29	4230	c.4065C>T	c.(4063-4065)TAC>TAT	p.Y1355Y	CACNA1E_uc009wxs.2_Silent_p.Y1243Y|CACNA1E_uc001gox.1_Silent_p.Y581Y|CACNA1E_uc009wxt.2_Silent_p.Y581Y	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1355	Extracellular (Potential).|III.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						AATTCCACTACGACAACATTA	0.493													18	56	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197313415	197313415	+	Silent	SNP	A	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr1:197313415A>G	uc001gtz.2	+	3	792	c.657A>G	c.(655-657)GTA>GTG	p.V219V	CRB1_uc010poz.1_Silent_p.V150V|CRB1_uc001gty.1_Silent_p.V219V|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Silent_p.V219V|CRB1_uc010ppc.1_RNA	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	219	Extracellular (Potential).|EGF-like 5; calcium-binding (Potential).				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						TAAAAGGTGTAAACTGTGAAT	0.398													6	398	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55561490	55561490	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:55561490C>A	uc002ryv.2	-	15	3309	c.2467G>T	c.(2467-2469)GAG>TAG	p.E823*	CCDC88A_uc010yoz.1_Nonsense_Mutation_p.E823*|CCDC88A_uc010ypa.1_Nonsense_Mutation_p.E823*|CCDC88A_uc010ypb.1_Nonsense_Mutation_p.E725*|CCDC88A_uc002ryu.2_Nonsense_Mutation_p.E106*|CCDC88A_uc002ryw.2_Nonsense_Mutation_p.E106*	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	823	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						TGAGAAGTCTCTTGCTCTAAT	0.318													5	301	---	---	---	---	PASS
BCL11A	53335	broad.mit.edu	37	2	60773250	60773250	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:60773250C>T	uc002sae.1	-	2	469	c.241G>A	c.(241-243)GTG>ATG	p.V81M	BCL11A_uc002sab.2_Missense_Mutation_p.V81M|BCL11A_uc002sac.2_Missense_Mutation_p.V81M|BCL11A_uc010ypi.1_Translation_Start_Site|BCL11A_uc010ypj.1_Missense_Mutation_p.V81M|BCL11A_uc002saf.1_Missense_Mutation_p.V81M|BCL11A_uc010fcg.2_Missense_Mutation_p.V81M	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	81	Required for nuclear body formation and for SUMO1 recruitment (By similarity).				negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GGCTTATCCACAGCTTTTTCT	0.483			T	IGH@	B-CLL								5	133	---	---	---	---	PASS
RGPD5	84220	broad.mit.edu	37	2	113127775	113127775	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:113127775G>C	uc002ths.1	-	23	5355	c.5278C>G	c.(5278-5280)CCT>GCT	p.P1760A	RGPD8_uc010fkk.1_Missense_Mutation_p.P1620A	NM_005054	NP_005045	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5 isoform	1760					intracellular transport	cytoplasm	binding				0						GAACGGGAAGGATTTTCTTCC	0.308													4	57	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141473639	141473639	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:141473639A>C	uc002tvj.1	-	37	6898	c.5926T>G	c.(5926-5928)TTA>GTA	p.L1976V		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1976	Extracellular (Potential).|LDL-receptor class B 20.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACTTCAATTAAGTTGAAACCA	0.343										TSP Lung(27;0.18)			92	216	---	---	---	---	PASS
CUL3	8452	broad.mit.edu	37	2	225379456	225379456	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:225379456T>C	uc002vny.2	-	4	796	c.412A>G	c.(412-414)AAC>GAC	p.N138D	CUL3_uc010zls.1_Missense_Mutation_p.N72D|CUL3_uc010fwy.1_Missense_Mutation_p.N144D	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	138					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TTGTAGACGTTCTCCACATTA	0.338													27	79	---	---	---	---	PASS
RNPEPL1	57140	broad.mit.edu	37	2	241516387	241516387	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:241516387C>T	uc002vzi.2	+	10	1764	c.1171C>T	c.(1171-1173)CGG>TGG	p.R391W	RNPEPL1_uc010fzf.2_Missense_Mutation_p.R297W|RNPEPL1_uc002vzj.2_Missense_Mutation_p.R39W	NM_018226	NP_060696	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like	391					leukotriene biosynthetic process|proteolysis		aminopeptidase activity|metallopeptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)		CCACAGGGTGCGGCGCTTCCT	0.647													4	111	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51101986	51101986	+	Silent	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:51101986G>A	uc011bds.1	+	6	446	c.423G>A	c.(421-423)GAG>GAA	p.E141E		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	141						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AGGTGCGGGAGGTTAAGCGGC	0.453													18	122	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51102013	51102013	+	Silent	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:51102013G>A	uc011bds.1	+	6	473	c.450G>A	c.(448-450)CTG>CTA	p.L150L		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	150						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CCGTGCGCCTGGACTGGGGTA	0.463													17	123	---	---	---	---	PASS
RYBP	23429	broad.mit.edu	37	3	72428496	72428496	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:72428496T>C	uc003dpe.2	-	2	328	c.211A>G	c.(211-213)AAG>GAG	p.K71E		NM_012234	NP_036366	Q8N488	RYBP_HUMAN	RING1 and YY1 binding protein	81	Lys-rich.				apoptosis|histone H2A monoubiquitination|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleoplasm	DNA binding|protein binding|transcription corepressor activity|zinc ion binding				0		Prostate(10;0.00174)|Lung NSC(201;0.0659)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;0.000197)|Epithelial(33;0.00068)|LUSC - Lung squamous cell carcinoma(21;0.00228)|Lung(16;0.00677)|KIRC - Kidney renal clear cell carcinoma(39;0.198)|Kidney(39;0.232)		ACTTTCTCCTTCTTCTCCTTT	0.408													65	193	---	---	---	---	PASS
OR5H14	403273	broad.mit.edu	37	3	97869007	97869007	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:97869007A>G	uc003dsg.1	+	1	778	c.778A>G	c.(778-780)ATG>GTG	p.M260V		NM_001005514	NP_001005514	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H,	260	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						CTTCATGTATATGGGCTCTGC	0.433													4	101	---	---	---	---	PASS
PLCXD2	257068	broad.mit.edu	37	3	111426940	111426940	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:111426940C>T	uc003dya.2	+	2	917	c.331C>T	c.(331-333)CGC>TGC	p.R111C	PLCXD2_uc003dyb.2_Missense_Mutation_p.R111C|PLCXD2_uc003dxz.2_Missense_Mutation_p.R111C	NM_001134478	NP_001127950	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X	111	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1						AGCTGGGATCCGCTACTTTGA	0.512													31	147	---	---	---	---	PASS
BOC	91653	broad.mit.edu	37	3	112993397	112993397	+	Silent	SNP	T	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:112993397T>C	uc003dzx.2	+	9	2031	c.1410T>C	c.(1408-1410)GCT>GCC	p.A470A	BOC_uc003dzy.2_Silent_p.A470A|BOC_uc003dzz.2_Silent_p.A470A|BOC_uc003eab.2_Silent_p.A171A	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	470	Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			GGCAGGGGGCTCCCGCCGAGG	0.687													5	29	---	---	---	---	PASS
COL29A1	256076	broad.mit.edu	37	3	130189738	130189738	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:130189738G>A	uc010htj.1	+	39	7995	c.7501G>A	c.(7501-7503)GAA>AAA	p.E2501K	COL29A1_uc010hti.1_RNA|COL29A1_uc010htk.1_Missense_Mutation_p.E540K	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2501	Nonhelical region.				axon guidance|cell adhesion	collagen					0						ATATCCCACCGAAGATATGAA	0.428													10	39	---	---	---	---	PASS
CDKL3	51265	broad.mit.edu	37	5	133634385	133634385	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:133634385C>T	uc003kzf.3	-	13	1855	c.1736G>A	c.(1735-1737)TGC>TAC	p.C579Y	CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_3'UTR	NM_001113575	NP_001107047	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3 isoform 1	579						cytoplasm	ATP binding|cyclin-dependent protein kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTTCCCCTCGCAATGGCCATC	0.348													37	126	---	---	---	---	PASS
FAM53C	51307	broad.mit.edu	37	5	137681219	137681219	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:137681219G>A	uc003lcv.2	+	4	1312	c.842G>A	c.(841-843)CGC>CAC	p.R281H	FAM53C_uc003lcw.2_Missense_Mutation_p.R281H|FAM53C_uc011cyq.1_RNA|FAM53C_uc011cyr.1_Missense_Mutation_p.A97T	NM_001135647	NP_001129119	Q9NYF3	FA53C_HUMAN	hypothetical protein LOC51307	281										ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CTGGATGCCCGCAAAACTGGG	0.642													4	171	---	---	---	---	PASS
PSD2	84249	broad.mit.edu	37	5	139189047	139189047	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:139189047T>C	uc003leu.1	+	2	227	c.22T>C	c.(22-24)TCT>CCT	p.S8P		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	8					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAGCTCTTATCTGCAGTGCC	0.627													3	21	---	---	---	---	PASS
GRIA1	2890	broad.mit.edu	37	5	153078545	153078545	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:153078545G>A	uc003lva.3	+	10	1729	c.1364G>A	c.(1363-1365)CGT>CAT	p.R455H	GRIA1_uc003luy.3_Missense_Mutation_p.R455H|GRIA1_uc003luz.3_Missense_Mutation_p.R360H|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Missense_Mutation_p.R375H|GRIA1_uc011dcx.1_Missense_Mutation_p.R386H|GRIA1_uc011dcy.1_Missense_Mutation_p.R465H|GRIA1_uc011dcz.1_Missense_Mutation_p.R465H|GRIA1_uc010jia.1_Missense_Mutation_p.R435H	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	455	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TACTCCTACCGTCTGGAGATT	0.542													33	75	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	159992774	159992774	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:159992774C>G	uc003lym.1	-	26	4919	c.4072G>C	c.(4072-4074)GTC>CTC	p.V1358L	ATP10B_uc010jit.1_Missense_Mutation_p.V608L	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1358	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTTCGGGGACAGGGGCAGGC	0.517													58	235	---	---	---	---	PASS
HLA-G	3135	broad.mit.edu	37	6	29797406	29797406	+	Silent	SNP	G	A	A	rs79264452		TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr6:29797406G>A	uc003nnw.2	+	5	1009	c.831G>A	c.(829-831)GAG>GAA	p.E277E	HLA-G_uc011dmb.1_Silent_p.E249E|HLA-G_uc003raj.3_Silent_p.E282E|HLA-G_uc003nnz.3_Silent_p.E185E|HLA-G_uc010jrn.2_Intron|HLA-G_uc003nny.3_RNA|HLA-G_uc003ran.1_5'Flank	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	277	Extracellular (Potential).|Ig-like C1-type.|Alpha-3.				antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						CTTCTGGAGAGGAGCAGAGAT	0.607													7	187	---	---	---	---	PASS
HLA-G	3135	broad.mit.edu	37	6	29797436	29797436	+	Silent	SNP	T	C	C	rs74547057		TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr6:29797436T>C	uc003nnw.2	+	5	1039	c.861T>C	c.(859-861)CAT>CAC	p.H287H	HLA-G_uc011dmb.1_Silent_p.H259H|HLA-G_uc003raj.3_Silent_p.H292H|HLA-G_uc003nnz.3_Silent_p.H195H|HLA-G_uc010jrn.2_Intron|HLA-G_uc003nny.3_RNA|HLA-G_uc003ran.1_5'Flank	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	287	Extracellular (Potential).|Ig-like C1-type.|Alpha-3.				antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						ATGTGCAGCATGAGGGGCTGC	0.577													6	179	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100345786	100345786	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr7:100345786G>T	uc003uwj.2	+	10	1215	c.1050G>T	c.(1048-1050)AAG>AAT	p.K350N	ZAN_uc003uwk.2_Missense_Mutation_p.K350N|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	350	MAM 2.|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TTTTTGGAAAGACCCCAGAGC	0.597													12	59	---	---	---	---	PASS
EBF2	64641	broad.mit.edu	37	8	25745360	25745360	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr8:25745360C>T	uc003xes.1	-	9	897	c.880G>A	c.(880-882)GAG>AAG	p.E294K	PPP2R2A_uc003xek.2_Intron|EBF2_uc010lug.1_RNA	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	294	IPT/TIG.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		CTGCTTACCTCGCTCCATACA	0.463													37	58	---	---	---	---	PASS
C8orf46	254778	broad.mit.edu	37	8	67428303	67428303	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr8:67428303G>T	uc003xwg.2	+	6	1009	c.616G>T	c.(616-618)GCC>TCC	p.A206S	C8orf46_uc003xwh.2_RNA|C8orf46_uc011let.1_3'UTR|C8orf46_uc003xwi.2_Missense_Mutation_p.A71S	NM_152765	NP_689978	Q8TAG6	CH046_HUMAN	hypothetical protein LOC254778	206										skin(2)	2			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			CGCCTTTGAGGCCGACTAAAG	0.557													6	44	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32632378	32632378	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:32632378G>A	uc003zrg.1	-	1	3290	c.3200C>T	c.(3199-3201)GCC>GTC	p.A1067V	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1067					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGATCCACGGGCAAATTTACT	0.468													5	306	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77427337	77427337	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:77427337C>T	uc004ajl.1	-	12	1559	c.1321G>A	c.(1321-1323)GAA>AAA	p.E441K	TRPM6_uc004ajk.1_Missense_Mutation_p.E436K|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.E441K|TRPM6_uc010mpd.1_Missense_Mutation_p.E441K|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	441	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						ATTGCTTGTTCCAGGGCATCA	0.363													51	91	---	---	---	---	PASS
IKBKAP	8518	broad.mit.edu	37	9	111662626	111662626	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:111662626C>T	uc004bdm.3	-	19	2564	c.2044G>A	c.(2044-2046)GTG>ATG	p.V682M	IKBKAP_uc004bdl.2_Missense_Mutation_p.V333M|IKBKAP_uc011lwc.1_Missense_Mutation_p.V568M|IKBKAP_uc010mtq.2_Missense_Mutation_p.V333M	NM_003640	NP_003631	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene	682					immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7						CCATGGGACACATGATTGCTG	0.458													22	108	---	---	---	---	PASS
WDR38	401551	broad.mit.edu	37	9	127618187	127618187	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:127618187C>A	uc004box.2	+	4	411	c.355C>A	c.(355-357)CAG>AAG	p.Q119K	WDR38_uc011lzn.1_Missense_Mutation_p.Q108K|WDR38_uc011lzo.1_Missense_Mutation_p.Q119K|WDR38_uc011lzp.1_Missense_Mutation_p.Q70K	NM_001045476	NP_001038941	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	119	WD 3.										0						TGACTCGAGACAGCTGGCATC	0.622											OREG0019485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	138	---	---	---	---	PASS
SCAI	286205	broad.mit.edu	37	9	127790688	127790688	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:127790688C>A	uc004bpe.2	-	5	477	c.396G>T	c.(394-396)CAG>CAT	p.Q132H	SCAI_uc004bpd.2_Missense_Mutation_p.Q155H|SCAI_uc010mwu.2_RNA	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2	132	Required for interaction with MKL1 (By similarity).|Necessary to inhibit MKL1-induced SRF transcriptional activity (By similarity).				negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						GATAGTATAGCTGCCCAATCT	0.338													10	139	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	Missense_Mutation	SNP	A	G	G	rs2257765		TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr10:38654432A>G	uc010qex.1	+	5	599	c.524A>G	c.(523-525)AAT>AGT	p.N175S	HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						TCATCTCGCAATGCAAGGAAA	0.453													7	122	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57077492	57077492	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:57077492G>A	uc001njr.2	-	5	3005	c.2693C>T	c.(2692-2694)GCC>GTC	p.A898V	TNKS1BP1_uc001njs.2_Missense_Mutation_p.A898V|TNKS1BP1_uc009ymd.1_Missense_Mutation_p.A349V	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	898	Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				ATCTTGGCTGGCATAAGCACC	0.532													6	414	---	---	---	---	PASS
NCAM1	4684	broad.mit.edu	37	11	113105824	113105824	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:113105824C>T	uc009yyq.1	+	15	2181	c.1487C>T	c.(1486-1488)GCG>GTG	p.A496V		NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3	588	Extracellular (Potential).|Fibronectin type-III 1.				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGGCTGGCGGCGCTCAATGGC	0.587													9	15	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118343971	118343971	+	Silent	SNP	T	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:118343971T>C	uc001pta.2	+	3	2120	c.2097T>C	c.(2095-2097)GCT>GCC	p.A699A	MLL_uc001ptb.2_Silent_p.A699A|MLL_uc001psz.1_Silent_p.A732A|MLL_uc001ptd.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	699					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		TTCTGAGAGCTCCAAGATTTA	0.453			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								33	124	---	---	---	---	PASS
OR10G9	219870	broad.mit.edu	37	11	123893785	123893785	+	Silent	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:123893785C>T	uc010sad.1	+	1	66	c.66C>T	c.(64-66)GAC>GAT	p.D22D		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CAGGGCTGGACGCCCCACTCT	0.587													18	413	---	---	---	---	PASS
OR10G7	390265	broad.mit.edu	37	11	123909643	123909643	+	Silent	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:123909643G>A	uc001pzq.1	-	1	66	c.66C>T	c.(64-66)GAC>GAT	p.D22D		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AGAGGGGGGCGTCCAGCCCTG	0.562													8	126	---	---	---	---	PASS
BARX2	8538	broad.mit.edu	37	11	129312807	129312807	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:129312807A>G	uc001qfc.3	+	3	616	c.566A>G	c.(565-567)AAG>AGG	p.K189R		NM_003658	NP_003649	Q9UMQ3	BARX2_HUMAN	BarH-like homeobox 2	189	Homeobox.										0	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		ATGAAATGGAAGAAAATGGTA	0.498													7	125	---	---	---	---	PASS
GALNT8	26290	broad.mit.edu	37	12	4830000	4830000	+	Missense_Mutation	SNP	T	G	G	rs10849133	byFrequency	TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:4830000T>G	uc001qne.1	+	1	249	c.157T>G	c.(157-159)TAC>GAC	p.Y53D		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	53	Lumenal (Potential).		Y -> N.			Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4						GAATAAACGCTACGGGGCAGT	0.468													3	150	---	---	---	---	PASS
ACCN2	41	broad.mit.edu	37	12	50474350	50474350	+	Silent	SNP	C	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:50474350C>A	uc001rvw.2	+	9	1504	c.1275C>A	c.(1273-1275)GCC>GCA	p.A425A	ACCN2_uc001rvv.2_Silent_p.A425A|ACCN2_uc009zln.2_Silent_p.A216A|ACCN2_uc009zlo.2_Silent_p.A425A	NM_001095	NP_001086	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	425	Extracellular (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)	AGAAGAAGGCCTATGAGATTG	0.448													3	92	---	---	---	---	PASS
NAP1L1	4673	broad.mit.edu	37	12	76446996	76446996	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:76446996G>A	uc001sxw.2	-	10	1317	c.905C>T	c.(904-906)GCC>GTC	p.A302V	NAP1L1_uc001sxv.2_Missense_Mutation_p.A260V|NAP1L1_uc001sxz.2_Missense_Mutation_p.A233V|NAP1L1_uc001sxx.2_Missense_Mutation_p.A302V|NAP1L1_uc001sxy.2_Missense_Mutation_p.A239V|NAP1L1_uc010sty.1_Missense_Mutation_p.A259V|NAP1L1_uc010stz.1_Missense_Mutation_p.A119V|NAP1L1_uc010sua.1_Missense_Mutation_p.A302V|NAP1L1_uc001syb.2_Missense_Mutation_p.A302V|NAP1L1_uc001sya.2_Missense_Mutation_p.A260V|NAP1L1_uc001syc.2_Missense_Mutation_p.A313V	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	302					DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)				TTCAGGAGGGGCAAAAAAGTT	0.328													5	197	---	---	---	---	PASS
SPIC	121599	broad.mit.edu	37	12	101876611	101876611	+	Silent	SNP	A	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:101876611A>G	uc001tid.2	+	5	411	c.252A>G	c.(250-252)CAA>CAG	p.Q84Q	SPIC_uc009zua.2_5'UTR|SPIC_uc010svp.1_Silent_p.Q83Q	NM_152323	NP_689536	Q8N5J4	SPIC_HUMAN	Spi-C transcription factor (Spi-1/PU.1 related)	84						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1						ATATTCATCAATCTCTGCAGA	0.299													130	333	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25169937	25169937	+	RNA	SNP	A	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr13:25169937A>C	uc001upm.2	+	11		c.1184A>C			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						AATCTTCCTAAATACTATGAC	0.264													3	18	---	---	---	---	PASS
FERMT2	10979	broad.mit.edu	37	14	53385917	53385917	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr14:53385917G>T	uc001xad.2	-	3	370	c.315C>A	c.(313-315)AAC>AAA	p.N105K	FERMT2_uc001xac.2_Missense_Mutation_p.N105K|FERMT2_uc001xae.2_Missense_Mutation_p.N105K|FERMT2_uc001xaf.2_Missense_Mutation_p.N105K	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1	105					actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)					CATACTTCATGTTGGGAAGCT	0.398													6	287	---	---	---	---	PASS
EML1	2009	broad.mit.edu	37	14	100405575	100405575	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr14:100405575G>A	uc001ygs.2	+	21	2302	c.2233G>A	c.(2233-2235)GTC>ATC	p.V745I	EML1_uc010tww.1_Missense_Mutation_p.V733I|EML1_uc001ygr.2_Missense_Mutation_p.V764I	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	745	WD 10.					cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				CATCAATGCCGTCTGTCGGGC	0.562													36	99	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107035002	107035002	+	RNA	SNP	A	G	G	rs72686845	byFrequency	TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr14:107035002A>G	uc010tyt.1	-	154		c.7231T>C			uc001ysz.2_Silent_p.S26S					Parts of antibodies, mostly variable regions.												0						CCTCTGCTCCAGACTGCACCA	0.567													5	32	---	---	---	---	PASS
SPTBN5	51332	broad.mit.edu	37	15	42145484	42145484	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr15:42145484A>C	uc001zos.2	-	59	10370	c.10037T>G	c.(10036-10038)GTG>GGG	p.V3346G		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3381	Spectrin 30.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GCTGTTGTCCACCAGCTGCTG	0.637													7	19	---	---	---	---	PASS
ZNF434	54925	broad.mit.edu	37	16	3440104	3440104	+	Silent	SNP	T	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr16:3440104T>A	uc002cuz.2	-	4	823	c.21A>T	c.(19-21)GTA>GTT	p.V7V	ZNF434_uc002cux.3_Silent_p.V218V|ZNF434_uc010uwx.1_Intron|ZNF434_uc002cuy.3_Intron|ZNF434_uc010uwy.1_Intron|ZNF434_uc010uwz.1_Silent_p.V218V|ZNF434_uc010uxa.1_Silent_p.V7V	NM_017810	NP_060280	Q9NX65	ZN434_HUMAN	zinc finger protein 434	7	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						GACAGAGGGATACAGCTCTGT	0.582													13	39	---	---	---	---	PASS
FAM86A	196483	broad.mit.edu	37	16	5140130	5140130	+	Missense_Mutation	SNP	C	T	T	rs112774542		TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr16:5140130C>T	uc002cyo.2	-	6	746	c.697G>A	c.(697-699)GTC>ATC	p.V233I	FAM86A_uc002cyp.2_Missense_Mutation_p.V199I	NM_201400	NP_958802	Q96G04	FA86A_HUMAN	hypothetical protein LOC196483 isoform 1	233											0						AGCTGATGGACCGTCGCGACG	0.592													5	106	---	---	---	---	PASS
FAM86A	196483	broad.mit.edu	37	16	5140136	5140136	+	Missense_Mutation	SNP	C	T	T	rs74684799		TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr16:5140136C>T	uc002cyo.2	-	6	740	c.691G>A	c.(691-693)GCG>ACG	p.A231T	FAM86A_uc002cyp.2_Missense_Mutation_p.A197T	NM_201400	NP_958802	Q96G04	FA86A_HUMAN	hypothetical protein LOC196483 isoform 1	231											0						TGGACCGTCGCGACGTCCCAG	0.597													4	119	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7734055	7734055	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr17:7734055G>A	uc002giu.1	+	78	12139	c.12125G>A	c.(12124-12126)GGC>GAC	p.G4042D	DNAH2_uc010cnm.1_Missense_Mutation_p.G980D	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	4042					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTCATTGCCGGCATCAACTAT	0.507													4	142	---	---	---	---	PASS
KIAA0100	9703	broad.mit.edu	37	17	26961608	26961608	+	Silent	SNP	A	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr17:26961608A>G	uc002hbu.2	-	16	3096	c.2997T>C	c.(2995-2997)CCT>CCC	p.P999P		NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	999						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					CAGGGGGAAAAGGGCTGCCTG	0.493													4	223	---	---	---	---	PASS
TMEM146	257062	broad.mit.edu	37	19	5768180	5768180	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:5768180A>C	uc002mda.2	+	18	1622	c.1561A>C	c.(1561-1563)AAA>CAA	p.K521Q	TMEM146_uc010duj.1_Missense_Mutation_p.K179Q	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor	521	Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						TGCTTGCAGCAAAGTTTCCGC	0.463													39	104	---	---	---	---	PASS
LDLR	3949	broad.mit.edu	37	19	11227612	11227612	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:11227612C>T	uc002mqk.3	+	12	1951	c.1783C>T	c.(1783-1785)CGG>TGG	p.R595W	LDLR_uc010xlk.1_Missense_Mutation_p.R595W|LDLR_uc010xll.1_Missense_Mutation_p.R554W|LDLR_uc010xlm.1_Missense_Mutation_p.R448W|LDLR_uc010xln.1_Missense_Mutation_p.R468W|LDLR_uc010xlo.1_Missense_Mutation_p.R427W	NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	595	LDL-receptor class B 5.|Extracellular (Potential).				cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	CGGGGGCAACCGGAAGACCAT	0.542													72	342	---	---	---	---	PASS
JAK3	3718	broad.mit.edu	37	19	17950419	17950419	+	Silent	SNP	T	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:17950419T>A	uc002nhn.3	-	10	1408	c.1308A>T	c.(1306-1308)GGA>GGT	p.G436G	JAK3_uc010ebh.2_RNA|JAK3_uc002nho.2_Silent_p.G436G|JAK3_uc010xpx.1_Silent_p.G436G	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	436	SH2; atypical.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56						GAAGGAAGGTTCCTGTGGGGC	0.612		2	Mis		acute megakaryocytic leukemia|								5	30	---	---	---	---	PASS
TSKS	60385	broad.mit.edu	37	19	50248602	50248602	+	Silent	SNP	C	T	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:50248602C>T	uc002ppm.2	-	7	1055	c.1044G>A	c.(1042-1044)GTG>GTA	p.V348V		NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate	348							protein binding			large_intestine(1)|skin(1)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GGGCTTCCTGCACCGCCCCCT	0.706													3	8	---	---	---	---	PASS
ZNF83	55769	broad.mit.edu	37	19	53117461	53117461	+	Silent	SNP	C	T	T	rs77404321	byFrequency	TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:53117461C>T	uc002pzu.3	-	2	1601	c.357G>A	c.(355-357)ACG>ACA	p.T119T	ZNF83_uc002pzv.3_Silent_p.T119T|ZNF83_uc010eps.2_Silent_p.T119T|ZNF83_uc010ept.2_Silent_p.T119T|ZNF83_uc010epu.2_Silent_p.T119T|ZNF83_uc010epv.2_Silent_p.T119T|ZNF83_uc010epw.2_Silent_p.T119T|ZNF83_uc010epx.2_Silent_p.T119T|ZNF83_uc010epy.2_Silent_p.T119T|ZNF83_uc010epz.2_Silent_p.T119T|ZNF83_uc010eqb.1_Silent_p.T119T	NM_018300	NP_060770	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform a	119						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		ATTTAAATTGCGTCTCTTTAG	0.338													56	146	---	---	---	---	PASS
ZSCAN1	284312	broad.mit.edu	37	19	58565060	58565060	+	Silent	SNP	C	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:58565060C>A	uc002qrc.1	+	6	1115	c.868C>A	c.(868-870)CGG>AGG	p.R290R		NM_182572	NP_872378	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	290					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CCGAGGTGGGCGGCCCTTCCA	0.652													4	100	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24659512	24659512	+	RNA	SNP	A	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr22:24659512A>G	uc002zzs.3	+	7		c.3244A>G			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						TGCCTGGGCCATGGAGCACTC	0.473													3	27	---	---	---	---	PASS
SNX12	29934	broad.mit.edu	37	X	70280884	70280884	+	Silent	SNP	C	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chrX:70280884C>A	uc004dyr.1	-	4	546	c.471G>T	c.(469-471)CCG>CCT	p.P157P	SNX12_uc004dyp.1_RNA|uc004dyq.2_5'Flank	NM_013346	NP_037478	Q9UMY4	SNX12_HUMAN	sorting nexin 12	157					cell communication|protein transport	membrane	phosphatidylinositol binding|protein binding				0	Renal(35;0.156)					GCACCTTCCCCGGGACGTAGT	0.512													3	22	---	---	---	---	PASS
ARL13A	392509	broad.mit.edu	37	X	100243476	100243476	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chrX:100243476C>G	uc004ego.2	+	8	970	c.854C>G	c.(853-855)ACG>AGG	p.T285R	ARL13A_uc011mrf.1_Missense_Mutation_p.T285R|ARL13A_uc010nng.2_Intron	NM_001012990	NP_001013008	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13 isoform a	285							GTP binding			ovary(1)	1						CAGAATACTACGAAGCTTTGC	0.378													3	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7026	7026	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chrM:7026G>A	uc011mfh.1	+	1	1173	c.125G>A	c.(124-126)AGC>AAC	p.S42N	uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		ACTACGTTGTAGCTCACTTCC	0.448													4	2	---	---	---	---	PASS
DBR1	51163	broad.mit.edu	37	3	137880741	137880743	+	In_Frame_Del	DEL	TCG	-	-	rs150114751	byFrequency	TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:137880741_137880743delTCG	uc003erv.2	-	8	1759_1761	c.1623_1625delCGA	c.(1621-1626)GATGAT>GAT	p.541_542DD>D	DBR1_uc003eru.2_In_Frame_Del_p.490_491DD>D|DBR1_uc003ert.2_In_Frame_Del_p.309_310DD>D	NM_016216	NP_057300	Q9UK59	DBR1_HUMAN	debranching enzyme homolog 1	541_542						nucleus	metal ion binding|RNA lariat debranching enzyme activity				0						TTAAGCTGCATCGTCATCATCAT	0.251													297	7	---	---	---	---	
MBD6	114785	broad.mit.edu	37	12	57920425	57920425	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:57920425delG	uc001soj.1	+	7	1721	c.1497delG	c.(1495-1497)CTGfs	p.L499fs	MBD6_uc001sok.1_Frame_Shift_Del_p.L366fs|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	499	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4						CCGAAGGACTGGGGATGGGGG	0.647													217	51	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106993939	106993941	+	RNA	DEL	TAC	-	-			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr14:106993939_106993941delTAC	uc010tyt.1	-	187		c.8506_8508delGTA								Parts of antibodies, mostly variable regions.												0						TAGTATATGGTACTACTACTACT	0.502													547	7	---	---	---	---	
