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
CHD5	26038	broad.mit.edu	37	1	6208965	6208965	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6208965G>T	uc001amb.1	-	9	1432	c.1332C>A	c.(1330-1332)AAC>AAA	p.N444K	CHD5_uc001amc.1_5'Flank	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	444	PHD-type 2.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCAGCGGCGGGTTGAGGCAAT	0.517													13	59	---	---	---	---	PASS
FBXO42	54455	broad.mit.edu	37	1	16583146	16583146	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16583146T>G	uc001ayg.2	-	5	827	c.611A>C	c.(610-612)GAG>GCG	p.E204A	FBXO42_uc001aye.3_5'Flank|FBXO42_uc001ayf.2_Missense_Mutation_p.E111A	NM_018994	NP_061867	Q6P3S6	FBX42_HUMAN	F-box protein 42	204	Kelch 2.									upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		AAAGAATCTCTCTGGCTGGTG	0.443													14	74	---	---	---	---	PASS
PRPF38B	55119	broad.mit.edu	37	1	109238748	109238748	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109238748G>T	uc001dvv.3	+	3	711	c.429G>T	c.(427-429)AAG>AAT	p.K143N	PRPF38B_uc001dvw.3_Missense_Mutation_p.K32N|PRPF38B_uc010ouz.1_5'UTR	NM_018061	NP_060531	Q5VTL8	PR38B_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	143					mRNA processing|RNA splicing	spliceosomal complex					0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		TAACTCGAAAGCAAGTGATGG	0.378													25	98	---	---	---	---	PASS
PRPF38B	55119	broad.mit.edu	37	1	109238749	109238749	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109238749C>T	uc001dvv.3	+	3	712	c.430C>T	c.(430-432)CAA>TAA	p.Q144*	PRPF38B_uc001dvw.3_Nonsense_Mutation_p.Q33*|PRPF38B_uc010ouz.1_5'UTR	NM_018061	NP_060531	Q5VTL8	PR38B_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	144					mRNA processing|RNA splicing	spliceosomal complex					0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		AACTCGAAAGCAAGTGATGGG	0.378													24	99	---	---	---	---	PASS
FAM40A	85369	broad.mit.edu	37	1	110582061	110582061	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110582061A>T	uc001dza.1	+	5	524	c.505A>T	c.(505-507)ATG>TTG	p.M169L	FAM40A_uc001dyz.1_Missense_Mutation_p.M74L|FAM40A_uc009wfp.1_5'UTR	NM_033088	NP_149079	Q5VSL9	FA40A_HUMAN	hypothetical protein LOC85369	169						nucleus	protein binding			ovary(3)|large_intestine(1)	4		all_cancers(81;8.51e-05)|all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0154)|all cancers(265;0.0732)|Epithelial(280;0.0781)|Colorectal(144;0.115)|LUSC - Lung squamous cell carcinoma(189;0.137)		GCAGTCCTGGATGCGCTACAA	0.547													10	24	---	---	---	---	PASS
CHRNB2	1141	broad.mit.edu	37	1	154543879	154543879	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154543879C>A	uc001ffg.2	+	5	844	c.580C>A	c.(580-582)CTG>ATG	p.L194M		NM_000748	NP_000739	P17787	ACHB2_HUMAN	neuronal nicotinic acetylcholine receptor beta 2	194	Extracellular (Potential).				B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)	GGTGGCCAGCCTGGACGACTT	0.587													11	39	---	---	---	---	PASS
ZBTB7B	51043	broad.mit.edu	37	1	154988705	154988705	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154988705G>T	uc001fgk.3	+	4	1322	c.1164G>T	c.(1162-1164)AAG>AAT	p.K388N	ZBTB7B_uc009wpa.2_Missense_Mutation_p.K388N|ZBTB7B_uc001fgj.3_Missense_Mutation_p.K422N|ZBTB7B_uc010peq.1_Missense_Mutation_p.K422N|ZBTB7B_uc001fgl.3_Missense_Mutation_p.K388N	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	388	C2H2-type 2.				cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGAACGACAAGCTGAAGATCC	0.632													4	74	---	---	---	---	PASS
CD5L	922	broad.mit.edu	37	1	157805891	157805891	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157805891A>C	uc001frk.3	-	3	253	c.110T>G	c.(109-111)GTG>GGG	p.V37G		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like precursor	37	SRCR 1.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TTCCACCTCCACCCGCCCTTC	0.632													10	91	---	---	---	---	PASS
C1orf112	55732	broad.mit.edu	37	1	169822055	169822055	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169822055G>A	uc001ggp.2	+	25	2799	c.2489G>A	c.(2488-2490)TGG>TAG	p.W830*	C1orf112_uc001ggj.2_RNA|C1orf112_uc001ggq.2_Nonsense_Mutation_p.W830*|C1orf112_uc009wvt.2_Nonsense_Mutation_p.W507*|C1orf112_uc001ggr.2_Nonsense_Mutation_p.W695*|C1orf112_uc010plv.1_Nonsense_Mutation_p.W772*|SCYL3_uc010plw.1_3'UTR|SCYL3_uc001ggs.2_3'UTR|SCYL3_uc001ggt.2_3'UTR|SCYL3_uc001ggu.2_RNA	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732	830											0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCTCCAGCCTGGCTTTCAATG	0.483													28	121	---	---	---	---	PASS
NR5A2	2494	broad.mit.edu	37	1	200014591	200014591	+	Silent	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200014591C>A	uc001gvb.2	+	4	548	c.342C>A	c.(340-342)GTC>GTA	p.V114V	NR5A2_uc001gvc.2_Silent_p.V68V|NR5A2_uc009wzh.2_Silent_p.V74V|NR5A2_uc010pph.1_Silent_p.V42V	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	114	Nuclear receptor.				embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)					AGCGAACAGTCCAAAATAATA	0.328													16	71	---	---	---	---	PASS
ATP2B4	493	broad.mit.edu	37	1	203652191	203652191	+	5'UTR	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203652191G>T	uc001gzw.2	+	2					ATP2B4_uc001gzv.2_5'UTR|ATP2B4_uc009xaq.2_5'UTR	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TATTGCACAAGATATATTCAA	0.512													4	15	---	---	---	---	PASS
HK2	3099	broad.mit.edu	37	2	75112644	75112644	+	Silent	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75112644A>G	uc002snd.2	+	13	3789	c.1863A>G	c.(1861-1863)AAA>AAG	p.K621K		NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2	621	Catalytic.|Substrate 2 binding.				apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2						AGTGGACAAAAGGCTTCAAGG	0.562													3	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	95552625	95552625	+	RNA	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95552625C>T	uc002stv.1	-	7		c.965G>A								Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																		GAACATACAGCCAAAAATCCA	0.333													8	58	---	---	---	---	PASS
LY75	4065	broad.mit.edu	37	2	160667078	160667078	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160667078A>G	uc002ubc.3	-	32	4727	c.4658T>C	c.(4657-4659)TTG>TCG	p.L1553S	LY75_uc002ubb.3_Missense_Mutation_p.L1553S|LY75_uc010fos.2_Missense_Mutation_p.L1553S	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor	1553	Extracellular (Potential).|C-type lectin 10.				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		AAAACTGTGCAATGCCTGATC	0.323													27	203	---	---	---	---	PASS
TLK1	9874	broad.mit.edu	37	2	171902831	171902831	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171902831C>T	uc002ugn.2	-	11	1494	c.1022G>A	c.(1021-1023)AGG>AAG	p.R341K	TLK1_uc002ugo.2_Missense_Mutation_p.R362K|TLK1_uc002ugp.2_Missense_Mutation_p.R293K|TLK1_uc002ugq.2_RNA|TLK1_uc010zdn.1_Missense_Mutation_p.R245K|TLK1_uc002ugr.1_Missense_Mutation_p.R124K	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1	341					cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						TTTCCTTTGCCTTTCAATATC	0.378													19	127	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179499489	179499489	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179499489C>T	uc010zfg.1	-	178	34632	c.34408G>A	c.(34408-34410)GCC>ACC	p.A11470T	TTN_uc010zfh.1_Missense_Mutation_p.A5165T|TTN_uc010zfi.1_Missense_Mutation_p.A5098T|TTN_uc010zfj.1_Missense_Mutation_p.A4973T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12397							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCATTAAGGGCCTGGTAGAGG	0.413													8	200	---	---	---	---	PASS
ABI2	10152	broad.mit.edu	37	2	204259426	204259426	+	Silent	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204259426G>A	uc002vaa.2	+	6	817	c.582G>A	c.(580-582)CGG>CGA	p.R194R	ABI2_uc010zig.1_Intron|ABI2_uc002uzz.2_Silent_p.R188R|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Silent_p.R188R|ABI2_uc010zij.1_Silent_p.R132R|ABI2_uc002vab.2_Silent_p.R143R|ABI2_uc010zik.1_Intron|ABI2_uc010zil.1_Silent_p.R29R|ABI2_uc010zim.1_Intron|ABI2_uc002vac.2_Intron|ABI2_uc010zin.1_5'UTR	NM_005759	NP_005750	Q9NYB9	ABI2_HUMAN	abl interactor 2	194	Pro-rich.				actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0						TTTGTAGGCGGCACTCCCCCT	0.473													4	157	---	---	---	---	PASS
NRP2	8828	broad.mit.edu	37	2	206640998	206640998	+	Intron	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206640998C>T	uc002vaw.2	+						NRP2_uc002vau.2_Silent_p.P823P|NRP2_uc002vav.2_Silent_p.P818P|NRP2_uc002vax.2_Intron|NRP2_uc002vay.2_Intron	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor						angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4						GGACCGAGCCCACAGTGGACA	0.597											OREG0015157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	121	---	---	---	---	PASS
HDAC4	9759	broad.mit.edu	37	2	240111615	240111615	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240111615G>C	uc002vyk.3	-	4	1045	c.253C>G	c.(253-255)CAG>GAG	p.Q85E	HDAC4_uc010fyz.1_Missense_Mutation_p.Q80E|HDAC4_uc010zoa.1_Missense_Mutation_p.Q80E|HDAC4_uc010fza.2_Missense_Mutation_p.Q85E|HDAC4_uc002vyl.1_RNA|HDAC4_uc010fyy.2_Missense_Mutation_p.Q37E	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	85	Potential.				B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ATCTGCCTCTGGATCTGCTGC	0.662													9	34	---	---	---	---	PASS
ATG7	10533	broad.mit.edu	37	3	11389435	11389435	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11389435G>T	uc003bwc.2	+	12	1327	c.1210G>T	c.(1210-1212)GAA>TAA	p.E404*	ATG7_uc003bwd.2_Nonsense_Mutation_p.E404*|ATG7_uc011aum.1_Nonsense_Mutation_p.E365*	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a	404					autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						CTATGAGTTTGAAGATTGCCT	0.522													26	86	---	---	---	---	PASS
KCNH8	131096	broad.mit.edu	37	3	19436689	19436689	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19436689G>A	uc003cbk.1	+	7	1258	c.1063G>A	c.(1063-1065)GTC>ATC	p.V355I	KCNH8_uc011awe.1_Missense_Mutation_p.V355I|KCNH8_uc010hex.1_5'UTR|KCNH8_uc011awf.1_5'UTR	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	355	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						CAGTACTATCGTCCTGACTCT	0.498													26	104	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121208173	121208173	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121208173T>G	uc003eee.3	-	16	3734	c.3605A>C	c.(3604-3606)GAA>GCA	p.E1202A	POLQ_uc003eed.2_Missense_Mutation_p.E374A	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1202					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		GCTTGTCTGTTCATGAGATTG	0.348								DNA_polymerases_(catalytic_subunits)					62	336	---	---	---	---	PASS
RASA2	5922	broad.mit.edu	37	3	141278763	141278763	+	Silent	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141278763A>G	uc003etz.1	+	9	789	c.789A>G	c.(787-789)CTA>CTG	p.L263L	RASA2_uc010huq.1_Silent_p.L263L|RASA2_uc003eua.1_Silent_p.L263L|RASA2_uc011bnc.1_5'UTR	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	263	C2 2.				intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6						ATGGAAACCTAGTCCAAGATG	0.393													11	68	---	---	---	---	PASS
CRYGS	1427	broad.mit.edu	37	3	186262113	186262113	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186262113C>T	uc003fqe.2	-	1	55	c.3G>A	c.(1-3)ATG>ATA	p.M1I	CRYGS_uc003fqf.2_Missense_Mutation_p.M1I	NM_017541	NP_060011	P22914	CRBS_HUMAN	crystallin, gamma S	1							structural constituent of eye lens				0	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		CAGTTTTAGACATTTTTGGTG	0.398													11	78	---	---	---	---	PASS
ZFYVE28	57732	broad.mit.edu	37	4	2275855	2275855	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2275855C>G	uc003gex.1	-	9	2459	c.2140G>C	c.(2140-2142)GAG>CAG	p.E714Q	ZFYVE28_uc011bvk.1_Missense_Mutation_p.E644Q|ZFYVE28_uc011bvl.1_Missense_Mutation_p.E684Q|ZFYVE28_uc003gew.1_Missense_Mutation_p.E600Q	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	714					negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						CGGATCTTCTCTCTTGTGGCC	0.627													4	72	---	---	---	---	PASS
FAM193A	8603	broad.mit.edu	37	4	2701737	2701737	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2701737C>A	uc010icl.2	+	17	3316	c.2965C>A	c.(2965-2967)CAT>AAT	p.H989N	FAM193A_uc010ick.2_Missense_Mutation_p.H1189N|FAM193A_uc003gfd.2_Missense_Mutation_p.H989N|FAM193A_uc011bvm.1_Missense_Mutation_p.H1011N|FAM193A_uc011bvn.1_Missense_Mutation_p.H989N|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Missense_Mutation_p.H843N	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	989										ovary(3)	3						CCCATCCAGGCATATGAACCA	0.547													4	115	---	---	---	---	PASS
YTHDC1	91746	broad.mit.edu	37	4	69195760	69195760	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69195760T>C	uc003hdx.2	-	9	1662	c.1309A>G	c.(1309-1311)AAA>GAA	p.K437E	YTHDC1_uc003hdy.2_Missense_Mutation_p.K419E	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	437	YTH.									upper_aerodigestive_tract(1)|ovary(1)	2						CCCAGCATTTTAGCACTCATT	0.363													3	103	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	69416530	69416530	+	IGR	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69416530C>T								YTHDC1 (200706 upstream) : UGT2B15 (95786 downstream)																							CAAGGGAATGCCCACCATAGG	0.458													5	266	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79437036	79437036	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79437036G>T	uc003hlb.2	+	66	10698	c.10258G>T	c.(10258-10260)GTG>TTG	p.V3420L		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3415	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						TGACCCCAGCGTGCGAGAGCC	0.552													3	75	---	---	---	---	PASS
SMARCAD1	56916	broad.mit.edu	37	4	95195916	95195916	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95195916G>T	uc003htc.3	+	13	1955	c.1700G>T	c.(1699-1701)TGG>TTG	p.W567L	SMARCAD1_uc003htb.3_Missense_Mutation_p.W567L|SMARCAD1_uc003htd.3_Missense_Mutation_p.W567L|SMARCAD1_uc010ila.2_Missense_Mutation_p.W430L|SMARCAD1_uc011cdw.1_Missense_Mutation_p.W137L	NM_020159	NP_064544	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated	567	Helicase ATP-binding.				chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		GTTAATTTATGGTGCCCTACT	0.323													4	155	---	---	---	---	PASS
AGXT2L1	64850	broad.mit.edu	37	4	109667938	109667938	+	Silent	SNP	T	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109667938T>C	uc003hzc.2	-	10	1333	c.1152A>G	c.(1150-1152)GAA>GAG	p.E384E	AGXT2L1_uc010imc.2_Silent_p.E378E|AGXT2L1_uc011cfm.1_Silent_p.E344E|AGXT2L1_uc011cfn.1_Silent_p.E311E|AGXT2L1_uc011cfo.1_Silent_p.E326E	NM_031279	NP_112569	Q8TBG4	AT2L1_HUMAN	alanine-glyoxylate aminotransferase 2-like 1	384					cellular amino acid metabolic process	mitochondrion	alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000281)		TGTGCTGAGCTTCAGCTGTGG	0.488													66	293	---	---	---	---	PASS
PCDH18	54510	broad.mit.edu	37	4	138450943	138450943	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138450943C>T	uc003ihe.3	-	1	2687	c.2300G>A	c.(2299-2301)GGC>GAC	p.G767D	PCDH18_uc003ihf.3_Missense_Mutation_p.G760D|PCDH18_uc011cgz.1_Intron|PCDH18_uc003ihg.3_Missense_Mutation_p.G547D|PCDH18_uc011cha.1_Intron	NM_019035	NP_061908	Q9HCL0	PCD18_HUMAN	protocadherin 18 precursor	767	Cytoplasmic (Potential).				brain development|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			pancreas(3)|skin(2)	5	all_hematologic(180;0.24)					GGGCAGAGTGCCATTTATGGT	0.517													14	89	---	---	---	---	PASS
RXFP1	59350	broad.mit.edu	37	4	159549854	159549854	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159549854G>A	uc003ipz.2	+	11	974	c.892G>A	c.(892-894)GAT>AAT	p.D298N	RXFP1_uc010iqj.1_Missense_Mutation_p.D127N|RXFP1_uc011cja.1_Missense_Mutation_p.D193N|RXFP1_uc010iqo.2_Missense_Mutation_p.D298N|RXFP1_uc011cjb.1_Missense_Mutation_p.D244N|RXFP1_uc010iqk.2_Missense_Mutation_p.D166N|RXFP1_uc011cjc.1_Missense_Mutation_p.D217N|RXFP1_uc011cjd.1_Missense_Mutation_p.D217N|RXFP1_uc010iql.2_Missense_Mutation_p.D142N|RXFP1_uc011cje.1_Missense_Mutation_p.D325N|RXFP1_uc010iqm.2_Missense_Mutation_p.D265N|RXFP1_uc011cjf.1_Missense_Mutation_p.D168N|RXFP1_uc010iqn.2_Missense_Mutation_p.D244N	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	298	Extracellular (Potential).|LRR 7.					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		CCAGAAACTGGATGAATTGTA	0.264													6	30	---	---	---	---	PASS
TRIML1	339976	broad.mit.edu	37	4	189068401	189068401	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189068401C>A	uc003izm.1	+	6	1397	c.1282C>A	c.(1282-1284)CTC>ATC	p.L428I	TRIML1_uc003izn.1_Missense_Mutation_p.L152I	NM_178556	NP_848651	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	428	B30.2/SPRY.				multicellular organismal development		ligase activity|zinc ion binding			ovary(1)|pancreas(1)|breast(1)|skin(1)	4		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GGATGAATCCCTCATCTACAG	0.512													4	200	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140594887	140594887	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140594887G>T	uc003lja.1	+	1	1379	c.1192G>T	c.(1192-1194)GAA>TAA	p.E398*		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	398	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAAATCCGCGGAAAACTTTTA	0.453													30	92	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176631295	176631295	+	Splice_Site	SNP	T	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176631295T>C	uc003mfr.3	+	4	1374	c.1236_splice	c.e4+2	p.K412_splice	NSD1_uc003mft.3_Splice_Site_p.K143_splice|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Splice_Site_p.K60_splice	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGGCATAAGGTAGGAAACGAA	0.323			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			14	85	---	---	---	---	PASS
RAB24	53917	broad.mit.edu	37	5	176729440	176729440	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176729440G>A	uc003mfv.2	-	6	760	c.391C>T	c.(391-393)CGT>TGT	p.R131C	RAB24_uc003mfu.2_Missense_Mutation_p.R102C|RAB24_uc003mfw.2_Missense_Mutation_p.R131C|PRELID1_uc003mfx.2_5'Flank|PRELID1_uc003mfy.2_5'Flank	NM_130781	NP_570137	Q969Q5	RAB24_HUMAN	RAB24 gene product	131					autophagy|protein transport|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|protein binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACACGTCGACGCCTCCGGTCT	0.577													42	127	---	---	---	---	PASS
IBTK	25998	broad.mit.edu	37	6	82950105	82950105	+	Silent	SNP	A	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82950105A>T	uc003pjl.1	-	2	626	c.99T>A	c.(97-99)ATT>ATA	p.I33I	IBTK_uc011dyv.1_Silent_p.I33I|IBTK_uc011dyw.1_Silent_p.I33I|IBTK_uc010kbi.1_5'UTR|IBTK_uc003pjm.2_Silent_p.I33I	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase	33					negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GAAAGGCCTTAATCTGGTTTT	0.473													27	130	---	---	---	---	PASS
IBTK	25998	broad.mit.edu	37	6	82950107	82950107	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82950107T>C	uc003pjl.1	-	2	624	c.97A>G	c.(97-99)ATT>GTT	p.I33V	IBTK_uc011dyv.1_Missense_Mutation_p.I33V|IBTK_uc011dyw.1_Missense_Mutation_p.I33V|IBTK_uc010kbi.1_5'UTR|IBTK_uc003pjm.2_Missense_Mutation_p.I33V	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase	33					negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AAGGCCTTAATCTGGTTTTCG	0.468													25	130	---	---	---	---	PASS
THEMIS	387357	broad.mit.edu	37	6	128222041	128222041	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128222041C>T	uc003qbi.2	-	2	356	c.37G>A	c.(37-39)GAC>AAC	p.D13N	THEMIS_uc011ebt.1_Missense_Mutation_p.D13N|THEMIS_uc010kfb.2_Intron	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	13	CABIT 1.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						GTCCTGAGGTCAAGGGAGTGG	0.473													6	183	---	---	---	---	PASS
NOX3	50508	broad.mit.edu	37	6	155743887	155743887	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155743887G>A	uc003qqm.2	-	10	1352	c.1249C>T	c.(1249-1251)CTT>TTT	p.L417F		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	417	Cytoplasmic (Potential).						electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GATTTCAGAAGAGCAGCGAAG	0.512													33	155	---	---	---	---	PASS
HOXA2	3199	broad.mit.edu	37	7	27142221	27142221	+	5'UTR	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27142221C>T	uc003syh.2	-	1						NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						GAAAAAAAATCTATCATAGAA	0.463													4	9	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48285181	48285181	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48285181A>G	uc003toq.2	+	12	1488	c.1463A>G	c.(1462-1464)AAG>AGG	p.K488R	ABCA13_uc010kyr.2_5'UTR	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	488					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						AAACTGGAAAAGGATGTGTTC	0.308													4	216	---	---	---	---	PASS
GNAI1	2770	broad.mit.edu	37	7	79818508	79818508	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79818508G>T	uc003uhb.1	+	3	601	c.264G>T	c.(262-264)ATG>ATT	p.M88I	GNAI1_uc011kgt.1_Missense_Mutation_p.M36I	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	88					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TTAGGGCTATGGGGAGGTTGA	0.403													3	94	---	---	---	---	PASS
MCM7	4176	broad.mit.edu	37	7	99693535	99693535	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99693535G>T	uc003usw.1	-	11	1967	c.1457C>A	c.(1456-1458)GCT>GAT	p.A486D	MCM7_uc003usv.1_Missense_Mutation_p.A310D|MCM7_uc003usx.1_Missense_Mutation_p.A310D|uc003usy.1_5'Flank|MIR25_hsa-mir-25|MI0000082_5'Flank|uc003usz.1_5'Flank|MIR93_hsa-mir-93|MI0000095_5'Flank|uc003uta.1_5'Flank|MIR106B_hsa-mir-106b|MI0000734_5'Flank	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	486	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)	GTTGGCGGCAGCCAGGATGGA	0.632													14	103	---	---	---	---	PASS
HYAL4	23553	broad.mit.edu	37	7	123517205	123517205	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123517205T>C	uc003vlc.2	+	5	2080	c.1442T>C	c.(1441-1443)TTG>TCG	p.L481S	HYAL4_uc011knz.1_3'UTR	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	481	Cytoplasmic (Potential).				fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity			skin(1)	1						AGCATTCAGTTGTGAGATAAT	0.378													17	91	---	---	---	---	PASS
HYAL4	23553	broad.mit.edu	37	7	123517206	123517206	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123517206G>T	uc003vlc.2	+	5	2081	c.1443G>T	c.(1441-1443)TTG>TTT	p.L481F	HYAL4_uc011knz.1_3'UTR	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	481	Cytoplasmic (Potential).				fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity			skin(1)	1						GCATTCAGTTGTGAGATAATT	0.373													17	89	---	---	---	---	PASS
GIMAP8	155038	broad.mit.edu	37	7	150174396	150174396	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150174396G>A	uc003whj.2	+	5	1856	c.1526G>A	c.(1525-1527)CGG>CAG	p.R509Q		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	509						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		GACCCATCCCGGTTAGAAGAG	0.532													3	73	---	---	---	---	PASS
FAM66D	100132923	broad.mit.edu	37	8	11985905	11985905	+	Intron	SNP	C	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11985905C>G	uc011kxo.1	+						FAM66D_uc011kxp.1_Intron|LOC392196_uc003wvb.1_RNA	NR_027425				Homo sapiens cDNA FLJ56781 complete cds.												0						TGCATGTCAACGCACTCAGGA	0.483													3	17	---	---	---	---	PASS
FZD3	7976	broad.mit.edu	37	8	28385020	28385020	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28385020T>C	uc003xgx.2	+	5	1221	c.743T>C	c.(742-744)GTA>GCA	p.V248A	FZD3_uc010lvb.2_Missense_Mutation_p.V248A	NM_017412	NP_059108	Q9NPG1	FZD3_HUMAN	frizzled 3 precursor	248	Helical; Name=2; (Potential).				canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TACATGATGGTATCCTTAATT	0.378													30	135	---	---	---	---	PASS
FGFR1	2260	broad.mit.edu	37	8	38282176	38282176	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38282176C>A	uc003xlp.2	-	7	1729	c.787G>T	c.(787-789)GCC>TCC	p.A263S	FGFR1_uc011lbo.1_Missense_Mutation_p.A261S|FGFR1_uc011lbp.1_Missense_Mutation_p.A174S|FGFR1_uc011lbq.1_Missense_Mutation_p.A172S|FGFR1_uc010lwk.2_Missense_Mutation_p.A255S|FGFR1_uc011lbr.1_RNA|FGFR1_uc011lbs.1_Missense_Mutation_p.A103S|FGFR1_uc011lbt.1_Missense_Mutation_p.A172S|FGFR1_uc011lbu.1_Missense_Mutation_p.A294S|FGFR1_uc011lbv.1_Missense_Mutation_p.A261S|FGFR1_uc011lbw.1_Missense_Mutation_p.A174S|FGFR1_uc011lbx.1_Missense_Mutation_p.A174S|FGFR1_uc003xlv.2_Missense_Mutation_p.A174S|FGFR1_uc003xlu.2_Missense_Mutation_p.A172S	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1	263	Ig-like C2-type 3.|Extracellular (Potential).				axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	GTTTTGTTGGCGGGCAACCCT	0.587		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						27	107	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125035809	125035809	+	Silent	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125035809C>T	uc003yqw.2	+	18	2465	c.2259C>T	c.(2257-2259)TGC>TGT	p.C753C	uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	753	Cytoplasmic (Potential).					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)			GCAAACACTGCGGCAAGATCA	0.493													6	67	---	---	---	---	PASS
PPP1R16A	84988	broad.mit.edu	37	8	145724303	145724303	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145724303G>A	uc003zdd.2	+	4	1248	c.335G>A	c.(334-336)TGC>TAC	p.C112Y	uc003zde.1_5'UTR|PPP1R16A_uc003zdf.2_Missense_Mutation_p.C112Y	NM_032902	NP_116291	Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	112	ANK 2.					plasma membrane	protein binding				0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TTGCAGTGCTGCATTGATGAT	0.652													10	46	---	---	---	---	PASS
CDC37L1	55664	broad.mit.edu	37	9	4685159	4685159	+	Splice_Site	SNP	G	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4685159G>T	uc003zio.2	+	2	624	c.414_splice	c.e2+1	p.K138_splice		NM_017913	NP_060383	Q7L3B6	CD37L_HUMAN	cell division cycle 37 homolog (S.							cytoplasm					0	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		TTTTAATAAGGTATGAGCTTT	0.413													4	119	---	---	---	---	PASS
MLANA	2315	broad.mit.edu	37	9	5897599	5897599	+	Silent	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5897599A>G	uc003zjo.1	+	3	173	c.120A>G	c.(118-120)TTA>TTG	p.L40L		NM_005511	NP_005502	Q16655	MAR1_HUMAN	melan-A	40	Helical; (Potential).					endoplasmic reticulum membrane|integral to plasma membrane|melanosome|trans-Golgi network	protein binding				0		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		TGGGAGTCTTACTGCTCATCG	0.483													18	101	---	---	---	---	PASS
MLANA	2315	broad.mit.edu	37	9	5897600	5897600	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5897600C>A	uc003zjo.1	+	3	174	c.121C>A	c.(121-123)CTG>ATG	p.L41M		NM_005511	NP_005502	Q16655	MAR1_HUMAN	melan-A	41	Helical; (Potential).					endoplasmic reticulum membrane|integral to plasma membrane|melanosome|trans-Golgi network	protein binding				0		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		GGGAGTCTTACTGCTCATCGG	0.488													17	103	---	---	---	---	PASS
BNC2	54796	broad.mit.edu	37	9	16418907	16418907	+	3'UTR	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16418907C>A	uc003zml.2	-	7					BNC2_uc011lmw.1_3'UTR|BNC2_uc003zmm.2_3'UTR|BNC2_uc011lmv.1_3'UTR|BNC2_uc003zmj.2_3'UTR|BNC2_uc003zmk.2_RNA|BNC2_uc003zmi.2_3'UTR	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)		acCCCAAGTACATAAGCGCAC	0.368													3	49	---	---	---	---	PASS
KIAA1797	54914	broad.mit.edu	37	9	20874780	20874780	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20874780C>T	uc003zog.1	+	21	2654	c.2291C>T	c.(2290-2292)TCA>TTA	p.S764L	KIAA1797_uc003zoh.1_Missense_Mutation_p.S200L	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914	764						integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		AAACTGTTGTCACTCACTCCC	0.403													48	203	---	---	---	---	PASS
ANUBL1	93550	broad.mit.edu	37	10	46121526	46121526	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46121526A>G	uc001jcp.3	-	7	1987	c.1745T>C	c.(1744-1746)TTA>TCA	p.L582S	ANUBL1_uc001jcl.3_Missense_Mutation_p.L102S|ANUBL1_uc001jcm.3_Missense_Mutation_p.L582S|ANUBL1_uc009xmu.2_Missense_Mutation_p.L508S|ANUBL1_uc001jcn.3_Missense_Mutation_p.L508S|ANUBL1_uc001jco.3_Intron	NM_001128324	NP_001121796	Q86XD8	ANUB1_HUMAN	AN1, ubiquitin-like, homolog	582							zinc ion binding				0						TGTGCTCTGTAATCTATTTCT	0.458													26	133	---	---	---	---	PASS
ARID5B	84159	broad.mit.edu	37	10	63662043	63662043	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63662043G>C	uc001jlt.1	+	2	173	c.147G>C	c.(145-147)AAG>AAC	p.K49N	ARID5B_uc010qil.1_Missense_Mutation_p.K49N	NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	49					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)					GTACGCCAAAGGATCCGATTT	0.453													4	120	---	---	---	---	PASS
AGAP5	729092	broad.mit.edu	37	10	75487058	75487058	+	5'UTR	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75487058G>A	uc001juu.3	-	3					BMS1P4_uc001juv.3_RNA|BMS1P4_uc010qkm.1_RNA	NM_001144000	NP_001137472	A6NIR3	AGAP5_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						TACCTGACACGATCATCACAG	0.498													16	104	---	---	---	---	PASS
NEURL	9148	broad.mit.edu	37	10	105344764	105344764	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105344764C>A	uc001kxh.2	+	4	1531	c.1121C>A	c.(1120-1122)CCT>CAT	p.P374H		NM_004210	NP_004201	O76050	NEU1A_HUMAN	neuralized-like	374	NHR 2.				nervous system development	perinuclear region of cytoplasm	zinc ion binding				0				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		CCTTTCAGCCCTGAGGCCCTG	0.746													3	10	---	---	---	---	PASS
C10orf79	80217	broad.mit.edu	37	10	105953637	105953637	+	Missense_Mutation	SNP	C	T	T	rs145913363	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105953637C>T	uc001kxw.2	-	11	1545	c.1429G>A	c.(1429-1431)GTG>ATG	p.V477M	C10orf79_uc001kxx.3_Missense_Mutation_p.V478M|C10orf79_uc001kxy.1_Missense_Mutation_p.V478M	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	477	WD 8.										0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)		ACGTGCTGCACGGACGATTCC	0.517													12	39	---	---	---	---	PASS
FGFR2	2263	broad.mit.edu	37	10	123239469	123239469	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123239469A>C	uc010qtk.1	-	19	3015	c.2368T>G	c.(2368-2370)TGT>GGT	p.C790G	FGFR2_uc010qtg.1_Missense_Mutation_p.C678G|FGFR2_uc010qth.1_Missense_Mutation_p.C675G|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Missense_Mutation_p.C791G|FGFR2_uc010qtl.1_Missense_Mutation_p.C674G|FGFR2_uc010qtm.1_Missense_Mutation_p.C673G|FGFR2_uc001lfg.3_Missense_Mutation_p.C398G|FGFR2_uc001lfk.1_RNA	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1	790	Cytoplasmic (Potential).				angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	CCTGAAGAACAAGAACTTCTT	0.428		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				5	173	---	---	---	---	PASS
FGFR2	2263	broad.mit.edu	37	10	123298145	123298145	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123298145A>G	uc010qtk.1	-	6	1356	c.709T>C	c.(709-711)TAC>CAC	p.Y237H	FGFR2_uc010qtg.1_Missense_Mutation_p.Y237H|FGFR2_uc010qth.1_Missense_Mutation_p.Y122H|FGFR2_uc010qti.1_Missense_Mutation_p.Y148H|FGFR2_uc010qtj.1_Missense_Mutation_p.Y237H|FGFR2_uc010qtl.1_Missense_Mutation_p.Y237H|FGFR2_uc010qtm.1_Missense_Mutation_p.Y122H|FGFR2_uc001lfl.3_Missense_Mutation_p.Y237H|FGFR2_uc001lfm.2_Missense_Mutation_p.Y148H|FGFR2_uc001lfn.3_RNA|FGFR2_uc010qtn.1_Missense_Mutation_p.Y256H|FGFR2_uc010qto.1_Missense_Mutation_p.Y141H|FGFR2_uc001lfo.1_Missense_Mutation_p.Y256H|FGFR2_uc010qtp.1_Missense_Mutation_p.Y256H|FGFR2_uc010qtq.1_Missense_Mutation_p.Y256H	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1	237	Ig-like C2-type 2.|Extracellular (Potential).				angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	ATGGACCCGTATTCATTCTCC	0.493		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				5	76	---	---	---	---	PASS
FGFR2	2263	broad.mit.edu	37	10	123298147	123298147	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123298147T>G	uc010qtk.1	-	6	1354	c.707A>C	c.(706-708)GAA>GCA	p.E236A	FGFR2_uc010qtg.1_Missense_Mutation_p.E236A|FGFR2_uc010qth.1_Missense_Mutation_p.E121A|FGFR2_uc010qti.1_Missense_Mutation_p.E147A|FGFR2_uc010qtj.1_Missense_Mutation_p.E236A|FGFR2_uc010qtl.1_Missense_Mutation_p.E236A|FGFR2_uc010qtm.1_Missense_Mutation_p.E121A|FGFR2_uc001lfl.3_Missense_Mutation_p.E236A|FGFR2_uc001lfm.2_Missense_Mutation_p.E147A|FGFR2_uc001lfn.3_RNA|FGFR2_uc010qtn.1_Missense_Mutation_p.E255A|FGFR2_uc010qto.1_Missense_Mutation_p.E140A|FGFR2_uc001lfo.1_Missense_Mutation_p.E255A|FGFR2_uc010qtp.1_Missense_Mutation_p.E255A|FGFR2_uc010qtq.1_Missense_Mutation_p.E255A	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1	236	Ig-like C2-type 2.|Extracellular (Potential).				angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	GGACCCGTATTCATTCTCCAC	0.488		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				4	78	---	---	---	---	PASS
RNH1	6050	broad.mit.edu	37	11	498772	498772	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:498772C>A	uc001lpk.1	-	5	2184	c.776G>T	c.(775-777)AGG>ATG	p.R259M	RNH1_uc001lpl.1_Missense_Mutation_p.R259M|RNH1_uc001lpm.1_Missense_Mutation_p.R259M|RNH1_uc001lpn.1_Missense_Mutation_p.R259M|RNH1_uc001lpo.1_Missense_Mutation_p.R259M|RNH1_uc009ybw.1_RNA|RNH1_uc001lpp.1_Missense_Mutation_p.R259M|RNH1_uc001lpt.1_Missense_Mutation_p.R16M|RNH1_uc001lpq.1_Missense_Mutation_p.R259M|RNH1_uc001lpr.1_Missense_Mutation_p.R259M|RNH1_uc001lps.1_Missense_Mutation_p.R259M	NM_203389	NP_976323	P13489	RINI_HUMAN	ribonuclease/angiogenin inhibitor	259	LRR 9.				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)		CCACAGGGTCCTGAGCCTGGA	0.706													3	19	---	---	---	---	PASS
PLCB3	5331	broad.mit.edu	37	11	64028903	64028903	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64028903A>T	uc001nzb.2	+	15	1763	c.1763A>T	c.(1762-1764)GAG>GTG	p.E588V	PLCB3_uc009ypg.1_Missense_Mutation_p.E588V|PLCB3_uc009yph.1_Missense_Mutation_p.E521V|PLCB3_uc009ypi.2_Missense_Mutation_p.E588V	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	588					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2						AATGCCACTGAGGAGATGTCC	0.617													15	84	---	---	---	---	PASS
ARHGAP20	57569	broad.mit.edu	37	11	110501395	110501395	+	Silent	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110501395C>T	uc001pkz.1	-	4	594	c.309G>A	c.(307-309)CGG>CGA	p.R103R	ARHGAP20_uc001pky.1_Silent_p.R80R|ARHGAP20_uc009yyb.1_Silent_p.R67R|ARHGAP20_uc001pla.1_Silent_p.R67R	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	103	PH.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GGAAAAGATGCCGCTCCTGCC	0.398													4	122	---	---	---	---	PASS
SIK3	23387	broad.mit.edu	37	11	116746997	116746997	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116746997A>G	uc001ppy.2	-	8	929	c.893T>C	c.(892-894)ATG>ACG	p.M298T	SIK3_uc001ppz.2_Missense_Mutation_p.M197T|SIK3_uc001pqa.2_Missense_Mutation_p.M298T	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK	298	UBA.					cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						GTCCAGTCCCATGTCCTCCAT	0.463													25	110	---	---	---	---	PASS
PZP	5858	broad.mit.edu	37	12	9344841	9344841	+	Silent	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9344841C>T	uc001qvl.2	-	13	1523	c.1494G>A	c.(1492-1494)AAG>AAA	p.K498K	PZP_uc009zgl.2_Silent_p.K367K	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						CGATGACTCCCTTAGCCATGA	0.463													11	55	---	---	---	---	PASS
PIK3C2G	5288	broad.mit.edu	37	12	18435099	18435099	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18435099T>G	uc001rdt.2	+	2	200	c.84T>G	c.(82-84)AAT>AAG	p.N28K	PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Missense_Mutation_p.N28K|PIK3C2G_uc010sic.1_5'UTR	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma	28					cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				TCTTTGTAAATCAACCCCATT	0.363													8	25	---	---	---	---	PASS
STAT2	6773	broad.mit.edu	37	12	56743970	56743970	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56743970G>A	uc001slc.2	-	13	1198	c.1120C>T	c.(1120-1122)CGG>TGG	p.R374W	STAT2_uc001slb.2_5'Flank|STAT2_uc001sld.2_Missense_Mutation_p.R370W|STAT2_uc010sqn.1_Missense_Mutation_p.R370W	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	374				R->A: Prevents the nuclear import; when associated with A-375.	interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3						TTGAACTTCCGGAAGCTGTTC	0.408													4	118	---	---	---	---	PASS
UPF3A	65110	broad.mit.edu	37	13	115047559	115047559	+	Silent	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115047559C>T	uc001vup.2	+	2	308	c.271C>T	c.(271-273)CTG>TTG	p.L91L	UPF3A_uc010tkn.1_Silent_p.L91L|UPF3A_uc001vuq.2_Silent_p.L91L|UPF3A_uc001vus.2_RNA|UPF3A_uc001vur.2_RNA	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	91	Required for interaction with UPF2.				mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCTGCGCCCGCTGCCAGCACA	0.731													3	5	---	---	---	---	PASS
FAM179B	23116	broad.mit.edu	37	14	45432114	45432114	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45432114C>T	uc001wvv.2	+	1	699	c.490C>T	c.(490-492)CGG>TGG	p.R164W	FAM179B_uc001wvw.2_Missense_Mutation_p.R164W|FAM179B_uc010anc.2_RNA|KLHL28_uc001wvq.2_5'Flank|KLHL28_uc001wvr.2_5'Flank|FAM179B_uc010anb.1_Missense_Mutation_p.R164W|FAM179B_uc001wvu.2_Missense_Mutation_p.R164W	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	164							binding			skin(2)|upper_aerodigestive_tract(1)	3						GGACGTTCTCCGGGGTCAGGG	0.567													27	180	---	---	---	---	PASS
LTBP2	4053	broad.mit.edu	37	14	74967715	74967715	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74967715C>T	uc001xqa.2	-	36	5725	c.5338G>A	c.(5338-5340)GAC>AAC	p.D1780N		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	1780	EGF-like 20; calcium-binding (Potential).				protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CCGTTCAAGTCATCACACTCA	0.577											OREG0022805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	19	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75513898	75513898	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75513898C>A	uc001xrd.1	-	2	2677	c.2461G>T	c.(2461-2463)GCA>TCA	p.A821S	MLH3_uc001xre.1_Missense_Mutation_p.A821S|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	821					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		ATGTGGCTTGCTGGTTGACAA	0.408								MMR					20	130	---	---	---	---	PASS
CCDC88C	440193	broad.mit.edu	37	14	91760563	91760563	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91760563T>A	uc010aty.2	-	23	4165	c.4066A>T	c.(4066-4068)AAC>TAC	p.N1356Y		NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE	1356	Potential.				microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				TTCTCCATGTTCTGCTCCAGA	0.552													7	208	---	---	---	---	PASS
RIN3	79890	broad.mit.edu	37	14	93125511	93125511	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93125511A>G	uc001yap.2	+	7	2184	c.2032A>G	c.(2032-2034)ATT>GTT	p.I678V	RIN3_uc010auk.2_Missense_Mutation_p.I340V|RIN3_uc001yaq.2_Missense_Mutation_p.I603V|RIN3_uc001yar.1_Missense_Mutation_p.I340V|RIN3_uc001yas.1_Missense_Mutation_p.I340V	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	678	Interaction with RAB5B.				endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding			lung(2)|ovary(1)	3		all_cancers(154;0.0701)				TGCAGAAGCAATTGTAGAGTC	0.537													9	537	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106237611	106237611	+	RNA	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106237611C>T	uc010tyt.1	-	3611		c.57272G>A			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						CTGGTCAGGGCGCCTGAGTTC	0.672													4	32	---	---	---	---	PASS
WHAMML1	339005	broad.mit.edu	37	15	23205108	23205108	+	RNA	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23205108C>T	uc001yvg.2	-	2		c.687G>A			WHAMML1_uc010ayc.2_RNA|WHAMML1_uc010ayd.2_RNA|WHAMML1_uc010aye.1_RNA	NR_003521				Homo sapiens mRNA; cDNA DKFZp313L2232 (from clone DKFZp313L2232).												0						GTGGTTGCCACGGTAACTAAT	0.393													3	20	---	---	---	---	PASS
LCMT2	9836	broad.mit.edu	37	15	43621613	43621613	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43621613C>A	uc001zrg.2	-	1	1279	c.1075G>T	c.(1075-1077)GGC>TGC	p.G359C	LCMT2_uc010udn.1_5'UTR|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	359					tRNA processing		methyltransferase activity|protein binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	GAGGCGTGGCCATATCTCTTC	0.567													9	41	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62254707	62254707	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62254707G>A	uc002agz.2	-	34	3540	c.3466C>T	c.(3466-3468)CGT>TGT	p.R1156C	VPS13C_uc002aha.2_Missense_Mutation_p.R1113C|VPS13C_uc002ahb.1_Missense_Mutation_p.R1156C|VPS13C_uc002ahc.1_Missense_Mutation_p.R1113C	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	1156					protein localization					ovary(2)	2						AAATTAAAACGGAAAACTTCA	0.378													5	195	---	---	---	---	PASS
ZNF710	374655	broad.mit.edu	37	15	90616473	90616473	+	Silent	SNP	C	G	G	rs146964408	byFrequency	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90616473C>G	uc002bov.1	+	3	1752	c.1629C>G	c.(1627-1629)CCC>CCG	p.P543P		NM_198526	NP_940928	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	543					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			TACACTCGCCCGTGAAGCCAT	0.592													18	108	---	---	---	---	PASS
MAPK3	5595	broad.mit.edu	37	16	30133218	30133218	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30133218G>A	uc002dws.2	-	2	380	c.280C>T	c.(280-282)CGC>TGC	p.R94C	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAPK3_uc002dwr.2_5'UTR|MAPK3_uc002dwv.3_Missense_Mutation_p.R94C|MAPK3_uc002dwt.2_Missense_Mutation_p.R94C|MAPK3_uc002dwu.2_RNA|MAPK3_uc010bzp.2_RNA	NM_002746	NP_002737	P27361	MK03_HUMAN	mitogen-activated protein kinase 3 isoform 1	94	Protein kinase.				activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|cellular response to mechanical stimulus|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|interleukin-1-mediated signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription initiation from RNA polymerase I promoter	cytosol|nucleoplasm	ATP binding|MAP kinase activity|phosphatase binding				0					Arsenic trioxide(DB01169)|Isoproterenol(DB01064)|Simvastatin(DB00641)|Sulindac(DB00605)	TGGCGGAAGCGCAGCAGGATC	0.592													5	30	---	---	---	---	PASS
CA7	766	broad.mit.edu	37	16	66887326	66887326	+	Silent	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66887326G>A	uc002eqi.2	+	7	829	c.720G>A	c.(718-720)AGG>AGA	p.R240R	uc002eqh.2_RNA|CA7_uc002eqj.2_Silent_p.R184R	NM_005182	NP_005173	P43166	CAH7_HUMAN	carbonic anhydrase VII isoform 1	240					one-carbon metabolic process	cytoplasm	carbonate dehydratase activity|zinc ion binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		ACGATGAGAGGATCCACATGG	0.602													9	59	---	---	---	---	PASS
KIAA0182	23199	broad.mit.edu	37	16	85701801	85701801	+	Silent	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85701801C>T	uc002fix.2	+	14	3260	c.3186C>T	c.(3184-3186)CAC>CAT	p.H1062H	KIAA0182_uc002fiw.2_Silent_p.H958H|KIAA0182_uc002fiy.2_Silent_p.H989H|KIAA0182_uc002fiz.2_Silent_p.H204H|KIAA0182_uc010cho.2_Silent_p.H242H	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	1062							protein binding			large_intestine(3)|ovary(1)|skin(1)	5						CGTCCGTCCACTACAACATTC	0.642													32	159	---	---	---	---	PASS
FLJ36000	284124	broad.mit.edu	37	17	21904125	21904125	+	RNA	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904125G>A	uc002gza.2	+	1		c.64G>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ggagtcgcaaggggccgagca	0.000													4	61	---	---	---	---	PASS
STAT5A	6776	broad.mit.edu	37	17	40461539	40461539	+	Intron	SNP	C	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40461539C>G	uc002hzj.1	+						STAT5A_uc010cya.1_Intron|STAT5A_uc010cyb.1_Intron|STAT5A_uc010cyc.1_Intron|STAT5A_uc010cye.1_3'UTR	NM_003152	NP_003143	P42229	STA5A_HUMAN	signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		AGGGGAAGAACTGGGGACTTG	0.617													9	26	---	---	---	---	PASS
CASP14	23581	broad.mit.edu	37	19	15164350	15164350	+	Silent	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15164350C>A	uc010dzv.1	+	3	393	c.85C>A	c.(85-87)CGG>AGG	p.R29R	CASP14_uc002naf.2_Silent_p.R29R	NM_012114	NP_036246	P31944	CASPE_HUMAN	caspase 14 precursor	29					apoptosis|cell differentiation|epidermis development|proteolysis	cytoplasm|nucleus	cysteine-type endopeptidase activity			skin(2)|ovary(1)|lung(1)	4						CACCAAAGCCCGGGAAGGTTC	0.517													4	145	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38976834	38976834	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38976834A>G	uc002oit.2	+	34	5669	c.5539A>G	c.(5539-5541)ACC>GCC	p.T1847A	RYR1_uc002oiu.2_Missense_Mutation_p.T1847A	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1847	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	GCTCGTGTCCACCCTGCTGGT	0.532													7	290	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39955501	39955501	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39955501T>A	uc002olo.3	+	11	867	c.688T>A	c.(688-690)TAC>AAC	p.Y230N	SUPT5H_uc002olp.3_Missense_Mutation_p.Y230N|SUPT5H_uc002olq.3_Missense_Mutation_p.Y226N|SUPT5H_uc002oln.3_Missense_Mutation_p.Y230N|SUPT5H_uc002olr.3_Missense_Mutation_p.Y230N|SUPT5H_uc002ols.1_5'Flank	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	230	Interaction with SUPT4H1.				cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CGTGGAGGCCTACAAGCAGAC	0.582													28	87	---	---	---	---	PASS
ZNF701	55762	broad.mit.edu	37	19	53085595	53085595	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53085595C>A	uc002pzs.1	+	4	410	c.283C>A	c.(283-285)CAT>AAT	p.H95N	ZNF701_uc010ydn.1_Missense_Mutation_p.H161N	NM_018260	NP_060730	Q9NV72	ZN701_HUMAN	zinc finger protein 701	95					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		GAAAGATATTCATGACTTTGT	0.398													4	157	---	---	---	---	PASS
RIN2	54453	broad.mit.edu	37	20	19977343	19977343	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19977343G>A	uc002wro.1	+	10	2257	c.2221G>A	c.(2221-2223)GCA>ACA	p.A741T	RIN2_uc010gcu.1_Missense_Mutation_p.A308T|RIN2_uc010gcv.1_Missense_Mutation_p.A535T	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	741	VPS9.				endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5						CTTGACAAGCGCATATGGAGC	0.517													3	48	---	---	---	---	PASS
KIF3B	9371	broad.mit.edu	37	20	30897808	30897808	+	Silent	SNP	G	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30897808G>C	uc002wxq.2	+	2	395	c.228G>C	c.(226-228)ACG>ACC	p.T76T	KIF3B_uc010ztv.1_Silent_p.T76T|KIF3B_uc010ztw.1_Silent_p.T76T	NM_004798	NP_004789	O15066	KIF3B_HUMAN	kinesin family member 3B	76	Kinesin-motor.				anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACGATGAGACGTTCCGACCAC	0.483													17	75	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11058168	11058168	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11058168A>T	uc002yit.1	-	3	480	c.272T>A	c.(271-273)CTG>CAG	p.L91Q	BAGE_uc002yiw.1_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TACATCTTTCAGGAGCTTGGT	0.388													4	131	---	---	---	---	PASS
TMPRSS3	64699	broad.mit.edu	37	21	43803192	43803192	+	Silent	SNP	G	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43803192G>A	uc002zbb.2	-	8	933	c.732C>T	c.(730-732)GGC>GGT	p.G244G	TMPRSS3_uc002zay.2_5'UTR|TMPRSS3_uc002zaz.2_Silent_p.G117G|TMPRSS3_uc002zba.2_Silent_p.G117G|TMPRSS3_uc002zbc.2_Silent_p.G244G|TMPRSS3_uc002zbd.2_Silent_p.G244G	NM_024022	NP_076927	P57727	TMPS3_HUMAN	transmembrane protease, serine 3 isoform 1	244	Peptidase S1.|Extracellular (Potential).				cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3						TGATGACAGAGCCCCCGCACA	0.597													8	29	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	G	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22664606A>G	uc011aim.1	+	31		c.2121A>G			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						GTCTTCATGCAAACTTGGTAT	0.398													4	34	---	---	---	---	PASS
ELFN2	114794	broad.mit.edu	37	22	37769171	37769171	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37769171C>A	uc003asq.3	-	3	3190	c.2404G>T	c.(2404-2406)GAG>TAG	p.E802*		NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	802	Cytoplasmic (Potential).					cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)					TGCAGATCCTCGTCCTTGGCG	0.637													12	87	---	---	---	---	PASS
MAGEB3	4114	broad.mit.edu	37	X	30254882	30254882	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30254882G>C	uc004dca.1	+	5	1578	c.841G>C	c.(841-843)GCT>CCT	p.A281P		NM_002365	NP_002356	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	281	MAGE.										0						AAGAGCCCATGCTGAAACCAG	0.488													14	30	---	---	---	---	PASS
MIR513A1	574509	broad.mit.edu	37	X	146295022	146295022	+	RNA	SNP	C	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146295022C>T	hsa-mir-513a-1|MI0003191	-			c.88C>T																				0						ttacccttctcagaaaggtga	0.194													16	24	---	---	---	---	PASS
PADI6	353238	broad.mit.edu	37	1	17723476	17723477	+	Intron	INS	-	CA	CA	rs144056968	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17723476_17723477insCA	uc001bak.1	+							NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AGGAATGCACCCAGGTGGCTGG	0.629													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	113433615	113433616	+	IGR	INS	-	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113433615_113433616insT								FAM19A3 (163761 upstream) : SLC16A1 (20856 downstream)																							ttattcacttattttttttttt	0.208													4	3	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120612040	120612041	+	5'UTR	INS	-	CCTCCGCCG	CCTCCGCCG			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120612040_120612041insCCTCCGCCG	uc001eik.2	-	1					NOTCH2_uc001eil.2_5'UTR|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGCCTCCTCCTccgccgccgcc	0.619			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	3	---	---	---	---	
B3GALNT2	148789	broad.mit.edu	37	1	235611535	235611536	+	3'UTR	INS	-	AAA	AAA	rs71576473		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235611535_235611536insAAA	uc001hxc.2	-	12					TBCE_uc001hwz.1_Intron|TBCE_uc001hxa.1_Intron|TBCE_uc010pxr.1_Intron|TBCE_uc001hxb.1_Intron	NM_152490	NP_689703	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			aagtcagtctcaaaaaaaaaaa	0.158													3	3	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	234113207	234113207	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234113207delG	uc010zmo.1	+	25	3564	c.3411delG	c.(3409-3411)CCGfs	p.P1137fs	INPP5D_uc010zmp.1_Frame_Shift_Del_p.P1136fs	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	1137	Pro-rich.				apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CGCCCACCCCGACGCCGCGGC	0.701													4	2	---	---	---	---	
ILKAP	80895	broad.mit.edu	37	2	239079802	239079802	+	Intron	DEL	T	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239079802delT	uc002vxv.2	-						ILKAP_uc010zns.1_Intron|ILKAP_uc002vxw.2_Intron	NM_030768	NP_110395	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated protein							cytoplasm|protein serine/threonine phosphatase complex	metal ion binding|protein binding			ovary(3)	3		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		ttcttttttcttttttttttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5124705	5124709	+	IGR	DEL	TTTTT	-	-	rs72175262		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5124705_5124709delTTTTT								BHLHE40 (97842 upstream) : ARL8B (39221 downstream)																							CATTTCAGCCttttttttttttttt	0.459													4	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52713876	52713877	+	5'Flank	INS	-	T	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52713876_52713877insT	uc003des.2	-						PBRM1_uc003dex.2_5'Flank|PBRM1_uc003deq.2_5'Flank|PBRM1_uc003der.2_5'Flank|PBRM1_uc003det.2_5'Flank|PBRM1_uc003deu.2_5'Flank|PBRM1_uc003dev.2_5'Flank|PBRM1_uc003dew.2_5'Flank|PBRM1_uc010hmk.1_5'Flank|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_5'Flank|PBRM1_uc003dfb.1_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CTAGCTATAAGTTTTTTTTTTT	0.361			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								4	2	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115439895	115439895	+	3'UTR	DEL	A	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115439895delA	uc003ebq.2	+	3					GAP43_uc003ebr.2_3'UTR	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		GCAAACatttaaaaaaaaaaa	0.413													4	2	---	---	---	---	
DNAJC13	23317	broad.mit.edu	37	3	132220414	132220414	+	Intron	DEL	A	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132220414delA	uc003eor.2	+							NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2						actctgtctcaaaaaaaaaaa	0.179													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190433401	190433402	+	IGR	INS	-	AG	AG	rs146341792	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190433401_190433402insAG								IL1RAP (57558 upstream) : LOC647309 (137124 downstream)																							TAAAATCAGAAAAAGTTCATTG	0.297													5	3	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68531131	68531132	+	Intron	INS	-	T	T	rs72340884		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68531131_68531132insT	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						CCAGCATAGTGtttttttttgt	0.243													13	7	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151642666	151642666	+	Intron	DEL	T	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151642666delT	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					AAGAACTGGGTTTTTTTTTTT	0.284													6	3	---	---	---	---	
NPR3	4883	broad.mit.edu	37	5	32739272	32739273	+	Intron	DEL	TG	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32739272_32739273delTG	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)	TGTTGCCTTCTGTGTGTGTGTG	0.411													7	5	---	---	---	---	
RIPK1	8737	broad.mit.edu	37	6	3081034	3081034	+	Intron	DEL	C	-	-	rs3830793		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3081034delC	uc010jni.2	+						RIPK1_uc003muv.3_Intron|RIPK1_uc003muw.3_Intron|RIPK1_uc011dhs.1_Intron|RIPK1_uc003mux.2_Intron	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine						activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				ATACCCTCTGCCCCCCCCCGA	0.383													4	2	---	---	---	---	
KATNA1	11104	broad.mit.edu	37	6	149959854	149959854	+	5'Flank	DEL	A	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149959854delA	uc003qmr.1	-						KATNA1_uc003qms.2_Intron|KATNA1_uc003qmt.2_Intron|KATNA1_uc011eed.1_5'Flank	NM_007044	NP_008975	O75449	KTNA1_HUMAN	katanin p60 subunit A 1						cell division|interphase of mitotic cell cycle|mitosis	microtubule|microtubule organizing center|spindle pole	ATP binding|microtubule binding|microtubule-severing ATPase activity|protein heterodimerization activity			skin(1)	1		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		TCACTCCTTTAAAAAAAACAT	0.194													3	3	---	---	---	---	
TNKS	8658	broad.mit.edu	37	8	9620574	9620574	+	Intron	DEL	T	-	-	rs66959741		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9620574delT	uc003wss.2	+						TNKS_uc011kww.1_Intron	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)		TTATTATGAAttttttttttt	0.274													3	3	---	---	---	---	
MSR1	4481	broad.mit.edu	37	8	16035612	16035613	+	Intron	INS	-	TTT	TTT			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16035612_16035613insTTT	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		TTCAGTTTTTCttttttttttt	0.139													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54445839	54445840	+	IGR	INS	-	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54445839_54445840insA								OPRK1 (281645 upstream) : ATP6V1H (182276 downstream)																							caaacaacaacaaaaaaaaaCA	0.178													4	2	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133184645	133184646	+	Intron	DEL	AC	-	-	rs138308682		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133184645_133184646delAC	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			GCACATTAATacacacacacac	0.342													3	4	---	---	---	---	
TMEM2	23670	broad.mit.edu	37	9	74337576	74337577	+	Intron	INS	-	G	G	rs76874061		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74337576_74337577insG	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ACTGTAAAAAAAAAAAAAACAG	0.238													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135455131	135455131	+	IGR	DEL	C	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135455131delC								FRG2B (14832 upstream) : LOC653544 (35148 downstream)																							TACAAAAAAACGATGAGGAAA	0.343													5	4	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116767743	116767744	+	Intron	DEL	AA	-	-	rs34854326		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116767743_116767744delAA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						actctgtttcaaaaaaaaaaaa	0.178													3	4	---	---	---	---	
NCAPD2	9918	broad.mit.edu	37	12	6640670	6640670	+	3'UTR	DEL	T	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6640670delT	uc001qoo.2	+	32					NCAPD2_uc010sfd.1_3'UTR|GAPDH_uc001qop.1_5'Flank|GAPDH_uc009zep.1_5'Flank|GAPDH_uc001qoq.1_5'Flank|GAPDH_uc001qor.1_5'Flank	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2						cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5						TGTCTGTCTCTTTTTTTTAAA	0.229													4	2	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32753640	32753641	+	Intron	INS	-	TG	TG	rs149633784	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32753640_32753641insTG	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TGTATTAAATTtgtgtgtgtgt	0.248													4	2	---	---	---	---	
MRPL46	26589	broad.mit.edu	37	15	89007756	89007756	+	Intron	DEL	A	-	-	rs66597211		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89007756delA	uc002bmj.2	-						MRPL46_uc002bmi.1_3'UTR|MRPL46_uc002bmk.2_Intron|MRPS11_uc002bmm.2_5'Flank|MRPS11_uc002bml.2_5'Flank|MRPS11_uc002bmn.2_5'Flank|MRPS11_uc010bnj.2_5'Flank	NM_022163	NP_071446	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46 precursor							mitochondrion|ribosome	hydrolase activity			central_nervous_system(1)	1	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			aaataaaaataaaaaaaaaat	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	12021299	12021340	+	IGR	DEL	TTCCACCTCAGCGGCCCTCCGCCTCTTGGGTTCGGGTGGTGA	-	-	rs141584024	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12021299_12021340delTTCCACCTCAGCGGCCCTCCGCCTCTTGGGTTCGGGTGGTGA								GSPT1 (10780 upstream) : TNFRSF17 (37624 downstream)																							gtgatgatggttccacctcagcGGCCCTCCGCCTCTTGGGTTCGGGTGGTGATTCCACCTCA	0.132													5	3	---	---	---	---	
CES3	23491	broad.mit.edu	37	16	67000964	67000964	+	Intron	DEL	T	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67000964delT	uc002eqt.2	+						CES3_uc010cdz.2_Intron|CES3_uc010cea.2_Intron|CES3_uc010viw.1_5'Flank	NM_024922	NP_079198	Q6UWW8	EST3_HUMAN	carboxylesterase 3 precursor							endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity			ovary(3)|central_nervous_system(2)	5		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		GTTGTTTTGCTTTTTTTTTTC	0.050													4	2	---	---	---	---	
SLC38A8	146167	broad.mit.edu	37	16	84065303	84065304	+	Intron	DEL	GA	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84065303_84065304delGA	uc002fhg.1	-							NM_001080442	NP_001073911	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8						amino acid transport|sodium ion transport	integral to membrane					0						GCAGCAGAAGGAGAGTGGCCCT	0.624													4	2	---	---	---	---	
NCOR1	9611	broad.mit.edu	37	17	15948310	15948311	+	Intron	INS	-	A	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15948310_15948311insA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_Intron|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AAGCTGAACTTAAGAAAAAAAA	0.366													5	3	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46423471	46423471	+	Intron	DEL	A	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46423471delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						CCAGTATTCGAAAAAAAAGTG	0.333													4	2	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	58761191	58761192	+	Intron	INS	-	CAAAA	CAAAA			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58761191_58761192insCAAAA	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			aaaccttgtctcaaaacaaaac	0.064													6	6	---	---	---	---	
SMARCD2	6603	broad.mit.edu	37	17	61913095	61913095	+	Intron	DEL	T	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61913095delT	uc010deb.1	-						SMARCD2_uc010wpt.1_Intron|SMARCD2_uc010dea.1_Intron|SMARCD2_uc010dec.1_Intron	NM_001098426	NP_001091896	Q92925	SMRD2_HUMAN	SWI/SNF-related matrix-associated						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	SWI/SNF complex	protein binding|transcription coactivator activity				0						agtcccagccttttttttttt	0.020													6	3	---	---	---	---	
KIAA1468	57614	broad.mit.edu	37	18	59894429	59894429	+	Intron	DEL	A	-	-	rs35190394		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59894429delA	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905	Q9P260	K1468_HUMAN	hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)				aaccgatcttaaaaaaaaaaa	0.085													3	3	---	---	---	---	
CCDC102B	79839	broad.mit.edu	37	18	66503861	66503862	+	Intron	INS	-	A	A	rs149330255	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66503861_66503862insA	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron|CCDC102B_uc002lkj.1_Intron	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				aagactctgtcaaaaataaaaa	0.119													7	4	---	---	---	---	
ADAMTSL5	339366	broad.mit.edu	37	19	1506711	1506711	+	Intron	DEL	C	-	-	rs76790056		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1506711delC	uc002ltd.2	-						ADAMTSL5_uc010dsl.2_Intron|ADAMTSL5_uc010xgq.1_Intron	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor							proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCACTCATCCCCCACCCTG	0.736													5	6	---	---	---	---	
ZCCHC3	85364	broad.mit.edu	37	20	278688	278690	+	In_Frame_Del	DEL	CGG	-	-	rs5839847		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:278688_278690delCGG	uc002wdf.2	+	1	485_487	c.461_463delCGG	c.(460-465)CCGGCG>CCG	p.A158del	ZCCHC3_uc002wdg.2_Intron	NM_033089	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	158	Poly-Ala.						nucleic acid binding|zinc ion binding				0		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CAGGATGAgccggcggcggcggc	0.635													5	5	---	---	---	---	
SFRS6	6431	broad.mit.edu	37	20	42086966	42086966	+	Intron	DEL	C	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42086966delC	uc010zwg.1	+						SFRS6_uc002xki.2_Intron|SFRS6_uc002xkk.2_Intron	NM_006275	NP_006266	Q13247	SRSF6_HUMAN	arginine/serine-rich splicing factor 6						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GCTAACGACTCCCCCGCGGTT	0.736													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9865569	9865570	+	IGR	INS	-	A	A	rs77497487	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9865569_9865570insA								None (None upstream) : None (None downstream)																							CTGCTGAGTTTAAATCTTCCTT	0.490													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15386126	15386139	+	IGR	DEL	ACAGCCAGGCTGAG	-	-	rs116193893	by1000genomes	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15386126_15386139delACAGCCAGGCTGAG								C21orf81 (33361 upstream) : LIPI (94998 downstream)																							GACACAAAACACAGCCAGGCTGAGGCAGCCAGAG	0.626													4	3	---	---	---	---	
PKNOX1	5316	broad.mit.edu	37	21	44438157	44438158	+	Intron	INS	-	AAAA	AAAA	rs60175567		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44438157_44438158insAAAA	uc002zcq.1	+						PKNOX1_uc002zcp.1_Intron|PKNOX1_uc011aex.1_Intron|PKNOX1_uc002zcr.2_3'UTR	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1								sequence-specific DNA binding			large_intestine(2)	2						cctgtctctacaaaaaaaaaaa	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44755961	44755961	+	IGR	DEL	C	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44755961delC								CRYAA (163048 upstream) : SIK1 (78437 downstream)																							accatcaccaccatcaccacc	0.000													4	2	---	---	---	---	
STS	412	broad.mit.edu	37	X	7193971	7193971	+	Intron	DEL	T	-	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7193971delT	uc004cry.3	+							NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor						female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	ttttcctcccttttttttttt	0.373									Ichthyosis				6	3	---	---	---	---	
