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
SMPDL3B	27293	broad.mit.edu	37	1	28282544	28282544	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28282544A>G	uc001bpg.2	+	7	1147	c.956A>G	c.(955-957)AAT>AGT	p.N319S	SMPDL3B_uc001bpf.2_Missense_Mutation_p.N319S|SMPDL3B_uc010ofq.1_Missense_Mutation_p.N113S|SMPDL3B_uc010ofr.1_Missense_Mutation_p.N271S	NM_014474	NP_055289	Q92485	ASM3B_HUMAN	acid sphingomyelinase-like phosphodiesterase 3B	319					sphingomyelin catabolic process	extracellular space	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity			ovary(3)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		GGGGCCAACAATCCAGCCATC	0.572													3	50	---	---	---	---	PASS
PARS2	25973	broad.mit.edu	37	1	55223346	55223346	+	3'UTR	SNP	A	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55223346A>T	uc001cxy.2	-	2						NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase (mitochondrial)(putative)						prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)	GGGTGTAGGAAAATGCAGTGT	0.488													5	21	---	---	---	---	PASS
ZZZ3	26009	broad.mit.edu	37	1	78098001	78098001	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78098001G>A	uc001dhq.2	-	5	1515	c.1039C>T	c.(1039-1041)CCA>TCA	p.P347S	ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Missense_Mutation_p.P347S|ZZZ3_uc001dhp.2_Missense_Mutation_p.P347S	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	347					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5						CCGGAGGCTGGCATACTCTCA	0.443													6	271	---	---	---	---	PASS
GLMN	11146	broad.mit.edu	37	1	92757048	92757048	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92757048C>A	uc001dor.2	-	4	327	c.212G>T	c.(211-213)CGA>CTA	p.R71L	GLMN_uc009wdg.2_RNA|GLMN_uc001dos.2_Missense_Mutation_p.R71L	NM_053274	NP_444504	Q92990	GLMN_HUMAN	glomulin	71					muscle cell differentiation|negative regulation of T cell proliferation|positive regulation of cytokine secretion|positive regulation of interleukin-2 biosynthetic process|positive regulation of phosphorylation|regulation of gene expression, epigenetic|vasculogenesis	intracellular	hepatocyte growth factor receptor binding			skin(1)	1		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		CAAAAGGCATCGAACAACAGG	0.343									Multiple_Glomus_Tumors_(of_the_Skin)_Familial				3	102	---	---	---	---	PASS
AMY2A	279	broad.mit.edu	37	1	104160101	104160101	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104160101C>A	uc001dut.2	+	1	103	c.39C>A	c.(37-39)TGC>TGA	p.C13*	AMY2A_uc010ouq.1_Nonsense_Mutation_p.C13*	NM_000699	NP_000690	P04746	AMYP_HUMAN	pancreatic amylase alpha 2A precursor	13					carbohydrate catabolic process|polysaccharide digestion	extracellular space	alpha-amylase activity|calcium ion binding|chloride ion binding			ovary(1)|skin(1)	2		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Bentiromide(DB00522)|Icodextrin(DB00702)|Miglitol(DB00491)|Pancrelipase(DB00085)	TTGGGTTCTGCTGGGCTCAGT	0.393													52	207	---	---	---	---	PASS
S100A12	6283	broad.mit.edu	37	1	153346341	153346341	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153346341C>T	uc001fbr.1	-	3	309	c.241G>A	c.(241-243)GCG>ACG	p.A81T		NM_005621	NP_005612	P80511	S10AC_HUMAN	S100 calcium-binding protein A12	81	EF-hand 2.				defense response to bacterium|defense response to fungus|inflammatory response|innate immune response|killing of cells of other organism|positive regulation of I-kappaB kinase/NF-kappaB cascade|xenobiotic metabolic process	cytosol|extracellular region|insoluble fraction|nucleus	calcium ion binding|RAGE receptor binding|zinc ion binding				0	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)		Amlexanox(DB01025)	GCCTTCAGCGCAATGGCTACC	0.443													21	110	---	---	---	---	PASS
PTPN7	5778	broad.mit.edu	37	1	202117740	202117740	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202117740G>C	uc001gxm.1	-	10	1208	c.1077C>G	c.(1075-1077)AGC>AGG	p.S359R	PTPN7_uc001gxl.1_Missense_Mutation_p.S398R|PTPN7_uc001gxn.1_Missense_Mutation_p.S359R|PTPN7_uc010ppv.1_Missense_Mutation_p.S178R|PTPN7_uc010ppw.1_Missense_Mutation_p.S307R|PTPN7_uc010ppx.1_Missense_Mutation_p.S433R|PTPN7_uc010ppy.1_RNA	NM_002832	NP_002823	P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type	359						cytosol|internal side of plasma membrane	protein binding|protein tyrosine phosphatase activity			skin(1)	1						GGGGTCAGGGGCTGGGTTCCT	0.642													7	40	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215987118	215987118	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215987118A>C	uc001hku.1	-	49	10086	c.9699T>G	c.(9697-9699)AAT>AAG	p.N3233K		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3233	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGCACTGATGATTTGGTTGTG	0.448										HNSCC(13;0.011)			35	152	---	---	---	---	PASS
CCDC104	112942	broad.mit.edu	37	2	55772134	55772134	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55772134T>C	uc002ryy.2	+	10	1217	c.1019T>C	c.(1018-1020)ATT>ACT	p.I340T	CCDC104_uc002ryx.2_Missense_Mutation_p.I365T	NM_080667	NP_542398	Q96G28	CC104_HUMAN	coiled-coil domain containing 104	340										ovary(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GAAGAAGTTATTAATAAGTAA	0.303													12	37	---	---	---	---	PASS
ANKRD36B	57730	broad.mit.edu	37	2	98201807	98201807	+	Silent	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98201807C>T	uc010yvc.1	-	2	496	c.216G>A	c.(214-216)CTG>CTA	p.L72L	ANKRD36B_uc010yve.1_RNA|ANKRD36B_uc010fif.2_RNA	NM_025190	NP_079466	Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B	72	ANK 2.										0						TTCTGGACACCAGGAGATGTA	0.473													5	8	---	---	---	---	PASS
CWC22	57703	broad.mit.edu	37	2	180818964	180818964	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180818964G>A	uc010frh.1	-	16	1957	c.1657C>T	c.(1657-1659)CAC>TAC	p.H553Y	CWC22_uc002uno.2_Missense_Mutation_p.H75Y|CWC22_uc002unp.2_Missense_Mutation_p.H553Y	NM_020943	NP_065994	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein homolog	553	MI.					catalytic step 2 spliceosome	protein binding|RNA binding				0						TATAAAAGGTGAGCAAACATC	0.358													19	66	---	---	---	---	PASS
PLCD4	84812	broad.mit.edu	37	2	219487602	219487602	+	Splice_Site	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219487602G>C	uc002vij.1	+	6	967	c.772_splice	c.e6+1	p.G258_splice	PLCD4_uc002vik.1_Splice_Site_p.G105_splice|PLCD4_uc010zkk.1_Intron	NM_032726	NP_116115	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4						intracellular signal transduction|lipid catabolic process	endoplasmic reticulum|membrane|nucleus	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)	3		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TCAGACAGTGGTAAGAGAAAT	0.502													37	137	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188248	10188248	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188248A>T	uc003bvc.2	+	2	604	c.391A>T	c.(391-393)AAC>TAC	p.N131Y	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	131	Involved in binding to CCT complex.		N -> T (in VHLD; type I).|N -> K (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.N131fs*28(4)|p.N131fs*27(2)|p.N131K(2)|p.N131fs*2(2)|p.N131fs*10(1)|p.N131*(1)|p.?fs(1)|p.N131Y(1)|p.V130fs*28(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GCTTCTGGTTAACCAAACTGA	0.418		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				79	210	---	---	---	---	PASS
FLNB	2317	broad.mit.edu	37	3	58128451	58128451	+	Silent	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58128451G>A	uc003djj.2	+	31	5421	c.5256G>A	c.(5254-5256)CCG>CCA	p.P1752P	FLNB_uc010hne.2_Silent_p.P1783P|FLNB_uc003djk.2_Silent_p.P1741P|FLNB_uc010hnf.2_Silent_p.P1728P|FLNB_uc003djl.2_Silent_p.P1572P|FLNB_uc003djm.2_Silent_p.P1559P	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	1752	Filamin 16.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TGGTCATTCCGTTTGCTGTCA	0.512													12	74	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164781312	164781312	+	Silent	SNP	G	A	A	rs139867598	byFrequency	TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164781312G>A	uc003fei.2	-	8	887	c.825C>T	c.(823-825)TAC>TAT	p.Y275Y		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	275	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	TTTGATGGCCGTATAAATTAT	0.254										HNSCC(35;0.089)			5	234	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505836G>C	uc011bto.1	-	3	12691	c.12231C>G	c.(12229-12231)CAC>CAG	p.H4077Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597													7	2	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515435	195515435	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515435C>T	uc011bto.1	-	2	3476	c.3016G>A	c.(3016-3018)GCC>ACC	p.A1006T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.582													3	7	---	---	---	---	PASS
MFI2	4241	broad.mit.edu	37	3	196753618	196753618	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196753618C>G	uc003fxk.3	-	3	330	c.217G>C	c.(217-219)GAC>CAC	p.D73H	MFI2_uc003fxl.3_Missense_Mutation_p.D73H|MFI2_uc011bua.1_Missense_Mutation_p.D73H	NM_005929	NP_005920	P08582	TRFM_HUMAN	melanoma-associated antigen p97 isoform 1	73	Transferrin-like 1.				cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		GTGATGGCGTCAGCCTCCTGG	0.622													9	51	---	---	---	---	PASS
GRID2	2895	broad.mit.edu	37	4	94547477	94547477	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94547477A>T	uc011cdt.1	+	14	2509	c.2251A>T	c.(2251-2253)ATC>TTC	p.I751F	GRID2_uc011cdu.1_Missense_Mutation_p.I656F	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	751	Extracellular (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	ATATGTGGCTATCAATGACCC	0.368													35	185	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104054940	104054940	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104054940T>C	uc003hxb.1	-	41	6722	c.6632A>G	c.(6631-6633)AAA>AGA	p.K2211R	CENPE_uc003hxc.1_Missense_Mutation_p.K2090R	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	2211	Kinetochore-binding domain.|Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GTGCTGTATTTTAATTAGCAA	0.294													24	83	---	---	---	---	PASS
CEP120	153241	broad.mit.edu	37	5	122685709	122685709	+	Silent	SNP	A	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122685709A>T	uc003ktk.2	-	20	2737	c.2655T>A	c.(2653-2655)CTT>CTA	p.L885L	CEP120_uc011cwq.1_Silent_p.L694L	NM_153223	NP_694955	Q8N960	CE120_HUMAN	coiled-coil domain containing 100	885	Potential.					centrosome				ovary(1)	1						CCTCAGCGGCAAGGTAACGTA	0.363													22	119	---	---	---	---	PASS
HNRNPH1	3187	broad.mit.edu	37	5	179047903	179047903	+	Silent	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179047903C>T	uc003mkf.3	-	4	493	c.387G>A	c.(385-387)CAG>CAA	p.Q129Q	HNRNPH1_uc011dgn.1_5'Flank|HNRNPH1_uc003mkg.3_Silent_p.Q37Q|HNRNPH1_uc003mke.3_Silent_p.Q129Q|HNRNPH1_uc003mkh.3_Silent_p.Q129Q	NM_005520	NP_005511	P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1	129	RRM 2.				regulation of RNA splicing	actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|poly(U) RNA binding|protein binding				0						CTGAGAAGAACTGAACAATTT	0.423													40	118	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54791201	54791201	+	Silent	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54791201T>C	uc003pck.2	+	3	593	c.477T>C	c.(475-477)GAT>GAC	p.D159D		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	159										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TATTTACAGATGTGGACATTT	0.303													46	113	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56394513	56394513	+	Silent	SNP	G	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56394513G>T	uc003pdf.2	-	60	10999	c.10971C>A	c.(10969-10971)GGC>GGA	p.G3657G	DST_uc003pcz.3_Silent_p.G3479G|DST_uc011dxj.1_Silent_p.G3508G|DST_uc011dxk.1_Silent_p.G3519G|DST_uc003pcy.3_Silent_p.G3153G	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5565	Spectrin 9.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTAAGGACTGGCCAATGCTAA	0.333													13	55	---	---	---	---	PASS
RBM16	22828	broad.mit.edu	37	6	155153658	155153658	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155153658C>T	uc003qqa.2	+	21	3177	c.2945C>T	c.(2944-2946)CCT>CTT	p.P982L	TIAM2_uc003qqb.2_5'Flank|RBM16_uc011efj.1_Missense_Mutation_p.P1048L|RBM16_uc011efk.1_Missense_Mutation_p.P1027L|RBM16_uc003qpz.2_Missense_Mutation_p.P982L|RBM16_uc010kji.2_Intron	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	982	Pro-rich.				mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)		CCAGAAAGACCTTTTTTAGCT	0.448													44	187	---	---	---	---	PASS
CCDC126	90693	broad.mit.edu	37	7	23650854	23650854	+	5'UTR	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23650854C>T	uc003swl.2	+	3					CCDC126_uc003swm.2_5'UTR|CCDC126_uc003swn.2_5'UTR	NM_138771	NP_620126	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126 precursor							extracellular region				ovary(1)|skin(1)	2						ATATTTTTTTCTTTTTTTTTT	0.289													8	71	---	---	---	---	PASS
ELN	2006	broad.mit.edu	37	7	73462860	73462860	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73462860C>T	uc003tzw.2	+	15	864	c.773C>T	c.(772-774)GCG>GTG	p.A258V	RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_RNA|ELN_uc011kfe.1_Missense_Mutation_p.A227V|ELN_uc003tzn.2_Missense_Mutation_p.A258V|ELN_uc003tzz.2_Missense_Mutation_p.A222V|ELN_uc003tzo.2_Missense_Mutation_p.A244V|ELN_uc003tzp.2_Missense_Mutation_p.A214V|ELN_uc003tzq.2_Missense_Mutation_p.A141V|ELN_uc003tzr.2_RNA|ELN_uc003tzs.2_Missense_Mutation_p.A258V|ELN_uc003tzt.2_Missense_Mutation_p.A263V|ELN_uc003tzu.2_Missense_Mutation_p.A263V|ELN_uc003tzv.2_Missense_Mutation_p.A248V|ELN_uc003tzx.2_Missense_Mutation_p.A248V|ELN_uc011kff.1_Missense_Mutation_p.A258V|ELN_uc003tzy.2_Missense_Mutation_p.A253V	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	258	Ala-rich.				blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)	gcagcagcagcggcagctaaa	0.507			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						12	98	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113518265	113518265	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113518265T>C	uc010ljy.1	-	4	2913	c.2882A>G	c.(2881-2883)CAG>CGG	p.Q961R		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	961					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						CTCAATACCCTGGATTTCTCT	0.393													6	281	---	---	---	---	PASS
SMO	6608	broad.mit.edu	37	7	128851985	128851985	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128851985C>T	uc003vor.2	+	12	2337	c.2057C>T	c.(2056-2058)GCG>GTG	p.A686V	SMO_uc003vos.2_3'UTR	NM_005631	NP_005622	Q99835	SMO_HUMAN	smoothened precursor	686	Cytoplasmic (Potential).				adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis	cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1)	37						TGCCCGCTGGCGCCGCCCCCT	0.582			Mis		skin basal cell 								2	2	---	---	---	---	PASS
FBXO43	286151	broad.mit.edu	37	8	101153613	101153613	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101153613G>C	uc003yjd.2	-	2	1582	c.869C>G	c.(868-870)ACA>AGA	p.T290R	FBXO43_uc003yje.2_Missense_Mutation_p.T256R|FBXO43_uc010mbp.1_Missense_Mutation_p.T290R	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b	290					meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			TCCACAAGTTGTTCCACTAAC	0.383													20	81	---	---	---	---	PASS
UHRF2	115426	broad.mit.edu	37	9	6420934	6420934	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6420934T>C	uc003zjy.2	+	2	516	c.176T>C	c.(175-177)TTT>TCT	p.F59S	UHRF2_uc003zjz.2_RNA	NM_152896	NP_690856	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains	59	Ubiquitin-like.				cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		TATACCTTATTTGATTATGAT	0.358													20	196	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	56077194	56077194	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56077194G>T	uc001jju.1	-	8	1108	c.713C>A	c.(712-714)GCC>GAC	p.A238D	PCDH15_uc010qhq.1_Missense_Mutation_p.A243D|PCDH15_uc010qhr.1_Missense_Mutation_p.A238D|PCDH15_uc010qhs.1_Missense_Mutation_p.A243D|PCDH15_uc010qht.1_Missense_Mutation_p.A238D|PCDH15_uc010qhu.1_Missense_Mutation_p.A238D|PCDH15_uc001jjv.1_Missense_Mutation_p.A216D|PCDH15_uc010qhv.1_Missense_Mutation_p.A238D|PCDH15_uc010qhw.1_Missense_Mutation_p.A201D|PCDH15_uc010qhx.1_Missense_Mutation_p.A238D|PCDH15_uc010qhy.1_Missense_Mutation_p.A243D|PCDH15_uc010qhz.1_Missense_Mutation_p.A238D|PCDH15_uc010qia.1_Missense_Mutation_p.A216D|PCDH15_uc010qib.1_Missense_Mutation_p.A216D|PCDH15_uc001jjw.2_Missense_Mutation_p.A238D	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	238	Extracellular (Potential).|Cadherin 2.				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				CAGATTTTGGGCACGGTCCTG	0.358										HNSCC(58;0.16)			54	189	---	---	---	---	PASS
MYOF	26509	broad.mit.edu	37	10	95191212	95191212	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95191212G>A	uc001kin.2	-	4	421	c.298C>T	c.(298-300)CCG>TCG	p.P100S	MYOF_uc001kio.2_Missense_Mutation_p.P100S|MYOF_uc001kip.3_Missense_Mutation_p.P100S|MYOF_uc009xuf.2_Missense_Mutation_p.P82S	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	100	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						AGCTTGTACGGCAGGGATCTG	0.473													3	85	---	---	---	---	PASS
PSMA1	5682	broad.mit.edu	37	11	14535155	14535155	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14535155G>T	uc001mlk.2	-	7	651	c.505C>A	c.(505-507)CGT>AGT	p.R169S	PSMA1_uc001mll.2_Missense_Mutation_p.R175S|PSMA1_uc010rcp.1_RNA|PSMA1_uc001mlj.2_Missense_Mutation_p.R144S	NM_002786	NP_002777	P25786	PSA1_HUMAN	proteasome alpha 1 subunit isoform 2	169					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2						AAGTAAGTACGAGCTGATTGG	0.393													3	81	---	---	---	---	PASS
CD44	960	broad.mit.edu	37	11	35208449	35208449	+	Splice_Site	SNP	T	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35208449T>A	uc001mvu.2	+	4	870	c.436_splice	c.e4+2	p.T146_splice	CD44_uc001mvv.2_Splice_Site_p.T146_splice|CD44_uc001mvw.2_Splice_Site_p.T146_splice|CD44_uc001mvx.2_Splice_Site_p.T146_splice|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Splice_Site_p.T146_splice|CD44_uc010rer.1_Splice_Site_p.T146_splice|CD44_uc009ykh.2_Splice_Site|CD44_uc010res.1_5'Flank|CD44_uc010ret.1_5'Flank|CD44_uc010reu.1_5'Flank	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor						cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	TTACCATAAGTATGTCTCTCT	0.358													43	178	---	---	---	---	PASS
SLC22A6	9356	broad.mit.edu	37	11	62744780	62744780	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62744780G>A	uc001nwk.2	-	9	1748	c.1441C>T	c.(1441-1443)CTC>TTC	p.L481F	SLC22A6_uc001nwl.2_Intron|SLC22A6_uc001nwj.2_Missense_Mutation_p.L481F|SLC22A6_uc001nwm.2_Intron	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a	481	Extracellular (Potential).				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0						GAGGGGTAGAGCTCGGCAGTC	0.647													21	67	---	---	---	---	PASS
FOLH1B	219595	broad.mit.edu	37	11	89395333	89395333	+	5'UTR	SNP	A	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89395333A>G	uc001pda.2	+	2						NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B						proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|skin(2)|central_nervous_system(1)	6						GCTTATAGGCATGGAATTGCA	0.348													3	81	---	---	---	---	PASS
SIK2	23235	broad.mit.edu	37	11	111591281	111591281	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111591281C>G	uc001plt.2	+	11	1693	c.1575C>G	c.(1573-1575)GAC>GAG	p.D525E		NM_015191	NP_056006	Q9H0K1	SIK2_HUMAN	SNF1-like kinase 2	525					intracellular protein kinase cascade|regulation of insulin receptor signaling pathway	Golgi apparatus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|skin(1)	3						TTCAGAGGGACCTGAACTTTC	0.473													40	128	---	---	---	---	PASS
PLBD1	79887	broad.mit.edu	37	12	14656715	14656715	+	Silent	SNP	A	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14656715A>G	uc001rcc.1	-	11	1814	c.1653T>C	c.(1651-1653)GAT>GAC	p.D551D		NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	551					lipid catabolic process	extracellular region	hydrolase activity				0						TTCATTTTATATCAAGTTTCA	0.358													40	182	---	---	---	---	PASS
GUCY2C	2984	broad.mit.edu	37	12	14832651	14832651	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14832651T>A	uc001rcd.2	-	6	907	c.770A>T	c.(769-771)AAG>ATG	p.K257M	GUCY2C_uc009zhz.2_Missense_Mutation_p.K257M	NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor	257	Extracellular (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(2)	6						ACCCTTCAGCTTGTAGAGGAA	0.423													41	162	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49420872	49420872	+	Silent	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49420872G>C	uc001rta.3	-	48	14877	c.14877C>G	c.(14875-14877)GCC>GCG	p.A4959A		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4959	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GCTTGGGTCGGGCTGATTCAG	0.637			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			26	143	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19445972	19445972	+	RNA	SNP	C	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19445972C>A	uc010tcj.1	-	1		c.138G>T				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						CTAGAATACTCAGGTTTCATT	0.328													21	107	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39420850	39420850	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39420850T>C	uc001uwv.2	+	7	6469	c.6160T>C	c.(6160-6162)TCT>CCT	p.S2054P	FREM2_uc001uww.2_Missense_Mutation_p.S140P	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	2054	Extracellular (Potential).|Calx-beta 3.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGATCCTCCCTCTGCAGATGG	0.463													35	147	---	---	---	---	PASS
NUDT15	55270	broad.mit.edu	37	13	48620101	48620101	+	3'UTR	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48620101T>C	uc001vbw.1	+	3						NM_018283	NP_060753	Q9NV35	NUD15_HUMAN	nudix-type motif 15								hydrolase activity|metal ion binding				0		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		CAGCCAGTACTTGAGAAAATT	0.323													4	9	---	---	---	---	PASS
FAM10A4	145165	broad.mit.edu	37	13	50746192	50746192	+	5'UTR	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50746192C>T	uc001vej.2	+	1					DLEU1_uc010adl.1_Intron|DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron	NR_002183				SubName: Full=ST13 protein;												0						AACCGGGCCGCAGCCCCCCGG	0.592													4	17	---	---	---	---	PASS
TGM1	7051	broad.mit.edu	37	14	24731316	24731316	+	Silent	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24731316G>A	uc001wod.2	-	2	367	c.243C>T	c.(241-243)GGC>GGT	p.G81G	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	81	Membrane anchorage region.				cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	AGCCCCGGGAGCCAGGTCTTC	0.652													32	81	---	---	---	---	PASS
SOS2	6655	broad.mit.edu	37	14	50626575	50626575	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50626575T>G	uc001wxs.3	-	10	1524	c.1426A>C	c.(1426-1428)ACT>CCT	p.T476P	SOS2_uc010tql.1_Missense_Mutation_p.T443P|SOS2_uc010tqm.1_RNA|SOS2_uc001wxt.2_Missense_Mutation_p.T164P	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	476	PH.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					GGAAGCCGAGTCTGGCCATGA	0.378													63	243	---	---	---	---	PASS
SNAPC1	6617	broad.mit.edu	37	14	62261727	62261727	+	3'UTR	SNP	T	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62261727T>G	uc001xft.2	+	10						NM_003082	NP_003073	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		TAGTTTTTAATTTTGAGTTTT	0.333													42	187	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106346892	106346892	+	RNA	SNP	G	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106346892G>T	uc010tyt.1	-	3227		c.50594C>A								Parts of antibodies, mostly variable regions.												0						TCTCACAGTGGTAGTAGCTCC	0.627													4	23	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106974612	106974612	+	RNA	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106974612C>T	uc010tyt.1	-	197		c.8749G>A								Parts of antibodies, mostly variable regions.												0						CGGCCCATCACGGAGTCTGCA	0.512													23	111	---	---	---	---	PASS
IL16	3603	broad.mit.edu	37	15	81591957	81591957	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81591957G>A	uc002bgh.3	+	14	2666	c.2290G>A	c.(2290-2292)GCC>ACC	p.A764T	IL16_uc010blq.1_Missense_Mutation_p.A718T|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.A806T|IL16_uc002bgg.2_Missense_Mutation_p.A764T|IL16_uc002bgi.1_Missense_Mutation_p.A154T|IL16_uc002bgj.2_Missense_Mutation_p.A258T|IL16_uc002bgk.2_Missense_Mutation_p.A63T|IL16_uc002bgl.1_Missense_Mutation_p.A63T|IL16_uc010unq.1_Missense_Mutation_p.A63T	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	764					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						GCTGGACACCGCCAATGGCAC	0.557													3	75	---	---	---	---	PASS
FANCA	2175	broad.mit.edu	37	16	89804179	89804179	+	3'UTR	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89804179C>T	uc002fou.1	-	43					ZNF276_uc010ciq.2_Intron|ZNF276_uc002fop.2_Intron|ZNF276_uc002foq.3_Intron|ZNF276_uc010cir.2_RNA|ZNF276_uc002for.3_Intron|ZNF276_uc010cis.2_Intron|ZNF276_uc002fos.3_Intron|ZNF276_uc002fot.3_Intron|ZNF276_uc010vpm.1_Intron|ZNF276_uc010cit.1_Intron|FANCA_uc010vpn.1_3'UTR	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GTTGGAGCATCAGGGGCCTGG	0.557			D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				11	71	---	---	---	---	PASS
MYH3	4621	broad.mit.edu	37	17	10543028	10543028	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10543028T>C	uc002gmq.1	-	22	2851	c.2774A>G	c.(2773-2775)GAG>GGG	p.E925G		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	925	Potential.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						TTCAGCTCTCTCTGTCACCTC	0.458													9	454	---	---	---	---	PASS
FAM83G	644815	broad.mit.edu	37	17	18880919	18880919	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18880919C>A	uc002guw.2	-	5	2227	c.2060G>T	c.(2059-2061)CGC>CTC	p.R687L	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	687										ovary(1)|central_nervous_system(1)	2						GTCTGTGGAGCGCTGGGCCTG	0.622													3	94	---	---	---	---	PASS
KRT16	3868	broad.mit.edu	37	17	39768515	39768515	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39768515G>C	uc002hxg.3	-	1	565	c.426C>G	c.(424-426)AAC>AAG	p.N142K	JUP_uc010wfs.1_Intron	NM_005557	NP_005548	P08779	K1C16_HUMAN	keratin 16	142	Coil 1A.|Rod.				cell proliferation|epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton			skin(1)	1		Breast(137;0.000307)				CCAGGTCGGCGTTGGCCTCCT	0.562													37	137	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31318800	31318800	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31318800G>A	uc010dmg.1	+	11	1487	c.1432G>A	c.(1432-1434)GAG>AAG	p.E478K	ASXL3_uc002kxq.2_Missense_Mutation_p.E185K	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	478					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						TGAATTTTCTGAGGAGGCTGA	0.388													13	78	---	---	---	---	PASS
APC2	10297	broad.mit.edu	37	19	1456344	1456344	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1456344C>A	uc002lsr.1	+	8	965	c.757C>A	c.(757-759)CCC>ACC	p.P253T	APC2_uc002lss.1_5'UTR|APC2_uc002lst.1_Missense_Mutation_p.P253T|APC2_uc002lsu.1_Missense_Mutation_p.P252T	NM_005883	NP_005874	O95996	APC2_HUMAN	adenomatosis polyposis coli 2	253					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|Wnt receptor signaling pathway	actin filament|catenin complex|cytoplasmic microtubule|Golgi membrane|lamellipodium membrane|perinuclear region of cytoplasm	beta-catenin binding|microtubule binding			breast(3)|pancreas(1)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGACGAGGACCCCGAGACAGA	0.682													3	15	---	---	---	---	PASS
C3	718	broad.mit.edu	37	19	6694615	6694615	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6694615G>C	uc002mfm.2	-	24	3043	c.2981C>G	c.(2980-2982)GCC>GGC	p.A994G	C3_uc002mfl.2_5'Flank	NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	994					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		CGCGTCGACGGCATCCTCTGT	0.627													4	38	---	---	---	---	PASS
ZNF302	55900	broad.mit.edu	37	19	35175869	35175869	+	Silent	SNP	A	G	G			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35175869A>G	uc002nvr.1	+	6	1322	c.1059A>G	c.(1057-1059)CAA>CAG	p.Q353Q	ZNF302_uc002nvp.1_Silent_p.Q309Q|ZNF302_uc002nvq.1_Silent_p.Q309Q|ZNF302_uc002nvs.1_Silent_p.Q309Q	NM_018443	NP_060913	Q9NR11	ZN302_HUMAN	zinc finger protein 302	388					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TTCATACGCAAGAAAAACGCT	0.418													34	110	---	---	---	---	PASS
ZNF350	59348	broad.mit.edu	37	19	52468847	52468847	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52468847C>T	uc002pyd.2	-	5	1087	c.859G>A	c.(859-861)GAG>AAG	p.E287K	uc002pyb.2_Intron|uc002pyc.2_Intron	NM_021632	NP_067645	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	287					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix|transcriptional repressor complex	DNA binding|protein binding|zinc ion binding			breast(1)	1		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		TAGGGTTTCTCTCCGGTATGT	0.408													8	330	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57326087	57326087	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57326087A>C	uc002qnu.2	-	7	4074	c.3723T>G	c.(3721-3723)AAT>AAG	p.N1241K	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.N1212K|PEG3_uc002qnv.2_Missense_Mutation_p.N1241K|PEG3_uc002qnw.2_Missense_Mutation_p.N1117K|PEG3_uc002qnx.2_Missense_Mutation_p.N1115K|PEG3_uc010etr.2_Missense_Mutation_p.N1241K	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	1241	C2H2-type 8.				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TCATATGCTCATTAAGGGCAG	0.498													18	64	---	---	---	---	PASS
PLCB4	5332	broad.mit.edu	37	20	9374306	9374306	+	Silent	SNP	G	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9374306G>T	uc002wnf.2	+	17	1531	c.1395G>T	c.(1393-1395)CTG>CTT	p.L465L	PLCB4_uc010gbw.1_Silent_p.L465L|PLCB4_uc010gbx.2_Silent_p.L465L|PLCB4_uc002wne.2_Silent_p.L465L|PLCB4_uc002wnh.2_Silent_p.L312L	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	465					intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						ACAAGCGGCTGAAACCTGAAG	0.363											OREG0025771	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	70	---	---	---	---	PASS
NINL	22981	broad.mit.edu	37	20	25442206	25442206	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25442206C>A	uc002wux.1	-	21	3722	c.3648G>T	c.(3646-3648)CAG>CAT	p.Q1216H	NINL_uc010gdn.1_Missense_Mutation_p.Q867H|NINL_uc002wuw.1_5'Flank	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	1216	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						ACCATGGCAGCTGCAGGCTCT	0.498													18	134	---	---	---	---	PASS
FAM182B	728882	broad.mit.edu	37	20	25848606	25848606	+	RNA	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25848606G>A	uc002wvd.1	-	1		c.181C>T								Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						atcaccgtccgggcaggcctg	0.000													4	10	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	31025137	31025137	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31025137G>C	uc002wxs.2	+	12	5048	c.4622G>C	c.(4621-4623)AGA>ACA	p.R1541T	ASXL1_uc010geb.2_Missense_Mutation_p.R1432T	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	1541					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						CTTGTGGTGAGATAATAAATT	0.383			F|N|Mis		MDS|CMML								40	240	---	---	---	---	PASS
RFPL1	5988	broad.mit.edu	37	22	29835224	29835224	+	Intron	SNP	T	C	C			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29835224T>C	uc003afn.2	+						RFPL1S_uc003afm.1_RNA	NM_021026	NP_066306	O75677	RFPL1_HUMAN	ret finger protein-like 1								zinc ion binding				0						AACTGGCCCCTCATTCCATAT	0.393													18	86	---	---	---	---	PASS
MIOX	55586	broad.mit.edu	37	22	50926751	50926751	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50926751G>A	uc003bll.1	+	5	502	c.388G>A	c.(388-390)GCC>ACC	p.A130T	MIOX_uc003blm.1_Missense_Mutation_p.A130T|MIOX_uc003bln.1_Nonsense_Mutation_p.W140*	NM_017584	NP_060054	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	130					inositol catabolic process	cytoplasm|inclusion body	aldo-keto reductase (NADP) activity|ferric iron binding|inositol oxygenase activity				0		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GAAGGTCCTGGCCCTGTTCGG	0.662													7	52	---	---	---	---	PASS
BHLHB9	80823	broad.mit.edu	37	X	102005104	102005104	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102005104G>T	uc010nog.2	+	4	1752	c.1181G>T	c.(1180-1182)GGG>GTG	p.G394V	BHLHB9_uc011mrq.1_Missense_Mutation_p.G394V|BHLHB9_uc011mrr.1_Missense_Mutation_p.G394V|BHLHB9_uc011mrs.1_Missense_Mutation_p.G394V|BHLHB9_uc011mrt.1_Missense_Mutation_p.G394V|BHLHB9_uc004ejo.2_Missense_Mutation_p.G394V|BHLHB9_uc011mru.1_Missense_Mutation_p.G394V|BHLHB9_uc011mrv.1_Missense_Mutation_p.G394V	NM_001142526	NP_001135998	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class	394						cytoplasm|nucleus	binding			ovary(2)	2						CCTCCTTCTGGGGATGAAAGA	0.378													32	77	---	---	---	---	PASS
C1orf38	9473	broad.mit.edu	37	1	28208353	28208354	+	Intron	INS	-	A	A			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28208353_28208354insA	uc001bpc.3	+						C1orf38_uc001boz.2_Intron|C1orf38_uc001bpa.2_Intron|C1orf38_uc010ofn.1_Intron|C1orf38_uc010ofo.1_Intron	NM_001105556	NP_001099026	Q5TEJ8	THMS2_HUMAN	basement membrane-induced gene isoform 3						cell adhesion|inflammatory response					ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;2.52e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)		aactccatctcaaaaaaaaaaa	0.272													4	2	---	---	---	---	
COL16A1	1307	broad.mit.edu	37	1	32122425	32122425	+	Intron	DEL	A	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32122425delA	uc001btk.1	-						COL16A1_uc001bti.1_Intron|COL16A1_uc001btj.1_Intron	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TACAGGGTTTAAAAAAAAAAA	0.343													4	3	---	---	---	---	
LEPR	3953	broad.mit.edu	37	1	65915368	65915368	+	Intron	DEL	T	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65915368delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		cctatttatcttttttttttt	0.224													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	207273434	207273439	+	IGR	DEL	TGTGTA	-	-	rs35665980		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207273434_207273439delTGTGTA								C4BPB (99 upstream) : C4BPA (4072 downstream)																							tgtgtgtgtgtgtgtatgtgtgtgtg	0.257													3	4	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242016438	242016439	+	Intron	DEL	TG	-	-	rs35698447		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242016438_242016439delTG	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			ATGGTAATCTTGTGTGTGTGTG	0.356								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89083941	89083942	+	Intron	INS	-	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89083941_89083942insT	uc010fhf.2	+						FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						GCCTGTATTCCTTTTTTTTCAG	0.347													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92318670	92318670	+	IGR	DEL	G	-	-	rs11491311		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92318670delG								FKSG73 (188176 upstream) : None (None downstream)																							catataaaaagcagacagcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128824754	128824754	+	IGR	DEL	A	-	-	rs113610724		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128824754delA								SAP130 (39121 upstream) : UGGT1 (24000 downstream)																							gactccatctaaaaaaaaaaa	0.174													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222809530	222809530	+	IGR	DEL	A	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222809530delA								EPHA4 (370608 upstream) : PAX3 (255077 downstream)																							TCTTTGATACAAAAAAAAAAA	0.294													3	3	---	---	---	---	
NT5DC2	64943	broad.mit.edu	37	3	52559178	52559181	+	Intron	DEL	GGGT	-	-	rs61419666		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52559178_52559181delGGGT	uc003deo.2	-						NT5DC2_uc003dem.2_Intron|NT5DC2_uc003den.2_Intron|NT5DC2_uc010hmi.2_Intron|NT5DC2_uc010hmj.2_Intron	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2								hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		GGGGGGGGGGGGGTTTCCTGGCCC	0.701													4	2	---	---	---	---	
SLC17A5	26503	broad.mit.edu	37	6	74320414	74320415	+	Intron	INS	-	A	A	rs139677205	by1000genomes	TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74320414_74320415insA	uc003phn.3	-						SLC17A5_uc010kax.2_Intron|SLC17A5_uc010kay.2_Intron|SLC17A5_uc011dyo.1_Intron	NM_012434	NP_036566	Q9NRA2	S17A5_HUMAN	sialin						anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6						AATTTCATGAGAAAAAAAAAAT	0.307													4	2	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	5985001	5985001	+	Intron	DEL	G	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5985001delG	uc003sph.1	-						RSPH10B2_uc003spg.1_Intron|RSPH10B2_uc010ktd.1_Intron|RSPH10B2_uc011jwk.1_Intron	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3						tgtaatcccagcactttggga	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15362229	15362230	+	IGR	INS	-	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15362229_15362230insT								TTC39B (54985 upstream) : SNAPC3 (60552 downstream)																							TTTCCCCTGTAttttttttttt	0.158													3	3	---	---	---	---	
FAM74A3	728495	broad.mit.edu	37	9	40715923	40715924	+	RNA	DEL	AA	-	-	rs62565543		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40715923_40715924delAA	uc010mmk.2	+	1		c.400_401delAA				NR_026801				Homo sapiens family with sequence similarity 74, member A3 (FAM74A3), non-coding RNA.											skin(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GAAGACGTGGAAAGAGCTCAGA	0.569													9	4	---	---	---	---	
CDC14B	8555	broad.mit.edu	37	9	99327506	99327506	+	Intron	DEL	T	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99327506delT	uc004awj.2	-						CDC14B_uc004awk.2_Intron|CDC14B_uc004awl.2_Intron|CDC14B_uc004awi.2_Intron	NM_033331	NP_201588	O60729	CC14B_HUMAN	CDC14 homolog B isoform 2						activation of anaphase-promoting complex activity|DNA repair|G2/M transition DNA damage checkpoint	nucleolus|nucleoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TTTAGGGAGGTTTTTTTTTTT	0.294													3	3	---	---	---	---	
KIAA0368	23392	broad.mit.edu	37	9	114170786	114170786	+	Intron	DEL	A	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114170786delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0						AACTGCACCTAAAAAAAAAAA	0.348													6	4	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27434230	27434231	+	Intron	INS	-	A	A	rs117799729		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27434230_27434231insA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						AAAAAAAAAACAAAAAAAAAAC	0.158													6	3	---	---	---	---	
MTPAP	55149	broad.mit.edu	37	10	30638287	30638287	+	5'Flank	DEL	G	-	-	rs112277654		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30638287delG	uc001iva.3	-						MTPAP_uc001ivb.3_Intron|MTPAP_uc001ivc.2_5'Flank	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						TCGGGGGGGAGGGGGGGGGCA	0.507													5	3	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	661459	661460	+	Intron	DEL	AC	-	-	rs149729869		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:661459_661460delAC	uc001qii.1	+						B4GALNT3_uc001qij.1_Intron|B4GALNT3_uc001qik.1_5'Flank	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CCTGAGTACTacacacacacac	0.475													3	3	---	---	---	---	
TMBIM6	7009	broad.mit.edu	37	12	50151817	50151817	+	Intron	DEL	A	-	-	rs80171037		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50151817delA	uc001rux.2	+						TMBIM6_uc010sml.1_Intron|TMBIM6_uc001ruy.2_Intron|TMBIM6_uc001ruz.2_Intron	NM_003217	NP_003208	P55061	BI1_HUMAN	testis enhanced gene transcript (BAX inhibitor						apoptosis|negative regulation of apoptosis	endoplasmic reticulum|insoluble fraction|integral to plasma membrane|nucleus					0						CTATTTCTATAAAAAAAAAAA	0.353													8	5	---	---	---	---	
SMARCC2	6601	broad.mit.edu	37	12	56562165	56562166	+	Intron	INS	-	T	T	rs72399911		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56562165_56562166insT	uc001skb.2	-						SMARCC2_uc001skd.2_Intron|SMARCC2_uc001ska.2_Intron|SMARCC2_uc001skc.2_Intron|SMARCC2_uc010sqf.1_Intron	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			tttcttttttcttttttttttt	0.104													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80658572	80658573	+	IGR	INS	-	T	T	rs138227519	by1000genomes	TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80658572_80658573insT								PPP1R12A (329337 upstream) : PTPRQ (179553 downstream)																							ACAATACACTATTTTTTTTCCT	0.332													4	2	---	---	---	---	
C14orf49	161176	broad.mit.edu	37	14	95884555	95884555	+	Intron	DEL	C	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95884555delC	uc001yei.3	-						C14orf49_uc010avi.2_Intron	NM_152592	NP_689805	Q6ZMZ3	SYNE3_HUMAN	nesprin-3						cytoskeletal anchoring at nuclear membrane	integral to membrane|nuclear outer membrane|SUN-KASH complex	actin binding			central_nervous_system(1)	1		all_cancers(154;0.0937)		COAD - Colon adenocarcinoma(157;0.245)		CTGCAGTTTTCCCAAAGCATT	0.403													4	2	---	---	---	---	
TMC7	79905	broad.mit.edu	37	16	19020932	19020932	+	Intron	DEL	A	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19020932delA	uc002dfq.2	+						TMC7_uc010vao.1_Intron|TMC7_uc002dfp.2_Intron|TMC7_uc010vap.1_Intron	NM_024847	NP_079123	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7 isoform a							integral to membrane				skin(2)|ovary(1)	3						cttAAAAAAGAAAAAAAAAAA	0.159													4	2	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153066	7153066	+	Intron	DEL	A	-	-	rs113402674		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153066delA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	acacccccccacacacacaca	0.050													4	2	---	---	---	---	
LDLR	3949	broad.mit.edu	37	19	11233654	11233655	+	Intron	DEL	TT	-	-	rs35951147		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11233654_11233655delTT	uc002mqk.3	+						LDLR_uc010xlk.1_Intron|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Intron|LDLR_uc010xlo.1_Intron	NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor						cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	acctggctaatttttttttttt	0.000													4	2	---	---	---	---	
ANO8	57719	broad.mit.edu	37	19	17434120	17434121	+	3'UTR	INS	-	TGTG	TGTG	rs141546754	by1000genomes	TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17434120_17434121insTGTG	uc002ngf.2	-	18					ANO8_uc010eap.2_RNA	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8							chloride channel complex	chloride channel activity			ovary(3)	3						ATCGCCTGTTCtgtgtgtgtgt	0.312													11	5	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55652163	55652165	+	Intron	DEL	TAA	-	-			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55652163_55652165delTAA	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron|TNNT1_uc002qjf.2_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		ataataatagtaataataataat	0.222													4	2	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20243448	20243449	+	Intron	INS	-	T	T	rs57744107		TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20243448_20243449insT	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc002wrw.2_Intron|C20orf26_uc002wrv.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		CTGTTTTTGTGTTTTTTTTTTT	0.233													4	5	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29633770	29633771	+	Intron	INS	-	AA	AA	rs145484297	by1000genomes	TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29633770_29633771insAA	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TATTTTAATATGTGTTGTGGTA	0.233													5	3	---	---	---	---	
KDM5C	8242	broad.mit.edu	37	X	53230876	53230877	+	Frame_Shift_Ins	INS	-	T	T			TCGA-B0-5108-01A-01D-1421-08	TCGA-B0-5108-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53230876_53230877insT	uc004drz.2	-	14	2449_2450	c.1916_1917insA	c.(1915-1917)TACfs	p.Y639fs	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Frame_Shift_Ins_p.Y572fs|KDM5C_uc004dsa.2_Frame_Shift_Ins_p.Y638fs	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	639					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18						AGAAGACGCAGTATCTCCGGAG	0.579			N|F|S		clear cell renal carcinoma								20	10	---	---	---	---	
