Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut	init_n_lod
LRRC47	57470	broad.mit.edu	37	1	3697831	3697831	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:3697831C>T	uc001akx.1	-	7	1601	c.1573G>A	c.(1573-1575)GAT>AAT	p.D525N		NM_020710	NP_065761	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	525					translation		phenylalanine-tRNA ligase activity|RNA binding			large_intestine(1)|ovary(1)	2	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		GAGACTGCATCGGCTTCAGTA	0.443													8	39					0	0	0.010729	0	0	
H6PD	9563	broad.mit.edu	37	1	9307041	9307041	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:9307041T>C	uc001apt.2	+	3	917	c.644T>C	c.(643-645)CTG>CCG	p.L215P		NM_004285	NP_004276	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase precursor	215	Glucose 1-dehydrogenase.					endoplasmic reticulum lumen	6-phosphogluconolactonase activity|glucose 1-dehydrogenase|glucose-6-phosphate dehydrogenase activity|NADP binding				0	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)	NADH(DB00157)	GCGCAGATCCTGCCTTTCCGA	0.607													14	48					0	0	0.003163	0	0	
PIK3CD	5293	broad.mit.edu	37	1	9778917	9778917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:9778917G>A	uc001aqb.3	+	9	1394	c.1186G>A	c.(1186-1188)GCC>ACC	p.A396T	PIK3CD_uc010oaf.1_Missense_Mutation_p.A396T|PIK3CD_uc001aqe.3_Missense_Mutation_p.A361T	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta	396					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)		TGCGCTGTACGCCGTGATCGA	0.647													7	39					0	0	0.008291	0	0	
CASZ1	54897	broad.mit.edu	37	1	10715762	10715762	+	Missense_Mutation	SNP	C	T	T	rs150917673	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:10715762C>T	uc001aro.2	-	9	1929	c.1609G>A	c.(1609-1611)GTC>ATC	p.V537I	CASZ1_uc001arp.1_Missense_Mutation_p.V537I|CASZ1_uc009vmx.2_Missense_Mutation_p.V561I	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	537					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TGGTAGTAGACGCTGCAGTCG	0.622													4	15					0	0	0.000602	0	0	
EXOSC10	5394	broad.mit.edu	37	1	11142746	11142746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:11142746G>A	uc001asa.2	-	10	1329	c.1279C>T	c.(1279-1281)CGC>TGC	p.R427C	EXOSC10_uc001asb.2_Missense_Mutation_p.R427C|EXOSC10_uc009vmy.1_Missense_Mutation_p.R427C	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1	427					CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CAAACTGACCGTATTCTCCAA	0.488													24	100					0	0	0.003954	0	0	
PRDM2	7799	broad.mit.edu	37	1	14057532	14057532	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:14057532C>T	uc001avi.2	+	3	903	c.47C>T	c.(46-48)GCT>GTT	p.A16V	PRDM2_uc001avg.2_Missense_Mutation_p.A16V|PRDM2_uc001avh.2_Missense_Mutation_p.A16V|PRDM2_uc001avj.2_RNA	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	16						Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GAGACCCTGGCTGAGGTACCC	0.512													17	51					0	0	0.006122	0	0	
SPEN	23013	broad.mit.edu	37	1	16258453	16258453	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:16258453C>T	uc001axk.1	+	11	5922	c.5718C>T	c.(5716-5718)AGC>AGT	p.S1906S	SPEN_uc010obp.1_Silent_p.S1865S	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1906					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ATGTAAGGAGCGTCTATGCAA	0.507													15	70					0	0	0.007413	0	0	
EPHA2	1969	broad.mit.edu	37	1	16464386	16464386	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:16464386C>T	uc001aya.1	-	5	1411	c.1274G>A	c.(1273-1275)CGC>CAC	p.R425H	EPHA2_uc010oca.1_Missense_Mutation_p.R425H	NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor	425	Extracellular (Potential).|Fibronectin type-III 1.				activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)	ACGGAAGCTGCGGCTGGTTAC	0.632													9	18					0	0	0.008291	0	0	
NBPF1	55672	broad.mit.edu	37	1	16892157	16892157	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:16892157T>C	uc009vos.1	-	28	4148	c.3260A>G	c.(3259-3261)AAA>AGA	p.K1087R	uc001ayw.2_5'Flank	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	1087	NBPF 7.					cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GCCAACATGTTTTTCCTCCAA	0.438													18	880					0	0	0.013537	0	0	
NBPF1	55672	broad.mit.edu	37	1	16907396	16907396	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:16907396C>T	uc009vos.1	-	16	2323	c.1435G>A	c.(1435-1437)GCC>ACC	p.A479T	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Missense_Mutation_p.A208T	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	479	NBPF 2.					cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CAAGTGATGGCACATTCCTCC	0.493													17	435					0	0	0.010818	0	0	
NBPF1	55672	broad.mit.edu	37	1	16913543	16913543	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:16913543A>G	uc009vos.1	-	11	1666	c.778_splice	c.e11+1	p.V260_splice	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		AATAGAGGCTACCTGGGAGAA	0.403													28	355					0	0	0.007291	0	0	
ATP13A2	23400	broad.mit.edu	37	1	17313587	17313587	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:17313587T>C	uc001baa.2	-	26	3227	c.3037A>G	c.(3037-3039)ACC>GCC	p.T1013A	ATP13A2_uc001azz.1_Missense_Mutation_p.T160A|ATP13A2_uc001bab.2_Missense_Mutation_p.T1008A|ATP13A2_uc001bac.2_Missense_Mutation_p.T969A	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1	1013	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		TGCACGCCGGTCACCAGGACC	0.711													9	23					0	0	0.006214	0	0	
PADI1	29943	broad.mit.edu	37	1	17566229	17566229	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:17566229A>T	uc001bah.1	+	14	1675	c.1583A>T	c.(1582-1584)AAT>ATT	p.N528I	PADI1_uc010oco.1_Missense_Mutation_p.N85I|PADI1_uc010ocp.1_Missense_Mutation_p.N85I|PADI1_uc010ocq.1_5'UTR|PADI1_uc009vpb.1_5'UTR	NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	528					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	AGAAGCATTAATGAGATGCTG	0.532													4	46					0	0	0.000602	0	0	
CAPZB	832	broad.mit.edu	37	1	19671710	19671710	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:19671710G>A	uc010ocz.1	-	7	1140	c.712C>T	c.(712-714)CAC>TAC	p.H238Y	CAPZB_uc001bce.2_Missense_Mutation_p.H209Y|CAPZB_uc009vpk.2_Missense_Mutation_p.H235Y|CAPZB_uc001bcd.2_Missense_Mutation_p.H197Y	NM_004930	NP_004921	P47756	CAPZB_HUMAN	F-actin capping protein beta subunit	209					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement	cytosol|F-actin capping protein complex|WASH complex	actin binding				0		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)		TTGGCTATGTGTGGGGAGCAG	0.567													4	75					0	0	0.000602	0	0	
TMCO4	255104	broad.mit.edu	37	1	20009604	20009604	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:20009604T>C	uc001bcn.2	-	16	2076	c.1834A>G	c.(1834-1836)ATG>GTG	p.M612V	TMCO4_uc001bcm.2_Missense_Mutation_p.M443V|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	612						integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		TTGGGGTCCATGCCATGGCTG	0.682													11	34					0	0	0.002450	0	0	
PLA2G2D	26279	broad.mit.edu	37	1	20442089	20442089	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:20442089T>C	uc001bcz.2	-	3	220	c.203A>G	c.(202-204)GAC>GGC	p.D68G	PLA2G2D_uc009vpo.2_Intron	NM_012400	NP_036532	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID precursor	68		Calcium (By similarity).			inflammatory response|lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ATAGCAGCAGTCATGGGTCTG	0.572										Multiple Myeloma(11;0.12)			7	51					0	0	0.004482	0	0	
NBPF3	84224	broad.mit.edu	37	1	21795231	21795231	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:21795231G>A	uc001ber.2	+	3	534	c.184G>A	c.(184-186)GGC>AGC	p.G62S	NBPF3_uc001bes.2_Missense_Mutation_p.G6S|NBPF3_uc009vqb.2_Missense_Mutation_p.G62S|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	62						cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGTATCTGCCGGCCCTTGGTC	0.517											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	26	119					0	0	0.005443	0	0	
ZBTB40	9923	broad.mit.edu	37	1	22839533	22839533	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:22839533G>A	uc001bft.2	+	13	3089	c.2578G>A	c.(2578-2580)GGG>AGG	p.G860R	ZBTB40_uc001bfu.2_Missense_Mutation_p.G860R|ZBTB40_uc009vqi.1_Missense_Mutation_p.G748R	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	860					bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CCTTCACACCGGGGACCGCCC	0.577													13	39					0	0	0.013537	0	0	
KDM1A	23028	broad.mit.edu	37	1	23409681	23409681	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:23409681C>T	uc001bgi.2	+	19	2532	c.2383C>T	c.(2383-2385)CGA>TGA	p.R795*	KDM1A_uc001bgj.2_Nonsense_Mutation_p.R819*	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b	795	Demethylase activity.				blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2						GCCGATTCCACGACTCTTCTT	0.458													10	43					0	0	0.008291	0	0	
IL22RA1	58985	broad.mit.edu	37	1	24448013	24448013	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:24448013T>C	uc001biq.1	-	7	1046	c.1007A>G	c.(1006-1008)CAG>CGG	p.Q336R	IL22RA1_uc010oeg.1_Missense_Mutation_p.Q268R|IL22RA1_uc009vrb.1_Missense_Mutation_p.Q200R|IL22RA1_uc010oeh.1_Missense_Mutation_p.Q336R	NM_021258	NP_067081	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1 precursor	336	Cytoplasmic (Potential).					integral to membrane	interferon receptor activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GTTGGAGGGCTGGAGGATGGA	0.637													11	30					0	0	0.002450	0	0	
CD52	1043	broad.mit.edu	37	1	26646688	26646688	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:26646688C>T	uc001bmc.2	+	2	179	c.81C>T	c.(79-81)AAC>AAT	p.N27N	UBXN11_uc001bma.2_5'Flank	NM_001803	NP_001794	P31358	CD52_HUMAN	CD52 antigen precursor	27					elevation of cytosolic calcium ion concentration|respiratory burst	anchored to membrane|integral to plasma membrane|membrane fraction					0		all_cancers(24;5.02e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	CAGGACAAAACGACACCAGCC	0.403													14	42					0	0	0.002450	0	0	
AIM1L	55057	broad.mit.edu	37	1	26669262	26669262	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:26669262G>T	uc001bmd.3	-	4	482	c.52C>A	c.(52-54)CTA>ATA	p.L18I		NM_001039775	NP_001034864	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	18							sugar binding			pancreas(1)	1		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		ACCCTCCTTAGGGAGCCGATG	0.507													21	104					3.57733e-08	3.90572e-08	0.009535	1	0	
RPS6KA1	6195	broad.mit.edu	37	1	26883502	26883502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:26883502G>A	uc001bmr.1	+	13	1158	c.995G>A	c.(994-996)CGT>CAT	p.R332H	RPS6KA1_uc010ofe.1_Missense_Mutation_p.R240H|RPS6KA1_uc010off.1_Missense_Mutation_p.R316H|RPS6KA1_uc001bms.1_Missense_Mutation_p.R341H|RPS6KA1_uc009vsl.1_Missense_Mutation_p.R175H	NM_002953	NP_002944	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	332	AGC-kinase C-terminal.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|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	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		CTATACCGTCGTGAGATCAAG	0.597													6	40					0	0	0.001984	0	0	
ARID1A	8289	broad.mit.edu	37	1	27094434	27094434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:27094434C>T	uc001bmv.1	+	11	3515	c.3142C>T	c.(3142-3144)CCT>TCT	p.P1048S	ARID1A_uc001bmt.1_Missense_Mutation_p.P1048S|ARID1A_uc001bmu.1_Missense_Mutation_p.P1048S|ARID1A_uc001bmw.1_Missense_Mutation_p.P665S	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1048	ARID.				androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGGTAGGAAACCTCTGGACCT	0.552			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								17	73					0	0	0.008871	0	0	
SLC9A1	6548	broad.mit.edu	37	1	27436202	27436202	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:27436202C>T	uc001bnm.2	-	3	1506	c.880G>A	c.(880-882)GGC>AGC	p.G294S	SLC9A1_uc010ofk.1_5'UTR|SLC9A1_uc001bnn.2_Missense_Mutation_p.G294S	NM_003047	NP_003038	P19634	SL9A1_HUMAN	solute carrier family 9, isoform A1	294	Extracellular (Potential).				regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	CTCAGGAAGCCGAGGAAGATG	0.612													18	65					0	0	0.006122	0	0	
HDAC1	3065	broad.mit.edu	37	1	32794717	32794717	+	Nonsense_Mutation	SNP	C	T	T	rs145372036		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:32794717C>T	uc001bvb.1	+	7	748	c.685C>T	c.(685-687)CGA>TGA	p.R229*	HDAC1_uc010ohf.1_Nonsense_Mutation_p.R200*|HDAC1_uc001bvc.1_5'Flank	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1	229	Histone deacetylase.				anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein 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)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	CTACCCGCTCCGAGACGGGAT	0.483													10	97					0	0	0.010729	0	0	
S100PBP	64766	broad.mit.edu	37	1	33318764	33318764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:33318764C>T	uc001bvz.2	+	6	1386	c.1109C>T	c.(1108-1110)ACG>ATG	p.T370M	S100PBP_uc001bwc.2_Missense_Mutation_p.T370M|S100PBP_uc001bwd.2_RNA	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a	370						nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GACCTCACCACGCGGTGAGTG	0.348													8	47					0	0	0.004482	0	0	
CSMD2	114784	broad.mit.edu	37	1	34046380	34046380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:34046380G>A	uc001bxn.1	-	49	7395	c.7366C>T	c.(7366-7368)CGG>TGG	p.R2456W	CSMD2_uc001bxm.1_Missense_Mutation_p.R2454W	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2456	CUB 14.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AAGCCCTTCCGATTGTAGGCG	0.517													9	40					0	0	0.013537	0	0	
CSMD2	114784	broad.mit.edu	37	1	34102053	34102053	+	Missense_Mutation	SNP	C	T	T	rs34594465		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:34102053C>T	uc001bxn.1	-	30	4785	c.4756G>A	c.(4756-4758)GGG>AGG	p.G1586R	CSMD2_uc001bxm.1_Missense_Mutation_p.G1626R|CSMD2_uc001bxo.1_Missense_Mutation_p.G499R	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1586	Extracellular (Potential).|Sushi 9.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCGTAGCCCCCGTGGCAGTAG	0.622													6	28					0	0	0.003080	0	0	
C1orf94	84970	broad.mit.edu	37	1	34666585	34666585	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:34666585C>T	uc001bxs.3	+	3	1051	c.652C>T	c.(652-654)CAG>TAG	p.Q218*	C1orf94_uc001bxt.2_Nonsense_Mutation_p.Q408*	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	218							protein binding				0		Myeloproliferative disorder(586;0.0393)				CCCAAGCGGGCAGCCGAGACT	0.592													4	10					0	0	0.000602	0	0	
DLGAP3	58512	broad.mit.edu	37	1	35334284	35334284	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:35334284G>A	uc001byc.2	-	7	2407	c.2407C>T	c.(2407-2409)CGG>TGG	p.R803W		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	803					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				ACCTCTGCCCGCAGCATCTTG	0.642													4	30					0	0	0.001984	0	0	
NCDN	23154	broad.mit.edu	37	1	36029369	36029369	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:36029369C>T	uc001bza.2	+	7	1739	c.1612C>T	c.(1612-1614)CGT>TGT	p.R538C	NCDN_uc001bzb.2_Missense_Mutation_p.R538C|NCDN_uc001bzc.2_Missense_Mutation_p.R521C	NM_001014839	NP_001014839	Q9UBB6	NCDN_HUMAN	neurochondrin isoform 1	538					neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTTTTCCAGGCGTGACGCCTG	0.527													26	72					0	0	0.008361	0	0	
C1orf216	127703	broad.mit.edu	37	1	36181448	36181448	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:36181448G>A	uc001bzh.1	-	2	963	c.475C>T	c.(475-477)CGC>TGC	p.R159C		NM_152374	NP_689587	Q8TAB5	CA216_HUMAN	hypothetical protein LOC127703	159										skin(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TCTTTGTAGCGCTCCTGGACT	0.627											OREG0013357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	88					0	0	0.004007	0	0	
EIF2C1	26523	broad.mit.edu	37	1	36380998	36380998	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:36380998G>A	uc001bzl.2	+	15	2096	c.1883G>A	c.(1882-1884)CGG>CAG	p.R628Q	EIF2C1_uc001bzk.2_Missense_Mutation_p.R553Q|EIF2C1_uc009vuy.2_RNA	NM_012199	NP_036331	Q9UL18	AGO1_HUMAN	eukaryotic translation initiation factor 2C, 1	628	Piwi.				negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GCTACTGTGCGGGTACAGCGA	0.532													4	66					0	0	0.000602	0	0	
ADPRHL2	54936	broad.mit.edu	37	1	36558054	36558054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:36558054C>T	uc001bzt.2	+	5	786	c.733C>T	c.(733-735)CGC>TGC	p.R245C	ADPRHL2_uc001bzu.2_Missense_Mutation_p.R91C	NM_017825	NP_060295	Q9NX46	ARHL2_HUMAN	ADP-ribosylhydrolase like 2	245						cytoplasm|nucleus	metal ion binding|poly(ADP-ribose) glycohydrolase activity			pancreas(1)	1		Myeloproliferative disorder(586;0.0393)				ATACTCCAGCCGCCTGAAGAA	0.602													9	31					0	0	0.008291	0	0	
MACF1	23499	broad.mit.edu	37	1	39823511	39823511	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:39823511A>G	uc010oiu.1	+	9	7340	c.7209A>G	c.(7207-7209)TTA>TTG	p.L2403L	MACF1_uc010ois.1_Silent_p.L1901L|MACF1_uc001cda.1_Silent_p.L1809L|MACF1_uc001cdc.1_Silent_p.L988L|MACF1_uc001cdb.1_Silent_p.L988L	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	3968					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTGGAAACTTAGTAAAGGACA	0.428													22	58					0	0	0.014323	0	0	
HPCAL4	51440	broad.mit.edu	37	1	40149806	40149806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:40149806C>T	uc001cdr.2	-	3	301	c.181G>A	c.(181-183)GCC>ACC	p.A61T	HPCAL4_uc010oix.1_Intron	NM_016257	NP_057341	Q9UM19	HPCL4_HUMAN	hippocalcin-like protein 4	61	EF-hand 2.				central nervous system development	intracellular	calcium ion binding			central_nervous_system(1)	1	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AACTTGGAGGCGTCGCCGTAG	0.692													6	23					0	0	0.001984	0	0	
SCMH1	22955	broad.mit.edu	37	1	41503057	41503057	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:41503057G>A	uc001cgo.2	-	13	1936	c.1625C>T	c.(1624-1626)GCT>GTT	p.A542V	SCMH1_uc010ojr.1_Missense_Mutation_p.A384V|SCMH1_uc001cgp.2_Missense_Mutation_p.A481V|SCMH1_uc001cgr.2_Missense_Mutation_p.A481V|SCMH1_uc001cgs.2_Missense_Mutation_p.A552V|SCMH1_uc001cgt.2_Missense_Mutation_p.A481V|SCMH1_uc001cgq.2_Missense_Mutation_p.A495V|SCMH1_uc010ojs.1_RNA	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1	542					anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CCTGCGCACAGCTGAGGCAGT	0.478													19	44					0	0	0.008871	0	0	
ZMYND12	84217	broad.mit.edu	37	1	42901019	42901019	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:42901019T>C	uc001chj.2	-	6	1025	c.755A>G	c.(754-756)TAT>TGT	p.Y252C	ZMYND12_uc010ojt.1_Missense_Mutation_p.Y142C	NM_032257	NP_115633	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12 isoform 1	252						intracellular	zinc ion binding			ovary(1)	1	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGGACTTGATAGTGATTGTT	0.478													30	136					0	0	0.012213	0	0	
TMEM125	128218	broad.mit.edu	37	1	43738712	43738712	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:43738712C>T	uc001cir.2	+	4	889	c.319C>T	c.(319-321)CGC>TGC	p.R107C	EBNA1BP2_uc001cio.2_5'Flank|TMEM125_uc001cis.2_Missense_Mutation_p.R107C	NM_144626	NP_653227	Q96AQ2	TM125_HUMAN	transmembrane protein 125	107			R -> L (in a breast cancer sample; somatic mutation).			integral to membrane		p.R107L(1)		breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCCCTGCTGCGCAGTGGTGG	0.687													3	13					0	0	0.004672	0	0	
KDM4A	9682	broad.mit.edu	37	1	44137442	44137442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:44137442G>A	uc001cjx.2	+	11	1796	c.1630G>A	c.(1630-1632)GTG>ATG	p.V544M	KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	544					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1						AGTTCTCACTGTGCACAGTTA	0.562													13	68					0	0	0.001855	0	0	
PLK3	1263	broad.mit.edu	37	1	45270162	45270162	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:45270162G>T	uc001cmn.2	+	12	1594	c.1494G>T	c.(1492-1494)TCG>TCT	p.S498S	PLK3_uc001cmo.2_RNA	NM_004073	NP_004064	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	498	POLO box 1.					membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)					TGGCCCTGTCGGCCAACAGAA	0.567													12	47					2.68362e-12	2.99231e-12	0.013537	1	0	
MUTYH	4595	broad.mit.edu	37	1	45799087	45799087	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:45799087G>A	uc001cnm.2	-	3	553	c.337C>T	c.(337-339)CGG>TGG	p.R113W	MUTYH_uc009vxn.2_Intron|MUTYH_uc001cnf.2_Missense_Mutation_p.R88W|MUTYH_uc009vxo.2_Missense_Mutation_p.R88W|MUTYH_uc001cng.2_Missense_Mutation_p.R99W|MUTYH_uc001cnj.2_Translation_Start_Site|MUTYH_uc001cni.2_Missense_Mutation_p.R88W|MUTYH_uc001cnh.2_Missense_Mutation_p.R89W|MUTYH_uc001cno.2_Translation_Start_Site|MUTYH_uc001cnk.2_Translation_Start_Site|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Missense_Mutation_p.R102W|MUTYH_uc009vxp.2_Missense_Mutation_p.R116W|MUTYH_uc001cnn.2_Missense_Mutation_p.R103W	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1	113					depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)					CTGCCTACCCGTCTTCTCCAT	0.582			Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				12	33					0	0	0.003163	0	0	
RAD54L	8438	broad.mit.edu	37	1	46736382	46736382	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:46736382G>A	uc009vye.2	+	11	1208	c.1094G>A	c.(1093-1095)CGA>CAA	p.R365Q	RAD54L_uc001cpl.2_Missense_Mutation_p.R365Q|RAD54L_uc001cpm.1_Missense_Mutation_p.R185Q	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein	365					meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		TTGAAGGGTCGAGACGCTGCT	0.468								Direct_reversal_of_damage|Homologous_recombination					12	57					0	0	0.001855	0	0	
RNF11	26994	broad.mit.edu	37	1	51736936	51736936	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:51736936G>A	uc001csi.3	+	3	891	c.407G>A	c.(406-408)TGC>TAC	p.C136Y		NM_014372	NP_055187	Q9Y3C5	RNF11_HUMAN	ring finger protein 11	136	RING-type.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	DNA binding|protein binding|zinc ion binding				0						TCCTTCACGTGCCCCTCCTGC	0.473													11	64					0	0	0.013537	0	0	
NRD1	4898	broad.mit.edu	37	1	52266266	52266266	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:52266266G>T	uc001ctc.3	-	23	2929	c.2607C>A	c.(2605-2607)ACC>ACA	p.T869T	NRD1_uc009vzb.2_Silent_p.T564T|NRD1_uc001ctd.3_Silent_p.T801T|NRD1_uc001cte.2_Silent_p.T737T|NRD1_uc001ctf.2_Silent_p.T801T|NRD1_uc010ong.1_RNA	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	800					cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0						TGTTAAAGTAGGTCTTCTTCA	0.398													6	102					5.18039e-06	5.59402e-06	0.003080	1	0	
MRPL37	51253	broad.mit.edu	37	1	54666207	54666207	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:54666207G>A	uc001cxa.3	+	1	368	c.291G>A	c.(289-291)CCG>CCA	p.P97P	CYB5RL_uc009vzo.2_5'Flank|CYB5RL_uc001cwx.3_5'Flank|CYB5RL_uc001cwy.3_5'Flank|MRPL37_uc009vzp.2_Missense_Mutation_p.R67H|MRPL37_uc001cxb.1_Silent_p.P97P|MRPL37_uc001cxc.3_Intron|MRPL37_uc010oob.1_RNA	NM_016491	NP_057575	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37 precursor	97					translation	mitochondrial ribosome	structural constituent of ribosome				0						ACGAGCATCCGCTGTACAAAG	0.527													14	41					0	0	0.004990	0	0	
DAB1	1600	broad.mit.edu	37	1	57610998	57610998	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:57610998C>T	uc001cys.1	-	5	846	c.172G>A	c.(172-174)GAC>AAC	p.D58N	DAB1_uc001cyt.1_Missense_Mutation_p.D58N|DAB1_uc001cyq.1_Missense_Mutation_p.D58N|DAB1_uc001cyr.1_Missense_Mutation_p.D58N|DAB1_uc009vzw.1_Missense_Mutation_p.D58N|DAB1_uc009vzx.1_Missense_Mutation_p.D58N	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	58	PID.				cell differentiation|nervous system development					skin(2)|ovary(1)	3						CATAACTTGTCTCCCCGAGCT	0.408													7	60					0	0	0.003080	0	0	
C1orf87	127795	broad.mit.edu	37	1	60499273	60499273	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:60499273T>C	uc001czs.1	-	7	996	c.904A>G	c.(904-906)AGG>GGG	p.R302G		NM_152377	NP_689590	Q8N0U7	CA087_HUMAN	hypothetical protein LOC127795	302							calcium ion binding			ovary(1)|breast(1)	2						AACAGACTCCTGTTCACTTCT	0.473													18	66					0	0	0.008871	0	0	
NFIA	4774	broad.mit.edu	37	1	61869831	61869831	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:61869831G>A	uc001czw.2	+	8	1615	c.1131G>A	c.(1129-1131)CAG>CAA	p.Q377Q	NFIA_uc001czy.2_Silent_p.Q369Q|NFIA_uc010oos.1_Silent_p.Q422Q|NFIA_uc001czv.2_Silent_p.Q377Q|NFIA_uc001czx.2_Silent_p.Q25Q|NFIA_uc009wae.2_5'Flank	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1	377					DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						CCATTATCCAGCAGCCTGGGC	0.507													17	96					0	0	0.012319	0	0	
INADL	10207	broad.mit.edu	37	1	62594566	62594566	+	Silent	SNP	C	T	T	rs113629200		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:62594566C>T	uc001dab.2	+	41	5334	c.5220C>T	c.(5218-5220)CAC>CAT	p.H1740H	INADL_uc001dac.2_RNA|INADL_uc009wag.2_Silent_p.H524H	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1740	PDZ 10.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						GGCTGTCTCACGCGGATGTGG	0.468													10	85					0	0	0.008291	0	0	
JAK1	3716	broad.mit.edu	37	1	65323363	65323363	+	Silent	SNP	G	A	A	rs55788790		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:65323363G>A	uc001dbu.1	-	10	1683	c.1434C>T	c.(1432-1434)ACC>ACT	p.T478T	JAK1_uc009wam.1_Silent_p.T466T	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	478	SH2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	p.T478S(1)|p.T478T(1)		haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		AGCAGGTGACGGTCATGAGGA	0.542			Mis		ALL								12	43					0	0	0.001855	0	0	
SYDE2	84144	broad.mit.edu	37	1	85656333	85656333	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:85656333G>A	uc009wcm.2	-	2	897	c.848C>T	c.(847-849)ACT>ATT	p.T283I	SYDE2_uc001dku.3_Missense_Mutation_p.T283I	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	283					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)		CTTTGAAACAGTGATGCTGTT	0.368													30	137					0	0	0.008361	0	0	
CLCA2	9635	broad.mit.edu	37	1	86905964	86905964	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:86905964G>T	uc001dlr.3	+	8	1499	c.1337G>T	c.(1336-1338)GGT>GTT	p.G446V		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	446	VWFA.|Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ATTGCCCTGGGTTCATCTGCA	0.423													14	65					6.72482e-11	7.46362e-11	0.003163	1	0	
GBP1	2633	broad.mit.edu	37	1	89520420	89520420	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:89520420T>C	uc001dmx.2	-	10	1830	c.1610A>G	c.(1609-1611)AAC>AGC	p.N537S		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	537					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		GACCCTGTCGTTCTCCATCTT	0.423													37	295					0	0	0.007835	0	0	
GBP1	2633	broad.mit.edu	37	1	89521715	89521715	+	Missense_Mutation	SNP	G	A	A	rs142020556		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:89521715G>A	uc001dmx.2	-	8	1572	c.1352C>T	c.(1351-1353)CCG>CTG	p.P451L		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	451					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CCCCTTCCTCGGTTCCTCATA	0.448													42	201					0	0	0.011902	0	0	
FNBP1L	54874	broad.mit.edu	37	1	93987691	93987691	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:93987691C>T	uc001dpw.2	+	3	193	c.193C>T	c.(193-195)CGG>TGG	p.R65W	FNBP1L_uc001dpv.2_Missense_Mutation_p.R65W	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1	65	FCH.|Induction of membrane tubulation (By similarity).				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		TGAAGAGCCACGGTAAATTAC	0.204													6	9					0	0	0.006214	0	0	
ARHGAP29	9411	broad.mit.edu	37	1	94639435	94639435	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:94639435T>C	uc001dqj.3	-	23	4145	c.3776A>G	c.(3775-3777)CAA>CGA	p.Q1259R	ARHGAP29_uc009wdq.1_Intron	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1	1259	Interaction with PTPN13/PTPL1.				Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CTACACAAATTGTGGAATTTC	0.408													33	138					0	0	0.004289	0	0	
ABCD3	5825	broad.mit.edu	37	1	94955520	94955520	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:94955520T>C	uc001dqn.3	+	15	1413	c.1311T>C	c.(1309-1311)GAT>GAC	p.D437D	ABCD3_uc010oto.1_Silent_p.D461D|ABCD3_uc010otp.1_Silent_p.D364D|ABCD3_uc009wdr.2_Silent_p.D327D|ABCD3_uc001dqo.3_Silent_p.D125D	NM_002858	NP_002849	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D, member 3	437					peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TTATTGCAGATAACATTATAA	0.318													19	86					0	0	0.012319	0	0	
EXTL2	2135	broad.mit.edu	37	1	101339853	101339853	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:101339853A>T	uc001dtk.1	-	5	975	c.638T>A	c.(637-639)ATT>AAT	p.I213N	EXTL2_uc001dtl.1_Missense_Mutation_p.I213N|EXTL2_uc010ouk.1_Missense_Mutation_p.I200N|EXTL2_uc001dtm.1_Missense_Mutation_p.I212N	NM_001439	NP_001430	Q9UBQ6	EXTL2_HUMAN	exostoses-like 2	213	Lumenal (Potential).				N-acetylglucosamine metabolic process|UDP-N-acetylgalactosamine metabolic process	extracellular region|integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,4-N-acetylgalactosaminyltransferase activity|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)		TGAGGCTCCAATCAGCACCAT	0.403													7	41					0	0	0.003080	0	0	
COL11A1	1301	broad.mit.edu	37	1	103345444	103345444	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:103345444G>T	uc001dul.2	-	66	5387	c.5069C>A	c.(5068-5070)TCC>TAC	p.S1690Y	COL11A1_uc001duk.2_Missense_Mutation_p.S886Y|COL11A1_uc001dum.2_Missense_Mutation_p.S1702Y|COL11A1_uc001dun.2_Missense_Mutation_p.S1651Y|COL11A1_uc009weh.2_Missense_Mutation_p.S1574Y	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1690	Fibrillar collagen NC1.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CATATTGATGGAATTTCCTTC	0.383													5	55					0.00116845	0.00122775	0.001168	1	0	
VAV3	10451	broad.mit.edu	37	1	108507464	108507464	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:108507464A>G	uc001dvk.1	-	1	82	c.28T>C	c.(28-30)TGG>CGG	p.W10R	VAV3_uc010ouw.1_Missense_Mutation_p.W10R|VAV3_uc001dvl.1_5'Flank|VAV3_uc010oux.1_Missense_Mutation_p.W10R	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	10	CH.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGGATGAGCCACTGCGCGCAC	0.627													4	23					0	0	0.000602	0	0	
FNDC7	163479	broad.mit.edu	37	1	109276020	109276020	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:109276020C>T	uc001dvx.2	+	10	2006	c.2006C>T	c.(2005-2007)ACG>ATG	p.T669M	FNDC7_uc010ova.1_Missense_Mutation_p.T436M	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	670	Fibronectin type-III 8.					extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GGCATTTTCACGTGCACCCCG	0.517													22	82					0	0	0.014323	0	0	
RBM15	64783	broad.mit.edu	37	1	110884339	110884339	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:110884339A>G	uc001dzl.1	+	1	2395	c.2312A>G	c.(2311-2313)GAT>GGT	p.D771G	RBM15_uc001dzm.1_Missense_Mutation_p.D771G|uc001dzj.2_5'Flank	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	771					interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		CAGAAACAGGATGGGGGGACA	0.547			T	MKL1	acute megakaryocytic leukemia								11	55					0	0	0.010729	0	0	
MAGI3	260425	broad.mit.edu	37	1	114092138	114092138	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:114092138C>T	uc001edk.2	+	2	499	c.318C>T	c.(316-318)GGC>GGT	p.G106G	MAGI3_uc001edh.3_Silent_p.G106G|MAGI3_uc001edi.3_Silent_p.G106G|MAGI3_uc010owm.1_Silent_p.G106G	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	106	PDZ 1.|Interaction with ADRB1 and TGFA (By similarity).				apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTGCTCCAGGCAAAGTCATTA	0.318													5	39					0	0	0.001984	0	0	
DCLRE1B	64858	broad.mit.edu	37	1	114454678	114454678	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:114454678G>T	uc001eeg.2	+	4	1635	c.1464G>T	c.(1462-1464)AAG>AAT	p.K488N	DCLRE1B_uc001eeh.2_Intron|DCLRE1B_uc001eei.2_Missense_Mutation_p.K362N	NM_022836	NP_073747	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B (PSO2 homolog, S.	488					cell cycle checkpoint|DNA repair|protection from non-homologous end joining at telomere|telomeric 3' overhang formation|telomeric loop formation	centrosome|chromosome, telomeric region|nucleus	5'-3' exonuclease activity|protein binding				0	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGCAAGGGCACCCCTC	0.532								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					19	94					6.94344e-10	7.66567e-10	0.006122	1	0	
AMPD1	270	broad.mit.edu	37	1	115231320	115231320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:115231320G>A	uc001efe.1	-	3	161	c.77C>T	c.(76-78)GCC>GTC	p.A26V	AMPD1_uc001eff.1_Missense_Mutation_p.A22V	NM_000036	NP_000027	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1 (isoform M)	26					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GACTTCAGAGGCAAACACTTT	0.413													25	144					0	0	0.004656	0	0	
IGSF3	3321	broad.mit.edu	37	1	117156651	117156651	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:117156651C>T	uc001egr.1	-	4	1273	c.568G>A	c.(568-570)GAG>AAG	p.E190K	IGSF3_uc001egq.1_Missense_Mutation_p.E190K	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	190	Ig-like C2-type 2.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		ACGGGCTTCTCGCCAACTTTC	0.612													10	39					0	0	0.008291	0	0	
VTCN1	79679	broad.mit.edu	37	1	117699263	117699263	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:117699263G>A	uc001ehb.2	-	3	450	c.378C>T	c.(376-378)GGC>GGT	p.G126G	VTCN1_uc001ehc.2_Silent_p.G31G|VTCN1_uc009whf.1_Intron	NM_024626	NP_078902	Q7Z7D3	VTCN1_HUMAN	V-set domain containing T cell activation	126	Ig-like V-type 1.|Extracellular (Potential).					integral to membrane|plasma membrane					0	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		ATTTGTAGGTGCCAGCATCTG	0.428													16	63					0	0	0.004990	0	0	
GDAP2	54834	broad.mit.edu	37	1	118455168	118455168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:118455168C>T	uc001ehf.2	-	4	753	c.454G>A	c.(454-456)GTA>ATA	p.V152I	GDAP2_uc001ehg.2_Missense_Mutation_p.V152I	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	152	Macro.									ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		AGTTGAAGTACGTTTCTGTAG	0.413													8	66					0	0	0.006214	0	0	
GDAP2	54834	broad.mit.edu	37	1	118461278	118461278	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:118461278G>A	uc001ehf.2	-	3	556	c.257C>T	c.(256-258)TCA>TTA	p.S86L	GDAP2_uc001ehg.2_Missense_Mutation_p.S86L	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	86	Macro.									ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		GATACTTTCTGACACAGGATT	0.363													12	64					0	0	0.002450	0	0	
ADAM30	11085	broad.mit.edu	37	1	120438783	120438783	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:120438783G>A	uc001eij.2	-	1	331	c.177C>T	c.(175-177)GTC>GTT	p.V59V		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	59					proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		ACACGGGACTGACCACACCCT	0.522													13	56					0	0	0.004990	0	0	
PDE4DIP	9659	broad.mit.edu	37	1	144865839	144865839	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:144865839A>G	uc001elw.3	-	35	6032	c.5741T>C	c.(5740-5742)CTT>CCT	p.L1914P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.L1808P|PDE4DIP_uc001elv.3_Missense_Mutation_p.L921P|PDE4DIP_uc001ema.2_Missense_Mutation_p.L101P	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1914	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTGAGCCTGAAGTCTTCGATT	0.483			T	PDGFRB	MPD								31	311					0	0	0.005524	0	0	
NBPF10	100132406	broad.mit.edu	37	1	146399620	146399620	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:146399620G>A	uc001emp.3	+	14	2570	c.1372G>A	c.(1372-1374)GCC>ACC	p.A458T	uc010ozk.1_5'UTR	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672	187											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGAATCATCTGCCCCCAGGTA	0.413													15	229					0	0	0.010504	0	0	
BCL9	607	broad.mit.edu	37	1	147096003	147096003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:147096003G>A	uc001epq.2	+	10	4264	c.3524G>A	c.(3523-3525)GGC>GAC	p.G1175D	BCL9_uc010ozr.1_Missense_Mutation_p.G1089D	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1175	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					CCAGGAGAAGGCCCCCTTGGC	0.647			T	IGH@|IGL@	B-ALL								7	21					0	0	0.001984	0	0	
SV2A	9900	broad.mit.edu	37	1	149884988	149884988	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:149884988G>A	uc001etg.2	-	2	896	c.405C>T	c.(403-405)GGC>GGT	p.G135G	SV2A_uc001eth.2_Silent_p.G135G	NM_014849	NP_055664	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2	135	Cytoplasmic (Potential).				neurotransmitter transport	cell junction|endoplasmic reticulum|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(6)|pancreas(1)	7	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	CCTCCCCCCGGCCCCCAGGGG	0.662													7	24					0	0	0.003080	0	0	
SF3B4	10262	broad.mit.edu	37	1	149898338	149898338	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:149898338T>C	uc001etj.1	-	3	687	c.636A>G	c.(634-636)GCA>GCG	p.A212A	SF3B4_uc001eti.1_5'Flank|SF3B4_uc001etk.1_Silent_p.A212A|SF3B4_uc009wll.1_Silent_p.A212A	NM_005850	NP_005841	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4	212						nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GAGGTGCATCTGCAAACAGCT	0.547													15	41					0	0	0.003163	0	0	
ADAMTSL4	54507	broad.mit.edu	37	1	150525383	150525383	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:150525383G>A	uc001eux.2	+	5	324	c.88G>A	c.(88-90)GGA>AGA	p.G30R	ADAMTSL4_uc001euw.2_Missense_Mutation_p.G30R|ADAMTSL4_uc009wlw.2_Missense_Mutation_p.G30R|ADAMTSL4_uc010pcg.1_Missense_Mutation_p.G30R	NM_019032	NP_061905	Q6UY14	ATL4_HUMAN	thrombospondin repeat containing 1 isoform 1	30					apoptosis|positive regulation of apoptosis		metalloendopeptidase activity|protease binding			ovary(1)|skin(1)	2	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGTGTTGTCCGGACACTCTCT	0.572													4	41					0	0	0.009096	0	0	
ANXA9	8416	broad.mit.edu	37	1	150958865	150958865	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:150958865C>T	uc001ewa.2	+	8	996	c.526C>T	c.(526-528)CAG>TAG	p.Q176*		NM_003568	NP_003559	O76027	ANXA9_HUMAN	annexin A9	176	Annexin 2.				cell-cell adhesion	cell surface|cytosol	acetylcholine receptor activity|calcium ion binding|calcium-dependent phospholipid binding|phosphatidylserine binding|protein homodimerization activity				0	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGGCATCTTGCAGGACCTGCT	0.572													10	29					0	0	0.013537	0	0	
THEM4	117145	broad.mit.edu	37	1	151861728	151861728	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:151861728G>A	uc001ezj.1	-	3	587	c.408C>T	c.(406-408)TGC>TGT	p.C136C	THEM4_uc001ezk.1_RNA	NM_053055	NP_444283	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	136					insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CTTGAAATAAGCAAACCATCC	0.443													5	44					0	0	0.001168	0	0	
TCHH	7062	broad.mit.edu	37	1	152081809	152081809	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:152081809T>C	uc001ezp.2	-	2	3884	c.3884A>G	c.(3883-3885)GAG>GGG	p.E1295G	TCHH_uc009wne.1_Missense_Mutation_p.E1295G	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1295	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTTCTTCCTCTGGGAAATG	0.552													19	95					0	0	0.008871	0	0	
FLG	2312	broad.mit.edu	37	1	152283466	152283466	+	Missense_Mutation	SNP	C	T	T	rs150251062	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:152283466C>T	uc001ezu.1	-	3	3932	c.3896G>A	c.(3895-3897)CGG>CAG	p.R1299Q	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1299	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			tgactgctcccgagaagatcc	0.378									Ichthyosis				39	184					0	0	0.006230	0	0	
S100A14	57402	broad.mit.edu	37	1	153588311	153588311	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:153588311G>A	uc001fce.2	-	2	122	c.24C>T	c.(22-24)AAC>AAT	p.N8N	S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723	Q9HCY8	S10AE_HUMAN	S100 calcium binding protein A14	8					calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCACCTCTGCGTTGGCTGACC	0.577													5	31					0	0	0.000602	0	0	
CRTC2	200186	broad.mit.edu	37	1	153924897	153924897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:153924897C>T	uc010ped.1	-	9	798	c.728G>A	c.(727-729)CGG>CAG	p.R243Q	CRTC2_uc001fde.3_RNA|CRTC2_uc001fdf.3_5'UTR	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	243					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TTCACAGGACCGAGGTCGGGA	0.532													20	80					0	0	0.008871	0	0	
AQP10	89872	broad.mit.edu	37	1	154296925	154296925	+	Missense_Mutation	SNP	C	T	T	rs141365858	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:154296925C>T	uc001feu.2	+	6	915	c.875C>T	c.(874-876)GCC>GTC	p.A292V	AQP10_uc001fev.2_3'UTR|ATP8B2_uc001few.2_5'Flank	NM_080429	NP_536354	Q96PS8	AQP10_HUMAN	aquaporin 10	292	Extracellular (Potential).				response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAAACTCCTGCCTCAGCTCAG	0.562											OREG0013832	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	51					0	0	0.002450	0	0	
CHRNB2	1141	broad.mit.edu	37	1	154544182	154544182	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:154544182C>T	uc001ffg.2	+	5	1147	c.883C>T	c.(883-885)CCG>TCG	p.P295S		NM_000748	NP_000739	P17787	ACHB2_HUMAN	neuronal nicotinic acetylcholine receptor beta 2	295					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)	CCTCGACGTGCCGCTCGTCGG	0.607													14	70					0	0	0.001855	0	0	
ZBTB7B	51043	broad.mit.edu	37	1	154988858	154988858	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:154988858C>T	uc001fgk.3	+	4	1475	c.1317C>T	c.(1315-1317)TTC>TTT	p.F439F	ZBTB7B_uc009wpa.2_Silent_p.F439F|ZBTB7B_uc001fgj.3_Silent_p.F473F|ZBTB7B_uc010peq.1_Silent_p.F473F|ZBTB7B_uc001fgl.3_Silent_p.F439F	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	439	C2H2-type 4; atypical.				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)			ACAAGGCTTTCGCCAAGGAGG	0.647													5	29					0	0	0.000602	0	0	
CLK2	1196	broad.mit.edu	37	1	155239459	155239459	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:155239459G>A	uc001fjy.2	-	3	509	c.219C>T	c.(217-219)TAC>TAT	p.Y73Y	RAG1AP1_uc010pey.1_Intron|CLK2_uc001fjw.2_Silent_p.Y73Y|CLK2_uc001fjx.2_5'UTR|CLK2_uc009wqm.2_Silent_p.Y73Y	NM_003993	NP_003984	P49760	CLK2_HUMAN	CDC-like kinase 2	73						nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AGCTGCCACAGTATCGCCGGT	0.488								Other_conserved_DNA_damage_response_genes					8	65					0	0	0.010729	0	0	
RUSC1	23623	broad.mit.edu	37	1	155292496	155292496	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:155292496G>A	uc001fkj.2	+	2	1161	c.932G>A	c.(931-933)CGG>CAG	p.R311Q	RAG1AP1_uc010pey.1_Intron|C1orf104_uc001fkh.1_5'Flank|C1orf104_uc001fki.2_Intron|RUSC1_uc001fkk.2_Missense_Mutation_p.R311Q|RUSC1_uc009wqn.1_RNA|RUSC1_uc009wqo.1_5'Flank|RUSC1_uc001fkl.2_5'Flank|RUSC1_uc001fkp.2_5'Flank|RUSC1_uc001fkq.2_5'Flank|RUSC1_uc010pgb.1_5'Flank|RUSC1_uc009wqp.1_5'Flank|RUSC1_uc001fkn.2_5'Flank|RUSC1_uc001fko.2_5'Flank|RUSC1_uc001fkr.2_5'Flank|RUSC1_uc001fks.2_5'Flank	NM_001105203	NP_001098673	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1 isoform a	311						cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			GTGCCCCACCGGACAATCACG	0.567													9	41					0	0	0.010729	0	0	
GON4L	54856	broad.mit.edu	37	1	155722380	155722380	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:155722380T>C	uc001flz.2	-	30	5941	c.5844A>G	c.(5842-5844)GCA>GCG	p.A1948A	GON4L_uc001flx.1_5'Flank|GON4L_uc009wrg.1_Splice_Site|GON4L_uc001fly.1_Splice_Site_p.G1948_splice|GON4L_uc009wrh.1_Splice_Site_p.G1948_splice|GON4L_uc001fma.1_Silent_p.A1948A	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	1948					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CTGCCAATCCTGCTTAGGAGG	0.502													4	7					0	0	0.009096	0	0	
VHLL	391104	broad.mit.edu	37	1	156268818	156268818	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:156268818G>A	uc001fok.2	-	1	611	c.163C>T	c.(163-165)CGG>TGG	p.R55W		NM_001004319	NP_001004319	Q6RSH7	VHLL_HUMAN	von Hippel-Lindau tumor suppressor-like	55	Beta-domain.				protein ubiquitination	nucleus				ovary(1)	1	Hepatocellular(266;0.158)					ATGATGATCCGGGAGAGCTCG	0.612													11	44					0	0	0.008291	0	0	
NTRK1	4914	broad.mit.edu	37	1	156844776	156844776	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:156844776C>T	uc001fqh.1	+	11	1386	c.1330C>T	c.(1330-1332)CGG>TGG	p.R444W	NTRK1_uc001fqf.1_Missense_Mutation_p.R408W|NTRK1_uc009wsi.1_Missense_Mutation_p.R143W|NTRK1_uc001fqi.1_Missense_Mutation_p.R438W|NTRK1_uc009wsk.1_Missense_Mutation_p.R438W	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	444	Cytoplasmic (Potential).				activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)	CAAATGTGGACGGAGAAACAA	0.567			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			16	76					0	0	0.006122	0	0	
ARHGEF11	9826	broad.mit.edu	37	1	156925516	156925516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:156925516G>A	uc001fqo.2	-	19	2667	c.1627C>T	c.(1627-1629)CCC>TCC	p.P543S	ARHGEF11_uc001fqn.2_Missense_Mutation_p.P583S|ARHGEF11_uc001fqp.1_Missense_Mutation_p.P72S	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	543					actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GAGCTTTTGGGCTTCCCAATG	0.498													24	165					0	0	0.007291	0	0	
FCRL5	83416	broad.mit.edu	37	1	157494244	157494244	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:157494244T>C	uc001fqu.2	-	10	2222	c.2064A>G	c.(2062-2064)CCA>CCG	p.P688P	FCRL5_uc009wsm.2_Silent_p.P688P|FCRL5_uc010phv.1_Silent_p.P688P|FCRL5_uc010phw.1_Silent_p.P603P	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	688	Extracellular (Potential).|Ig-like C2-type 7.					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				AGTACAGGATTGGGGAGGAGC	0.577													12	50					0	0	0.002450	0	0	
FCRL3	115352	broad.mit.edu	37	1	157665164	157665164	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:157665164C>A	uc001frb.2	-	8	1658	c.1366G>T	c.(1366-1368)GGC>TGC	p.G456C	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Missense_Mutation_p.G456C|FCRL3_uc009wsn.2_RNA|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_Missense_Mutation_p.G182C|FCRL3_uc001frc.1_Missense_Mutation_p.G456C	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	456	Ig-like C2-type 5.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					GCCCCCAGGCCATTGTCTGCA	0.532													22	102					1.96895e-08	2.1553e-08	0.002780	1	0	
FCRL3	115352	broad.mit.edu	37	1	157666067	157666067	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:157666067G>A	uc001frb.2	-	7	1187	c.895C>T	c.(895-897)CTG>TTG	p.L299L	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Silent_p.L299L|FCRL3_uc009wsn.2_RNA|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_Silent_p.L25L|FCRL3_uc001frc.1_Silent_p.L299L	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	299	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					CCTTCAATCAGCTGCCCTCCG	0.517													10	117					0	0	0.010729	0	0	
ATP1A2	477	broad.mit.edu	37	1	160094924	160094924	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:160094924A>G	uc001fvc.2	+	7	763	c.631_splice	c.e7-2	p.V211_splice	ATP1A2_uc001fvb.2_Splice_Site_p.V211_splice|ATP1A2_uc010piz.1_Splice_Site_p.V56_splice|ATP1A2_uc001fvd.2_5'Flank	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein						ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CTTCCTCCTCAGGTGGATAAC	0.542													4	27					0	0	0.001168	0	0	
ATP1A4	480	broad.mit.edu	37	1	160156152	160156152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:160156152C>T	uc001fve.3	+	21	3535	c.3056C>T	c.(3055-3057)CCG>CTG	p.P1019L	ATP1A4_uc001fvf.3_RNA|ATP1A4_uc001fvg.2_Missense_Mutation_p.P522L|ATP1A4_uc001fvh.2_Missense_Mutation_p.P155L	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1	1019	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CGTCAGCACCCGGATGGTGAG	0.562													20	96					0	0	0.008871	0	0	
SLAMF6	114836	broad.mit.edu	37	1	160465878	160465878	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:160465878G>T	uc001fwe.1	-	2	415	c.355C>A	c.(355-357)CTG>ATG	p.L119M	SLAMF6_uc001fwd.1_Missense_Mutation_p.L119M|SLAMF6_uc010pjh.1_Missense_Mutation_p.L70M|SLAMF6_uc010pji.1_Intron|SLAMF6_uc010pjj.1_Intron|SLAMF6_uc009wtm.1_Missense_Mutation_p.L70M	NM_052931	NP_443163	Q96DU3	SLAF6_HUMAN	activating NK receptor precursor	119	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			TAACTGGACAGCTTTGCAGAG	0.418													14	81					6.94344e-10	7.66567e-10	0.006122	1	0	
NDUFS2	4720	broad.mit.edu	37	1	161183198	161183198	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:161183198T>G	uc001fyv.2	+	12	1593	c.1145T>G	c.(1144-1146)TTT>TGT	p.F382C	NDUFS2_uc001fyw.2_Missense_Mutation_p.F382C|NDUFS2_uc010pkj.1_Missense_Mutation_p.F331C|NDUFS2_uc001fyx.2_Missense_Mutation_p.F356C|FCER1G_uc001fyz.1_5'Flank|FCER1G_uc001fza.1_5'Flank	NM_004550	NP_004541	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2	382					mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity|protein binding|quinone binding			skin(1)	1	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		NADH(DB00157)	ATTCATCACTTTAAGTTGTAT	0.483													3	17					0	0	0.004672	0	0	
FMO3	2328	broad.mit.edu	37	1	171076863	171076863	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:171076863C>T	uc001ghi.2	+	4	480	c.369C>T	c.(367-369)GGC>GGT	p.G123G	FMO3_uc001ghh.2_Silent_p.G123G|FMO3_uc010pmb.1_Silent_p.G103G|FMO3_uc010pmc.1_Silent_p.G60G	NM_001002294	NP_001002294	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	123					xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CAACTACTGGCCAGTGGGATG	0.393													23	62					0	0	0.002780	0	0	
RC3H1	149041	broad.mit.edu	37	1	173930312	173930312	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:173930312C>T	uc001gju.3	-	12	2360	c.2273G>A	c.(2272-2274)CGA>CAA	p.R758Q	RC3H1_uc010pms.1_Missense_Mutation_p.R758Q|RC3H1_uc001gjv.2_Missense_Mutation_p.R758Q|RC3H1_uc010pmt.1_Missense_Mutation_p.R758Q	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin	758	Pro-rich.				cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						TATTTCCTTTCGTCGGCGATG	0.453													22	63					0	0	0.002780	0	0	
GPR52	9293	broad.mit.edu	37	1	174417414	174417414	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:174417414T>C	uc001gka.1	+	1	203	c.165T>C	c.(163-165)ATT>ATC	p.I55I	RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjx.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_005684	NP_005675	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	55	Helical; Name=1; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			skin(1)	1						TTCTGATCATTGCTGGGAATC	0.438													18	90					0	0	0.004990	0	0	
PAPPA2	60676	broad.mit.edu	37	1	176671867	176671867	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:176671867T>C	uc001gkz.2	+	9	4525	c.3361T>C	c.(3361-3363)TCA>CCA	p.S1121P	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1121					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TGGGAAGGTGTCAGAGTGAGT	0.318													6	40					0	0	0.001984	0	0	
LHX4	89884	broad.mit.edu	37	1	180235536	180235536	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:180235536C>T	uc001goe.1	+	3	481	c.258C>T	c.(256-258)GGC>GGT	p.G86G		NM_033343	NP_203129	Q969G2	LHX4_HUMAN	LIM homeobox protein 4	86	LIM zinc-binding 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						GGCGCTTCGGCACAAAATGCA	0.607													5	28					0	0	0.001168	0	0	
CACNA1E	777	broad.mit.edu	37	1	181706764	181706764	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:181706764G>A	uc001gow.2	+	23	3691	c.3526G>A	c.(3526-3528)GTC>ATC	p.V1176I	CACNA1E_uc009wxs.2_Missense_Mutation_p.V1064I|CACNA1E_uc001gox.1_Missense_Mutation_p.V402I|CACNA1E_uc009wxt.2_Missense_Mutation_p.V402I	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1176	Extracellular (Potential).|III.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						AGAGGACCCCGTCCTGACCAA	0.617													18	58					0	0	0.012319	0	0	
CACNA1E	777	broad.mit.edu	37	1	181731743	181731743	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:181731743T>C	uc001gow.2	+	33	4804	c.4639T>C	c.(4639-4641)TTC>CTC	p.F1547L	CACNA1E_uc009wxs.2_Missense_Mutation_p.F1435L|CACNA1E_uc001gox.1_Missense_Mutation_p.F773L|CACNA1E_uc009wxt.2_Missense_Mutation_p.F773L	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1547	Helical; Name=S3 of repeat IV.|IV.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						TATCTTTGACTTCATCACCGT	0.398													11	39					0	0	0.001855	0	0	
ZNF648	127665	broad.mit.edu	37	1	182025786	182025786	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:182025786C>T	uc001goz.2	-	2	1568	c.1360G>A	c.(1360-1362)GGC>AGC	p.G454S		NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	454	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AAGGCCACGCCGCAGTCAGCG	0.677													4	10					0	0	0.009096	0	0	
APOBEC4	403314	broad.mit.edu	37	1	183617241	183617241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:183617241C>T	uc001gqn.2	-	2	948	c.676G>A	c.(676-678)GCA>ACA	p.A226T	RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron	NM_203454	NP_982279	Q8WW27	ABEC4_HUMAN	apolipoprotein B	226					mRNA processing		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0						ATTTCATATGCGTTGTGCCTG	0.433													16	93					0	0	0.004990	0	0	
IVNS1ABP	10625	broad.mit.edu	37	1	185270128	185270128	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:185270128T>C	uc001grl.2	-	10	1719	c.1096A>G	c.(1096-1098)ATG>GTG	p.M366V	IVNS1ABP_uc001gri.2_Missense_Mutation_p.M26V|IVNS1ABP_uc001grj.2_Missense_Mutation_p.M26V|IVNS1ABP_uc009wyj.2_Missense_Mutation_p.M148V|IVNS1ABP_uc009wyk.2_RNA|IVNS1ABP_uc001grm.2_Missense_Mutation_p.M26V	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	366	Sufficient for AHR interaction and signaling.				interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5						TTGCCATTCATCTCTGCTGTT	0.433													12	58					0	0	0.003163	0	0	
HMCN1	83872	broad.mit.edu	37	1	185931751	185931751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:185931751G>A	uc001grq.1	+	12	2159	c.1930G>A	c.(1930-1932)GCC>ACC	p.A644T	HMCN1_uc001grr.1_5'UTR	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	644	Ig-like C2-type 3.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						ACCAAAGATTGCCTGGACCGT	0.428													21	135					0	0	0.008871	0	0	
HMCN1	83872	broad.mit.edu	37	1	186092202	186092202	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:186092202C>T	uc001grq.1	+	81	12578	c.12349C>T	c.(12349-12351)CGT>TGT	p.R4117C		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4117	Ig-like C2-type 40.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						TAAAGATGGGCGTGCAATTGT	0.512													12	31					0	0	0.002450	0	0	
HMCN1	83872	broad.mit.edu	37	1	186113746	186113746	+	Missense_Mutation	SNP	G	A	A	rs149329415		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:186113746G>A	uc001grq.1	+	91	14406	c.14177G>A	c.(14176-14178)GGC>GAC	p.G4726D	HMCN1_uc001grs.1_Missense_Mutation_p.G295D	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4726	TSP type-1 4.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AGAACAAGGGGCTGCTCCGAC	0.542													15	69					0	0	0.003163	0	0	
PRG4	10216	broad.mit.edu	37	1	186276755	186276755	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:186276755C>T	uc001gru.3	+	7	1955	c.1904C>T	c.(1903-1905)ACC>ATC	p.T635I	PRG4_uc001grt.3_Missense_Mutation_p.T594I|PRG4_uc009wyl.2_Missense_Mutation_p.T542I|PRG4_uc009wym.2_Missense_Mutation_p.T501I|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	635	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CTCGCACCCACCACCCCTGAG	0.682													6	18					0	0	0.001984	0	0	
TPR	7175	broad.mit.edu	37	1	186328983	186328983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:186328983C>T	uc001grv.2	-	12	1634	c.1337G>A	c.(1336-1338)CGT>CAT	p.R446H	TPR_uc010pop.1_Missense_Mutation_p.R522H	NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	446	Potential.				carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTTCTGTGCACGTTCATATTC	0.368			T	NTRK1	papillary thyroid								16	59					0	0	0.004007	0	0	
FAM5C	339479	broad.mit.edu	37	1	190129847	190129847	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:190129847G>A	uc001gse.1	-	7	1367	c.1135C>T	c.(1135-1137)CTT>TTT	p.L379F	FAM5C_uc010pot.1_Missense_Mutation_p.L277F	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	379						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					CTCTTGCTAAGGCTAAAAAGC	0.393													19	63					0	0	0.012319	0	0	
FAM5C	339479	broad.mit.edu	37	1	190129967	190129967	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:190129967A>G	uc001gse.1	-	7	1247	c.1015T>C	c.(1015-1017)TCT>CCT	p.S339P	FAM5C_uc010pot.1_Missense_Mutation_p.S237P	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	339						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					ATTATAGTAGATGTGTTGAGG	0.308													20	94					0	0	0.008871	0	0	
ASPM	259266	broad.mit.edu	37	1	197098315	197098315	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:197098315A>G	uc001gtu.2	-	9	3017	c.2760_splice	c.e9+1	p.K920_splice	ASPM_uc001gtv.2_Splice_Site_p.K920_splice|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly						mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						TGAAAAGCATACCTTGAATTC	0.299													11	59					0	0	0.013537	0	0	
DENND1B	163486	broad.mit.edu	37	1	197564380	197564380	+	Silent	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:197564380A>C	uc001guf.3	-	14	1343	c.1005T>G	c.(1003-1005)GCT>GCG	p.A335A	DENND1B_uc010ppe.1_Silent_p.A315A|DENND1B_uc010ppf.1_RNA|DENND1B_uc001gue.3_Silent_p.A305A	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2	335	dDENN.					clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0						CAAACAAAGCAGCCTGTGCTC	0.428													35	200					0	0	0.008740	0	0	
CACNA1S	779	broad.mit.edu	37	1	201023674	201023674	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:201023674T>G	uc001gvv.2	-	29	3852	c.3625A>C	c.(3625-3627)AGC>CGC	p.S1209R		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1209	IV.|Extracellular (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	AGTCCCCCGCTGGAGGCCAGG	0.403													3	15					0	0	0.009096	0	0	
PPP1R12B	4660	broad.mit.edu	37	1	202465946	202465946	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:202465946C>T	uc001gya.1	+	18	2630	c.2486C>T	c.(2485-2487)ACG>ATG	p.T829M	PPP1R12B_uc001gxz.1_Missense_Mutation_p.T829M|PPP1R12B_uc001gyb.1_Missense_Mutation_p.T55M|PPP1R12B_uc001gyc.1_Missense_Mutation_p.T55M	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	829					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			GTCAAAGAAACGTGGGTAAGT	0.403													18	66					0	0	0.006122	0	0	
TMEM183A	92703	broad.mit.edu	37	1	202985125	202985125	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:202985125C>T	uc001gyu.1	+	5	623	c.565C>T	c.(565-567)CGA>TGA	p.R189*	TMEM183A_uc009xai.1_Nonsense_Mutation_p.R189*|TMEM183A_uc001gyv.1_RNA|TMEM183A_uc001gyw.1_Nonsense_Mutation_p.R188*|TMEM183A_uc001gyx.1_Nonsense_Mutation_p.R188*	NM_001079809	NP_001073277	Q8IXX5	T183A_HUMAN	transmembrane protein 183B	189						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)			TTTGCGTCTGCGACCAGAGTC	0.502													19	83					0	0	0.006320	0	0	
FMOD	2331	broad.mit.edu	37	1	203316449	203316449	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:203316449T>C	uc001gzr.2	-	2	1086	c.950A>G	c.(949-951)AAC>AGC	p.N317S	FMOD_uc010pqi.1_RNA	NM_002023	NP_002014	Q06828	FMOD_HUMAN	fibromodulin precursor	317	LRR 10.				transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)			GAGGTAGAGGTTCTCCAGGTT	0.532													6	88					0	0	0.001984	0	0	
PIK3C2B	5287	broad.mit.edu	37	1	204400821	204400821	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:204400821A>C	uc001haw.2	-	29	4735	c.4256T>G	c.(4255-4257)CTC>CGC	p.L1419R	PIK3C2B_uc010pqv.1_Missense_Mutation_p.L1391R	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	1419	PX.				cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			AGAAGGGAAGAGCAGCCGCAA	0.542											OREG0014134	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	70					0	0	0.001855	0	0	
PIK3C2B	5287	broad.mit.edu	37	1	204418318	204418318	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:204418318G>T	uc001haw.2	-	15	2820	c.2341C>A	c.(2341-2343)CTG>ATG	p.L781M	PIK3C2B_uc010pqv.1_Missense_Mutation_p.L781M	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	781					cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CTCACCTGCAGGATGACACTG	0.552													5	9					1.23904e-05	1.33197e-05	0.000602	1	0	
SLC41A1	254428	broad.mit.edu	37	1	205766095	205766095	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:205766095G>A	uc001hdh.1	-	8	1901	c.1029C>T	c.(1027-1029)GAC>GAT	p.D343D	SLC41A1_uc001hdg.1_5'Flank|uc001hdi.1_5'Flank	NM_173854	NP_776253	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 member 1	343						integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			skin(2)	2	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CAAAGTTGGGGTCTGAGACAG	0.522													4	22					0	0	0.000602	0	0	
SRGAP2	23380	broad.mit.edu	37	1	206611390	206611390	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:206611390G>T	uc001hdy.2	+	13	1782	c.1449G>T	c.(1447-1449)CGG>CGT	p.R483R	SRGAP2_uc010prt.1_Silent_p.R406R|SRGAP2_uc001hdx.2_Silent_p.R483R|SRGAP2_uc010pru.1_Silent_p.R406R|SRGAP2_uc010prv.1_Silent_p.R407R	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	570	Rho-GAP.				axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					TTTACTTCCGGGGGCTGGAAC	0.552													10	34					9.70103e-10	1.0696e-09	0.008291	1	0	
CD34	947	broad.mit.edu	37	1	208061172	208061172	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:208061172G>A	uc001hgw.1	-	8	1327	c.1069C>T	c.(1069-1071)CGA>TGA	p.R357*	CD34_uc001hgv.1_Nonsense_Mutation_p.R199*|CD34_uc001hgx.1_3'UTR|CD34_uc010psj.1_Nonsense_Mutation_p.R222*	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a	357	Cytoplasmic (Potential).				cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						TGAGCCCCTCGGTTCACACTG	0.592													4	39					0	0	0.000602	0	0	
SERTAD4	56256	broad.mit.edu	37	1	210411408	210411408	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:210411408G>A	uc001hhy.2	+	2	282	c.103G>A	c.(103-105)GGA>AGA	p.G35R	SERTAD4_uc009xcw.2_Missense_Mutation_p.G35R	NM_019605	NP_062551	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	35							protein binding			ovary(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TGACAGCTACGGAGGCCCAAG	0.602													21	80					0	0	0.010504	0	0	
TRAF5	7188	broad.mit.edu	37	1	211546014	211546014	+	Silent	SNP	C	T	T	rs147270768	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:211546014C>T	uc001hih.2	+	11	1704	c.1644C>T	c.(1642-1644)GCC>GCT	p.A548A	TRAF5_uc001hii.2_Silent_p.A548A|TRAF5_uc010psx.1_Silent_p.A559A|TRAF5_uc010psy.1_Silent_p.A442A|TRAF5_uc001hij.2_Silent_p.A548A	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	548	MATH.				apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TGAAAGTGGCCGTGGACTTAA	0.468													12	54					0	0	0.013537	0	0	
NEK2	4751	broad.mit.edu	37	1	211843642	211843642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:211843642G>A	uc001hir.1	-	5	892	c.746C>T	c.(745-747)ACG>ATG	p.T249M	NEK2_uc001hiq.1_Missense_Mutation_p.T249M|NEK2_uc001his.3_Missense_Mutation_p.T249M|NEK2_uc001hit.1_RNA	NM_002497	NP_002488	P51955	NEK2_HUMAN	NIMA-related kinase 2	249	Protein kinase.				cell division|centrosome separation|G2/M transition of mitotic cell cycle|meiosis|protein autophosphorylation|regulation of mitosis	centrosome|condensed chromosome kinetochore|cytosol|nucleolus	ATP binding|metal ion binding|protein binding|protein phosphatase binding|protein serine/threonine kinase activity			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		TAACATCCTCGTAATAATTTC	0.353													22	114					0	0	0.003330	0	0	
TMEM206	55248	broad.mit.edu	37	1	212560431	212560431	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:212560431C>T	uc001hjc.3	-	3	313	c.145G>A	c.(145-147)GAG>AAG	p.E49K	TMEM206_uc010pte.1_Missense_Mutation_p.E110K	NM_018252	NP_060722	Q9H813	TM206_HUMAN	transmembrane protein 206	49	Cytoplasmic (Potential).					integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		GAGGCGGACTCGCTGTCCAGG	0.587													15	41					0	0	0.003163	0	0	
CENPF	1063	broad.mit.edu	37	1	214792011	214792011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:214792011C>T	uc001hkm.2	+	4	629	c.455C>T	c.(454-456)CCA>CTA	p.P152L		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	152	Interaction with SNAP25 and required for localization to the cytoplasm (By similarity).|Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TTTACAACTCCACTAACACCA	0.353													12	45					0	0	0.001855	0	0	
CENPF	1063	broad.mit.edu	37	1	214819293	214819293	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:214819293G>A	uc001hkm.2	+	13	6554	c.6380G>A	c.(6379-6381)CGC>CAC	p.R2127H		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2223	Potential.|2-1.|2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding	p.R2127H(1)		ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CTGAGAGTTCGCATTGAGGCC	0.498													20	89					0	0	0.012319	0	0	
SPATA17	128153	broad.mit.edu	37	1	217955552	217955552	+	Missense_Mutation	SNP	C	T	T	rs145142638	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:217955552C>T	uc001hlh.1	+	8	786	c.760C>T	c.(760-762)CGC>TGC	p.R254C	SPATA17_uc009xdr.1_RNA|SPATA17_uc001hli.2_Missense_Mutation_p.R254C	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	254						cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		ATTAGAACAACGCTACAGGCC	0.458													8	55					0	0	0.008291	0	0	
RAB3GAP2	25782	broad.mit.edu	37	1	220324711	220324711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:220324711G>A	uc010puk.1	-	35	4228	c.4064C>T	c.(4063-4065)GCA>GTA	p.A1355V	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Missense_Mutation_p.A935V|RAB3GAP2_uc001hmh.2_3'UTR	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	1355					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		AGCTGTTGTTGCAATTGGCAC	0.368													22	99					0	0	0.004656	0	0	
DISP1	84976	broad.mit.edu	37	1	223177546	223177546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:223177546C>T	uc001hnu.1	+	8	2954	c.2807C>T	c.(2806-2808)GCT>GTT	p.A936V		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	936					diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)		TTCACACTGGCTTATGAAAAG	0.473													6	39					0	0	0.001168	0	0	
CAPN2	824	broad.mit.edu	37	1	223943271	223943271	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:223943271G>A	uc001hob.3	+	10	1449	c.1225G>A	c.(1225-1227)GTG>ATG	p.V409M	CAPN2_uc010puy.1_Missense_Mutation_p.V331M|CAPN2_uc001hoc.2_5'Flank	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1	409	Domain III.				proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)		CACCTTCCTGGTGGGGCTCAT	0.493													4	17					0	0	0.000602	0	0	
OBSCN	84033	broad.mit.edu	37	1	228509533	228509533	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:228509533C>T	uc009xez.1	+	55	15035	c.14991C>T	c.(14989-14991)AGC>AGT	p.S4997S	OBSCN_uc001hsn.2_Silent_p.S4997S	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	4997					apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				AAGCCGAGAGCTCCTCTGGGG	0.617													4	33					0	0	0.000602	0	0	
COG2	22796	broad.mit.edu	37	1	230798937	230798937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:230798937G>A	uc001htw.2	+	4	502	c.351G>A	c.(349-351)ATG>ATA	p.M117I	COG2_uc001htx.2_Missense_Mutation_p.M117I|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	117					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				ATGAACGAATGTCTAAACAAG	0.338													16	61					0	0	0.007413	0	0	
SIPA1L2	57568	broad.mit.edu	37	1	232626723	232626723	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:232626723T>C	uc001hvg.2	-	3	1861	c.1703A>G	c.(1702-1704)GAA>GGA	p.E568G		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	568					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TTCCAAAACTTCTTTGAGAGG	0.473													13	73					0	0	0.002450	0	0	
PCNXL2	80003	broad.mit.edu	37	1	233134062	233134062	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:233134062G>A	uc001hvl.2	-	32	5961	c.5726C>T	c.(5725-5727)GCA>GTA	p.A1909V	PCNXL2_uc001hvk.1_Missense_Mutation_p.A561V|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1909						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				GGGCTGTTCTGCGCTGCTCTC	0.622													4	22					0	0	0.009096	0	0	
ACTN2	88	broad.mit.edu	37	1	236902754	236902754	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:236902754C>A	uc001hyf.2	+	10	1233	c.1029C>A	c.(1027-1029)ATC>ATA	p.I343I	ACTN2_uc001hyg.2_Silent_p.I135I|ACTN2_uc009xgi.1_Silent_p.I343I|ACTN2_uc010pxu.1_Intron|ACTN2_uc001hyh.2_Silent_p.I31I	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	343	Spectrin 1.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			AGCTGGAGATCAACTTCAACA	0.582													13	64					3.27435e-08	3.57726e-08	0.002450	1	0	
ACTN2	88	broad.mit.edu	37	1	236920825	236920825	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:236920825G>A	uc001hyf.2	+	18	2398	c.2194G>A	c.(2194-2196)GCC>ACC	p.A732T	ACTN2_uc001hyg.2_Missense_Mutation_p.A524T|ACTN2_uc009xgi.1_Missense_Mutation_p.A732T|ACTN2_uc010pxu.1_Missense_Mutation_p.A421T|ACTN2_uc001hyh.2_Missense_Mutation_p.A420T	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	732	Spectrin 4.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			GACAACCATCGCCAGAACCAT	0.507													10	79					0	0	0.006214	0	0	
Unknown	0	broad.mit.edu	37	1	237167436	237167436	+	RNA	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:237167436C>T	uc001hyk.1	-	1		c.283G>A								Homo sapiens metallothionein 1H-like protein mRNA, complete cds.																		AAAAAAATCCCGGACTTTACG	0.433													4	9					0	0	0.000602	0	0	
CHRM3	1131	broad.mit.edu	37	1	240072247	240072247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:240072247C>T	uc001hyp.2	+	5	2275	c.1496C>T	c.(1495-1497)GCC>GTC	p.A499V		NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	499	Helical; Name=6; (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	ATCTTGCTTGCCTTCATCATC	0.498													24	87					0	0	0.006320	0	0	
SCCPDH	51097	broad.mit.edu	37	1	246890298	246890298	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:246890298G>A	uc001ibr.2	+	2	642	c.295G>A	c.(295-297)GTA>ATA	p.V99I		NM_016002	NP_057086	Q8NBX0	SCPDH_HUMAN	saccharopine dehydrogenase (putative)	99						midbody	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity			ovary(1)	1	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)		CCTCAATTGCGTAGGACCAGT	0.398													13	32					0	0	0.013537	0	0	
AHCTF1	25909	broad.mit.edu	37	1	247063740	247063740	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:247063740A>T	uc001ibu.1	-	8	1156	c.1149T>A	c.(1147-1149)TTT>TTA	p.F383L	AHCTF1_uc001ibv.1_Missense_Mutation_p.F392L|AHCTF1_uc009xgs.1_5'Flank	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	383	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CCTGCCAGGTAAAGACTGAAA	0.348													17	43					0	0	0.006122	0	0	
OR6F1	343169	broad.mit.edu	37	1	247875374	247875374	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:247875374G>A	uc001idj.1	-	1	684	c.684C>T	c.(682-684)ATC>ATT	p.I228I		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	228	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TGGCAGAGGGGATCCTGAGGA	0.527													9	86					0	0	0.006214	0	0	
OR1C1	26188	broad.mit.edu	37	1	247920953	247920953	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:247920953G>A	uc010pza.1	-	1	756	c.756C>T	c.(754-756)TAC>TAT	p.Y252Y		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TGGCTGTGCCGTAAAACAACA	0.522													9	35					0	0	0.010729	0	0	
OR2W3	343171	broad.mit.edu	37	1	248059482	248059482	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:248059482C>T	uc001idp.1	+	3	863	c.594C>T	c.(592-594)ACC>ACT	p.T198T	OR2W3_uc010pzb.1_Silent_p.T198T	NM_001001957	NP_001001957	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W,	198	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|pancreas(1)	3	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCGAAGGCACCGTCTTTGTCC	0.587													10	63					0	0	0.006122	0	0	
PFKP	5214	broad.mit.edu	37	10	3146003	3146003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:3146003G>A	uc001igp.2	+	5	523	c.487G>A	c.(487-489)GCC>ACC	p.A163T	PFKP_uc001igq.2_Missense_Mutation_p.A155T|PFKP_uc009xhr.2_Missense_Mutation_p.A125T|PFKP_uc009xhs.1_5'Flank	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	163					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GCAGAAGTACGCCTACCTCAA	0.622													8	36					0	0	0.008291	0	0	
KIN	22944	broad.mit.edu	37	10	7829837	7829837	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:7829837C>T	uc001ijt.2	-	1	108	c.60G>A	c.(58-60)GGG>GGA	p.G20G	KIN_uc010qaz.1_RNA|KIN_uc009xip.2_Silent_p.G20G|KIN_uc010qba.1_5'UTR|ATP5C1_uc010qbb.1_5'Flank|ATP5C1_uc009xiq.1_5'Flank|ATP5C1_uc010qbc.1_5'Flank|ATP5C1_uc001iju.2_5'Flank|ATP5C1_uc001ijv.2_5'Flank	NM_012311	NP_036443	O60870	KIN17_HUMAN	HsKin17 protein	20					DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						GCTTCTGCAGCCCCTTGGACT	0.612													12	59					0	0	0.003163	0	0	
TAF3	83860	broad.mit.edu	37	10	8007484	8007484	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:8007484G>A	uc010qbd.1	+	3	2011	c.2011G>A	c.(2011-2013)GCC>ACC	p.A671T		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	671	Lys-rich.				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						CCCTGCCACAGCCTCCAGGGT	0.423													8	46					0	0	0.013537	0	0	
FAM188A	80013	broad.mit.edu	37	10	15885239	15885239	+	Silent	SNP	C	T	T	rs140140984		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:15885239C>T	uc001iod.1	-	3	428	c.207G>A	c.(205-207)TCG>TCA	p.S69S	FAM188A_uc001ioe.1_5'UTR|FAM188A_uc001iof.1_Silent_p.S69S	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97	69					apoptosis	nucleus	calcium ion binding			ovary(1)	1						AAGACTTCTCCGAAGAAAACA	0.323													19	93					0	0	0.014323	0	0	
NEBL	10529	broad.mit.edu	37	10	21141488	21141488	+	Missense_Mutation	SNP	C	T	T	rs150518045	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:21141488C>T	uc001iqi.2	-	10	1391	c.994G>A	c.(994-996)GTC>ATC	p.V332I	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	332	Nebulin 9.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						CTTTGGAGGACGGCATTGCCT	0.493													4	33					0	0	0.009096	0	0	
BMI1	648	broad.mit.edu	37	10	22618263	22618263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:22618263C>T	uc001irh.2	+	10	1412	c.773C>T	c.(772-774)GCC>GTC	p.A258V	BMI1_uc009xkg.2_Missense_Mutation_p.A401V	NM_005180	NP_005171	P35226	BMI1_HUMAN	BMI1 polycomb ring finger oncogene	258	Pro/Ser-rich.				hemopoiesis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent	cytoplasm|nucleolus|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			ovary(1)|skin(1)	2						AGTGACAAGGCCAACAGCCCA	0.493													16	67					0	0	0.004007	0	0	
KIAA1217	56243	broad.mit.edu	37	10	24833918	24833918	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:24833918C>T	uc001iru.3	+	20	5623	c.5220C>T	c.(5218-5220)AGC>AGT	p.S1740S	KIAA1217_uc001irs.2_Silent_p.S1061S|KIAA1217_uc001irt.3_Silent_p.S1106S|KIAA1217_uc010qcy.1_Silent_p.S1171S|KIAA1217_uc010qcz.1_Silent_p.S1146S|KIAA1217_uc001irw.2_Silent_p.S890S|KIAA1217_uc001irz.2_Silent_p.S824S|KIAA1217_uc001irx.2_Silent_p.S1423S|KIAA1217_uc001iry.2_Silent_p.S864S	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	1740					embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						AGGGCTCCAGCGGGGCCCCAC	0.607													13	51					0	0	0.013537	0	0	
MYO3A	53904	broad.mit.edu	37	10	26414415	26414415	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:26414415A>G	uc001isn.2	+	19	2352	c.1992A>G	c.(1990-1992)CGA>CGG	p.R664R	MYO3A_uc009xko.1_Silent_p.R664R|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	664	Myosin head-like.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						CAATTATACGACCCAATACTG	0.418													14	93					0	0	0.003163	0	0	
GAD2	2572	broad.mit.edu	37	10	26506539	26506539	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:26506539C>T	uc001isp.2	+	2	580	c.77C>T	c.(76-78)GCG>GTG	p.A26V	GAD2_uc009xkr.2_Missense_Mutation_p.A26V|GAD2_uc001isq.2_Missense_Mutation_p.A26V	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	glutamate decarboxylase 2	26					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)	TTCCTTGCAGCGCGAGCCTGG	0.592													3	11					0	0	0.009096	0	0	
ACBD5	91452	broad.mit.edu	37	10	27497331	27497331	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:27497331C>T	uc010qdp.1	-	10	1439	c.1248G>A	c.(1246-1248)CAG>CAA	p.Q416Q	ACBD5_uc010qdm.1_Silent_p.Q414Q|ACBD5_uc010qdn.1_Silent_p.Q307Q|ACBD5_uc010qdo.1_Silent_p.Q239Q|ACBD5_uc001ito.2_Silent_p.Q381Q|ACBD5_uc001itp.2_Silent_p.Q307Q|ACBD5_uc001itq.2_Silent_p.Q307Q|ACBD5_uc001itr.1_Silent_p.Q205Q	NM_145698	NP_663736	Q5T8D3	ACBD5_HUMAN	acyl-Coenzyme A binding domain containing 5	425					transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0						CACTTCCCACCTGCCGGCCCT	0.512													7	39					0	0	0.004482	0	0	
PTCHD3	374308	broad.mit.edu	37	10	27702350	27702350	+	Missense_Mutation	SNP	G	A	A	rs147881350		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:27702350G>A	uc001itu.2	-	1	948	c.830C>T	c.(829-831)ACG>ATG	p.T277M		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	277					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4						CAGGTTGAGCGTTTTGTTCAC	0.612													7	34					0	0	0.001984	0	0	
MTPAP	55149	broad.mit.edu	37	10	30611528	30611528	+	Silent	SNP	G	A	A	rs139195646	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:30611528G>A	uc001iva.3	-	6	1074	c.1011C>T	c.(1009-1011)TCC>TCT	p.S337S	MTPAP_uc001ivb.3_Silent_p.S467S	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor	337					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						AAAGGAGTTCGGAACTTGTCA	0.378													7	30					0	0	0.003080	0	0	
ZNF33A	7581	broad.mit.edu	37	10	38343774	38343774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:38343774A>G	uc001izh.2	+	5	897	c.719A>G	c.(718-720)AAC>AGC	p.N240S	ZNF33A_uc001izg.2_Missense_Mutation_p.N241S|ZNF33A_uc010qev.1_Missense_Mutation_p.N247S|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	240						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						AAGAGAGAGAACGCAGAAGAG	0.383													9	86					0	0	0.006214	0	0	
HSD17B7P2	158160	broad.mit.edu	37	10	38658885	38658885	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:38658885G>A	uc001izq.2	+	6		c.729G>A				NR_003086				Homo sapiens 17-beta-hydroxysteroid dehydrogenase type VII isoform mRNA, complete cds.												0						CTGCAGCTTCGCTTTTTTGCA	0.318													8	36					0	0	0.006214	0	0	
LOC441666	441666	broad.mit.edu	37	10	42832171	42832171	+	RNA	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:42832171C>A	uc010qey.1	-	3		c.1804G>T				NR_024380				Homo sapiens noncoding mRNA sequence.												0						TATGAATTCTCTTATGTATAG	0.353													7	26					5.18039e-06	5.59402e-06	0.003080	1	0	
OR13A1	79290	broad.mit.edu	37	10	45798942	45798942	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:45798942A>G	uc001jcc.1	-	4	1238	c.929T>C	c.(928-930)TTG>TCG	p.L310S	OR13A1_uc001jcd.1_Missense_Mutation_p.L306S	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	310	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CTTGTTTCTCAAAGTATAGAT	0.483													18	75					0	0	0.007413	0	0	
MARCH8	220972	broad.mit.edu	37	10	45956826	45956826	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:45956826G>T	uc001jci.1	-	5	515	c.276C>A	c.(274-276)CCC>CCA	p.P92P	MARCH8_uc001jch.2_Silent_p.P374P|MARCH8_uc001jcj.1_Silent_p.P92P|MARCH8_uc001jck.1_Silent_p.P92P|MARCH8_uc001jcg.1_5'UTR	NM_001002266	NP_001002266	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform	92	RING-CH-type.					cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						GGGTGATCAGGGGGCTCTCAT	0.582													7	23					0.000157383	0.000167469	0.003080	1	0	
RBP3	5949	broad.mit.edu	37	10	48385926	48385926	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:48385926G>A	uc001jez.2	-	2	3280	c.3166C>T	c.(3166-3168)CTC>TTC	p.L1056F		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	1056	4 X approximate tandem repeats.|4.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)	ACCTGGGTGAGCAGCTCACCG	0.512													16	49					0	0	0.003163	0	0	
OGDHL	55753	broad.mit.edu	37	10	50959917	50959917	+	Silent	SNP	G	A	A	rs149339959		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:50959917G>A	uc001jie.2	-	6	847	c.705C>T	c.(703-705)AGC>AGT	p.S235S	OGDHL_uc009xog.2_Silent_p.S262S|OGDHL_uc010qgt.1_Silent_p.S178S|OGDHL_uc010qgu.1_Silent_p.S26S|OGDHL_uc009xoh.2_Silent_p.S26S	NM_018245	NP_060715	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like isoform a	235					glycolysis	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1						GCTTCTCCTCGCTGGAGAACT	0.607													23	91					0	0	0.014323	0	0	
CSTF2T	23283	broad.mit.edu	37	10	53458059	53458059	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:53458059C>T	uc001jjp.2	-	1	1297	c.1251G>A	c.(1249-1251)GCG>GCA	p.A417A	PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit	417	Gly-rich.				mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		GAGTCTCCATCGCTCGAGAAT	0.512													16	83					0	0	0.007413	0	0	
ANK3	288	broad.mit.edu	37	10	61835822	61835822	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:61835822G>A	uc001jky.2	-	37	5009	c.4817C>T	c.(4816-4818)ACG>ATG	p.T1606M	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1606	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						CGTAGCTTCCGTGACTGCTGG	0.483													17	98					0	0	0.008871	0	0	
ARID5B	84159	broad.mit.edu	37	10	63759914	63759914	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:63759914G>A	uc001jlt.1	+	4	593	c.567G>A	c.(565-567)TCG>TCA	p.S189S	ARID5B_uc010qil.1_Silent_p.S189S	NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	189					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)					GGTACCGCTCGATGCTGAAAC	0.532													14	75					0	0	0.004007	0	0	
AIFM2	84883	broad.mit.edu	37	10	71880941	71880941	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:71880941C>T	uc010qjg.1	-	3	334	c.321G>A	c.(319-321)CTG>CTA	p.L107L	AIFM2_uc001jqp.1_Silent_p.L107L	NM_032797	NP_116186	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor (AIF)-like	107					apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1						TGCCCGTGGCCAGGATAAGAT	0.443													12	23					0	0	0.013537	0	0	
NPFFR1	64106	broad.mit.edu	37	10	72025905	72025905	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:72025905T>C	uc010qjk.1	-	1	250	c.244A>G	c.(244-246)AAC>GAC	p.N82D		NM_022146	NP_071429	Q9GZQ6	NPFF1_HUMAN	neuropeptide FF receptor 1	84	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	neuropeptide receptor activity				0						ACAGCCAGGTTGAGGATGAAC	0.562													7	49					0	0	0.004482	0	0	
CDH23	64072	broad.mit.edu	37	10	73538008	73538008	+	Silent	SNP	C	T	T	rs111033487	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:73538008C>T	uc001jrx.3	+	38	5507	c.5130C>T	c.(5128-5130)ATC>ATT	p.I1710I		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1710	Cadherin 16.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						ACACCCTGATCGTCACTGCCA	0.607													10	32					0	0	0.001855	0	0	
ASCC1	51008	broad.mit.edu	37	10	73912658	73912658	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:73912658C>T	uc001jst.1	-	8	907	c.799G>A	c.(799-801)GCC>ACC	p.A267T	ASCC1_uc001jsr.1_Missense_Mutation_p.A154T|ASCC1_uc001jss.1_Missense_Mutation_p.A239T|ASCC1_uc001jsu.1_Missense_Mutation_p.A239T|ASCC1_uc010qju.1_Missense_Mutation_p.A260T			Q8N9N2	ASCC1_HUMAN	RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;	267					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0						TGGACTTTGGCGTAAAGAACA	0.408													10	54					0	0	0.008291	0	0	
CBARA1	10367	broad.mit.edu	37	10	74268011	74268011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:74268011C>T	uc001jtb.1	-	7	693	c.560G>A	c.(559-561)CGA>CAA	p.R187Q	CBARA1_uc010qjw.1_5'UTR|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_RNA	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1	185					calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1						AAATTTTTCTCGTTCCTGGGA	0.338													4	18					0	0	0.009096	0	0	
PLAU	5328	broad.mit.edu	37	10	75674570	75674570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:75674570C>T	uc001jwa.2	+	9	1012	c.866C>T	c.(865-867)GCG>GTG	p.A289V	C10orf55_uc001jvz.1_Intron|PLAU_uc010qkw.1_Missense_Mutation_p.A272V|PLAU_uc010qkx.1_Missense_Mutation_p.A203V|PLAU_uc001jwb.2_RNA|PLAU_uc001jwc.2_Missense_Mutation_p.A289V|PLAU_uc009xrq.1_Missense_Mutation_p.A253V	NM_002658	NP_002649	P00749	UROK_HUMAN	plasminogen activator, urokinase isoform 1	289	Peptidase S1.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(2)|kidney(1)	3	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)	GGCAGGTGTGCGCAGCCATCC	0.552													8	19					0	0	0.003080	0	0	
MYST4	23522	broad.mit.edu	37	10	76788343	76788343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:76788343G>A	uc001jwn.1	+	18	4254	c.3761G>A	c.(3760-3762)CGC>CAC	p.R1254H	MYST4_uc001jwo.1_Missense_Mutation_p.R962H|MYST4_uc001jwp.1_Missense_Mutation_p.R1071H	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1254					histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					GGAACAAAGCGCGGTCTATCT	0.438			T	CREBBP	AML								22	83					0	0	0.002780	0	0	
SFTPD	6441	broad.mit.edu	37	10	81701740	81701740	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:81701740G>A	uc001kbh.2	-	5	563	c.520C>T	c.(520-522)CGT>TGT	p.R174C	MBL1P_uc001kbf.2_Intron	NM_003019	NP_003010	P35247	SFTPD_HUMAN	pulmonary surfactant-associated protein D	174	Collagen-like.				cell junction assembly|innate immune response|lung alveolus development|macrophage chemotaxis|negative regulation of interleukin-2 biosynthetic process|negative regulation of T cell proliferation|positive regulation of phagocytosis|reactive oxygen species metabolic process|receptor-mediated endocytosis|respiratory gaseous exchange|surfactant homeostasis	collagen|endocytic vesicle|extracellular space|lysosome	bacterial cell surface binding|protein binding|sugar binding			skin(1)	1	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			GGGACTCCACGCTCACCAGGG	0.627													10	42					0	0	0.010729	0	0	
NRG3	10718	broad.mit.edu	37	10	84711311	84711311	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:84711311T>C	uc001kco.2	+	5	1168	c.1141T>C	c.(1141-1143)TTC>CTC	p.F381L	NRG3_uc010qlz.1_Missense_Mutation_p.F380L|NRG3_uc001kcp.2_Missense_Mutation_p.F160L|NRG3_uc001kcq.2_Missense_Mutation_p.F31L|NRG3_uc001kcr.2_Missense_Mutation_p.F31L	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	381	Helical; Note=Internal signal sequence; (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		CTGTGCAGCATTCTACTTCAA	0.378													26	118					0	0	0.005443	0	0	
RGR	5995	broad.mit.edu	37	10	86014126	86014126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:86014126C>T	uc001kdc.1	+	5	595	c.557C>T	c.(556-558)GCC>GTC	p.A186V	RGR_uc001kdd.1_Missense_Mutation_p.A190V|RGR_uc001kde.1_Missense_Mutation_p.A186V	NM_001012720	NP_001012738	P47804	RGR_HUMAN	retinal G-protein coupled receptor isoform 2	186	Helical; Name=5; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity|protein binding			ovary(1)	1						TTCAACTTCGCCATGCCCCTC	0.542													13	63					0	0	0.001855	0	0	
GRID1	2894	broad.mit.edu	37	10	87407104	87407104	+	Missense_Mutation	SNP	C	T	T	rs76097378	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:87407104C>T	uc001kdl.1	-	13	2149	c.2048G>A	c.(2047-2049)CGG>CAG	p.R683Q	GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Missense_Mutation_p.R254Q|uc001kdm.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	683	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	AGCAGAATCCCGGACAGTGCC	0.527										Multiple Myeloma(13;0.14)			56	214					0	0	0.014410	0	0	
PTEN	5728	broad.mit.edu	37	10	89653868	89653868	+	Splice_Site	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:89653868T>C	uc001kfb.2	+	3	1195	c.164_splice	c.e3+2	p.R55_splice		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.Y27fs*1(2)|p.?(2)|p.V54fs*29(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGTAGTAAGGTAAGAATGCTT	0.299		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			14	61					0	0	0.006122	0	0	
FAS	355	broad.mit.edu	37	10	90774042	90774042	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:90774042G>A	uc001kfr.2	+	9	1189	c.843G>A	c.(841-843)TGG>TGA	p.W281*	FAS_uc010qna.1_RNA|FAS_uc001kfs.2_3'UTR|FAS_uc001kft.2_Nonsense_Mutation_p.W260*|FAS_uc010qnb.1_RNA|FAS_uc010qnc.1_RNA|FAS_uc001kfw.2_3'UTR|FAS_uc010qnd.1_RNA|FAS_uc010qne.1_RNA|FAS_uc009xtp.2_RNA	NM_000043	NP_000034	P25445	TNR6_HUMAN	tumor necrosis factor receptor superfamily,	281	Death.|Interaction with HIPK3 (By similarity).|Cytoplasmic (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death	cytosol|extracellular region|integral to membrane|soluble fraction	identical protein binding|kinase binding			upper_aerodigestive_tract(1)|breast(1)	2		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)		TTCGTAATTGGCATCAACTTC	0.368									Autoimmune_Lymphoproliferative_syndrome_type_I				22	107					0	0	0.003330	0	0	
MYOF	26509	broad.mit.edu	37	10	95169361	95169361	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:95169361C>T	uc001kin.2	-	6	692	c.569G>A	c.(568-570)CGG>CAG	p.R190Q	MYOF_uc001kio.2_Missense_Mutation_p.R190Q|MYOF_uc001kip.3_Missense_Mutation_p.R190Q|MYOF_uc009xuf.2_Missense_Mutation_p.R172Q	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	190	C2 2.|Cytoplasmic (Potential).|Necessary for interaction with EHD2.				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						TGACAGCATCCGCCGGCTGTT	0.542													28	174					0	0	0.013726	0	0	
PIPSL	266971	broad.mit.edu	37	10	95719121	95719121	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:95719121C>T	uc009xuj.2	-	1	2552	c.2033G>A	c.(2032-2034)GGT>GAT	p.G678D		NR_002319				RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha;          Short=PtdIns(4)P-5-kinase alpha;          Short=PIP5KIalpha;          EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha;												0						CATGGCACCACCTTCACCAGC	0.507													9	63					0	0	0.004482	0	0	
SORBS1	10580	broad.mit.edu	37	10	97194450	97194450	+	Missense_Mutation	SNP	C	T	T	rs139115529		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:97194450C>T	uc001kkp.2	-	3	146	c.101G>A	c.(100-102)CGC>CAC	p.R34H	SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Missense_Mutation_p.R22H|SORBS1_uc001kko.2_Missense_Mutation_p.R34H|SORBS1_uc001kkq.2_Missense_Mutation_p.R34H|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Missense_Mutation_p.R34H|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Missense_Mutation_p.R34H|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	34					focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		AGAAATAGAGCGTGCGCGTAA	0.473													17	61					0	0	0.006122	0	0	
TLL2	7093	broad.mit.edu	37	10	98146799	98146799	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:98146799C>T	uc001kml.1	-	14	1989	c.1763G>A	c.(1762-1764)TGC>TAC	p.C588Y		NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	588	EGF-like 1; calcium-binding (Potential).			EVDECSWPDHGGCEHRCV -> GKKKKKKKKKKKKKKKKK (in Ref. 5; AAH13871).	cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GCGATGCTCGCACCCGCCGTG	0.597													6	21					0	0	0.004482	0	0	
SLIT1	6585	broad.mit.edu	37	10	98760984	98760984	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:98760984C>T	uc001kmw.2	-	37	4742	c.4490G>A	c.(4489-4491)TGC>TAC	p.C1497Y		NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	1497	CTCK.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GCCCTGGCAGCAGCCCTGGCC	0.642													7	34					0	0	0.004482	0	0	
CRTAC1	55118	broad.mit.edu	37	10	99655720	99655720	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:99655720G>A	uc001kou.1	-	10	1595	c.1239C>T	c.(1237-1239)GAC>GAT	p.D413D	CRTAC1_uc001kov.2_Silent_p.D402D|CRTAC1_uc001kot.1_Silent_p.D203D	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	413	FG-GAP 4; atypical.					proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TCCCGTCTCCGTCGAAGTCGG	0.582													8	33					0	0	0.004482	0	0	
TLX1	3195	broad.mit.edu	37	10	102896641	102896641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:102896641G>A	uc001ksw.2	+	3	1202	c.964G>A	c.(964-966)GTC>ATC	p.V322I		NM_005521	NP_005512	P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	322						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		AATCACTAGCGTCACGTCGGT	0.647			T	TRB@|TRD@	T-ALL								9	32					0	0	0.010729	0	0	
MGEA5	10724	broad.mit.edu	37	10	103563735	103563735	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:103563735C>T	uc001ktv.2	-	7	1236	c.793G>A	c.(793-795)GAA>AAA	p.E265K	MGEA5_uc010qqe.1_Missense_Mutation_p.E265K|MGEA5_uc009xws.2_Missense_Mutation_p.E265K|MGEA5_uc001ktw.2_Missense_Mutation_p.E265K|MGEA5_uc009xwt.2_Intron	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	265					glycoprotein catabolic process	cytoplasm|nucleus	histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		GAAACCTCTTCGATGGACTCT	0.353													15	89					0	0	0.003163	0	0	
NT5C2	22978	broad.mit.edu	37	10	104850727	104850727	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:104850727C>T	uc001kwo.2	-	17	1424	c.1238G>A	c.(1237-1239)CGT>CAT	p.R413H	NT5C2_uc010qqp.1_Missense_Mutation_p.R384H|NT5C2_uc001kwq.2_Missense_Mutation_p.R413H|NT5C2_uc001kwp.2_Missense_Mutation_p.R260H	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	413					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	GATGTCTGGACGCTCATTGCT	0.328													12	73					0	0	0.001855	0	0	
INA	9118	broad.mit.edu	37	10	105046873	105046873	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:105046873C>T	uc001kws.2	+	2	1196	c.1147C>T	c.(1147-1149)CTC>TTC	p.L383F		NM_032727	NP_116116	Q16352	AINX_HUMAN	internexin neuronal intermediate filament	383	Coil 2.|Rod.				cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton			ovary(1)|breast(1)	2				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		CCAGGACTTGCTCAATGTCAA	0.488													7	35					0	0	0.003080	0	0	
SORCS1	114815	broad.mit.edu	37	10	108431115	108431115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:108431115C>T	uc001kym.2	-	16	2077	c.2069G>A	c.(2068-2070)TGT>TAT	p.C690Y	SORCS1_uc001kyl.2_Missense_Mutation_p.C690Y|SORCS1_uc009xxs.2_Missense_Mutation_p.C690Y|SORCS1_uc001kyn.1_Missense_Mutation_p.C690Y|SORCS1_uc001kyo.2_Missense_Mutation_p.C690Y	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	690	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TCCCATGATACATGCTTCCCC	0.448													20	112					0	0	0.014323	0	0	
SORCS1	114815	broad.mit.edu	37	10	108439027	108439027	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:108439027T>G	uc001kym.2	-	12	1735	c.1727A>C	c.(1726-1728)AAC>ACC	p.N576T	SORCS1_uc001kyl.2_Missense_Mutation_p.N576T|SORCS1_uc009xxs.2_Missense_Mutation_p.N576T|SORCS1_uc001kyn.1_Missense_Mutation_p.N576T|SORCS1_uc001kyo.2_Missense_Mutation_p.N576T	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	576	Lumenal (Potential).|BNR 4.					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TCTCCAGGTGTTCCCTGCATC	0.398													9	63					0	0	0.010729	0	0	
HABP2	3026	broad.mit.edu	37	10	115338458	115338458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:115338458C>T	uc001lai.3	+	7	744	c.641C>T	c.(640-642)GCG>GTG	p.A214V	HABP2_uc010qrz.1_RNA|HABP2_uc010qry.1_3'UTR	NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	214	Kringle.				cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)		AACCAGCATGCGTGCCTTTAC	0.488													25	71					0	0	0.004656	0	0	
VWA2	340706	broad.mit.edu	37	10	116021030	116021030	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:116021030C>T	uc001lbl.1	+	5	668	c.347C>T	c.(346-348)GCA>GTA	p.A116V	VWA2_uc001lbk.1_Missense_Mutation_p.A116V|VWA2_uc009xyf.1_5'UTR	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	116	VWFA 1.					extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)		GAAGTGAAGGCAAGAATCAAG	0.463													10	86					0	0	0.008291	0	0	
INPP5F	22876	broad.mit.edu	37	10	121583376	121583376	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:121583376G>A	uc001leo.2	+	19	2377	c.2211G>A	c.(2209-2211)ATG>ATA	p.M737I	INPP5F_uc001lep.2_Missense_Mutation_p.M127I	NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F	737							phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AGCAAGCCATGGGATCGGATT	0.388													4	48					0	0	0.003080	0	0	
DMBT1	1755	broad.mit.edu	37	10	124380630	124380630	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:124380630G>A	uc001lgk.1	+	41	5061	c.4955G>A	c.(4954-4956)CGA>CAA	p.R1652Q	DMBT1_uc001lgl.1_Missense_Mutation_p.R1642Q|DMBT1_uc001lgm.1_Missense_Mutation_p.R1024Q|DMBT1_uc009xzz.1_Missense_Mutation_p.R1652Q|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yab.1_Missense_Mutation_p.R355Q|DMBT1_uc009yac.1_5'UTR	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1652	SRCR 13.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TGTCGAGGCCGAGTGGAGGTC	0.557													54	205					0	0	0.014410	0	0	
CHST15	51363	broad.mit.edu	37	10	125801922	125801922	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:125801922C>T	uc001lhl.2	-	3	1441	c.928G>A	c.(928-930)GTG>ATG	p.V310M	CHST15_uc001lhm.2_Missense_Mutation_p.V310M|CHST15_uc001lhn.2_Missense_Mutation_p.V310M|CHST15_uc010que.1_Missense_Mutation_p.V310M|CHST15_uc001lho.2_Missense_Mutation_p.V310M	NM_015892	NP_056976	Q7LFX5	CHSTF_HUMAN	B cell RAG associated protein	310	Lumenal (Potential).				hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1						TAATCTTCCACGGGATAGCGG	0.522													7	39					0	0	0.003080	0	0	
MGMT	4255	broad.mit.edu	37	10	131506287	131506287	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:131506287A>G	uc001lkh.2	+	3	373	c.347A>G	c.(346-348)CAC>CGC	p.H116R		NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	85										ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)		CCGGCTCTTCACCATCCCGTT	0.537								Direct_reversal_of_damage					14	72					0	0	0.004007	0	0	
EBF3	253738	broad.mit.edu	37	10	131639112	131639112	+	Silent	SNP	G	A	A	rs147171591		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr10:131639112G>A	uc001lki.1	-	14	1589	c.1530C>T	c.(1528-1530)TAC>TAT	p.Y510Y		NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3	519	Pro/Ser/Thr-rich.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		ACTTACTGCCGTAGGGAGAGT	0.507													15	57					0	0	0.003163	0	0	
NLRP6	171389	broad.mit.edu	37	11	281195	281195	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:281195C>T	uc010qvs.1	+	4	1461	c.1461C>T	c.(1459-1461)GGC>GGT	p.G487G	NLRP6_uc010qvt.1_Silent_p.G487G	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	487	NACHT.|LRR 1.					cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGCTGCCGGGCGTGCTGGAGA	0.612													19	76					0	0	0.008871	0	0	
ANO9	338440	broad.mit.edu	37	11	418746	418746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:418746G>A	uc001lpi.2	-	22	2189	c.2104C>T	c.(2104-2106)CGC>TGC	p.R702C	SIGIRR_uc001lpf.2_5'Flank|SIGIRR_uc001lpe.1_5'Flank|ANO9_uc001lph.2_Missense_Mutation_p.R395C|ANO9_uc010qvv.1_Missense_Mutation_p.R558C	NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN	tumor protein p53 inducible protein 5	702	Extracellular (Potential).					chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4						AAGGCCAGGCGGATGGCCAGG	0.607													17	54					0	0	0.004007	0	0	
PTDSS2	81490	broad.mit.edu	37	11	487453	487453	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:487453C>A	uc001lpj.2	+	6	780	c.604C>A	c.(604-606)CTT>ATT	p.L202I		NM_030783	NP_110410	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	202	Extracellular (Potential).					integral to membrane					0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	CGCGCACTTTCTTGGCTGGTA	0.637													11	54					3.27435e-08	3.57726e-08	0.002450	1	0	
TALDO1	6888	broad.mit.edu	37	11	763457	763457	+	Missense_Mutation	SNP	G	A	A	rs151052416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:763457G>A	uc001lqz.2	+	5	625	c.575G>A	c.(574-576)CGC>CAC	p.R192H	TALDO1_uc001lra.2_Missense_Mutation_p.R192H	NM_006755	NP_006746	P37837	TALDO_HUMAN	transaldolase 1	192					energy reserve metabolic process|xylulose biosynthetic process	cytosol	protein binding|sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;4.66e-26)|Epithelial(43;2.97e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.48e-19)|BRCA - Breast invasive adenocarcinoma(625;4.41e-05)|Lung(200;0.0595)|LUSC - Lung squamous cell carcinoma(625;0.0712)		TTTGTTGGGCGCATCCTTGAT	0.582													24	82					0	0	0.004656	0	0	
LRDD	55367	broad.mit.edu	37	11	799897	799897	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:799897G>A	uc001lro.1	-	15	2534	c.2392C>T	c.(2392-2394)CGT>TGT	p.R798C	SLC25A22_uc009yci.2_5'Flank|SLC25A22_uc001lrj.2_5'Flank|LRDD_uc009yck.1_RNA|LRDD_uc001lrk.1_Missense_Mutation_p.R781C|LRDD_uc001lrl.1_Missense_Mutation_p.R641C|LRDD_uc001lrm.1_Missense_Mutation_p.R485C|LRDD_uc001lrn.1_Missense_Mutation_p.R641C|LRDD_uc001lrp.1_3'UTR	NM_145886	NP_665893	Q9HB75	PIDD_HUMAN	leucine rich repeat and death domain containing	798	Death.				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGACCCAGACGCCCAGCCACA	0.692													3	10					0	0	0.009096	0	0	
MUC5B	727897	broad.mit.edu	37	11	1263879	1263879	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:1263879G>A	uc009ycr.1	+	47	7974	c.7848G>A	c.(7846-7848)ACG>ACA	p.T2616T	MUC5B_uc001ltb.2_Silent_p.T1926T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1923	7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CTGGATCCACGGCCACCCCGA	0.647													16	73					0	0	0.008361	0	0	
BRSK2	9024	broad.mit.edu	37	11	1467040	1467040	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:1467040C>T	uc001lti.2	+	12	1515	c.1129C>T	c.(1129-1131)CGG>TGG	p.R377W	BRSK2_uc009ycv.1_Missense_Mutation_p.R377W|BRSK2_uc001lth.1_Missense_Mutation_p.R377W|BRSK2_uc001ltj.2_Missense_Mutation_p.R377W|BRSK2_uc001ltk.2_RNA|BRSK2_uc001ltl.2_Missense_Mutation_p.R377W|BRSK2_uc001ltm.2_Missense_Mutation_p.R423W|BRSK2_uc001ltn.2_RNA|BRSK2_uc010qwx.1_RNA	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	377					establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CGGCAAGCGGCGGCCAGAACG	0.697													5	29					0	0	0.001984	0	0	
OSBPL5	114879	broad.mit.edu	37	11	3111807	3111807	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:3111807C>T	uc001lxk.2	-	20	2537	c.2379G>A	c.(2377-2379)CAG>CAA	p.Q793Q	OSBPL5_uc010qxq.1_Silent_p.Q704Q|OSBPL5_uc009ydw.2_Silent_p.Q725Q|OSBPL5_uc001lxl.2_Silent_p.Q725Q|OSBPL5_uc001lxj.2_Silent_p.Q247Q	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	793					cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		AGTCACCATCCTGCTCCTCGT	0.677													6	14					0	0	0.001168	0	0	
LOC650368	650368	broad.mit.edu	37	11	3423077	3423077	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:3423077G>A	uc010qxs.1	+	4		c.376G>A			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						TGGGCGGCACGCACTCTCCGT	0.567													4	26					0	0	0.009096	0	0	
ART5	116969	broad.mit.edu	37	11	3661166	3661166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:3661166G>A	uc001lyb.1	-	2	886	c.493C>T	c.(493-495)CTT>TTT	p.L165F	ART5_uc001lyc.1_Missense_Mutation_p.L165F|ART5_uc001lyd.2_Missense_Mutation_p.L165F|ART5_uc009yea.2_Missense_Mutation_p.L165F	NM_053017	NP_443750	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5 precursor	165						extracellular region	NAD(P)+-protein-arginine ADP-ribosyltransferase activity			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCAAAGCGAAGGCTGCCCACA	0.632													7	36					0	0	0.003080	0	0	
STIM1	6786	broad.mit.edu	37	11	4103494	4103494	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:4103494G>A	uc001lyv.2	+	8	1618	c.1050G>A	c.(1048-1050)TGG>TGA	p.W350*	STIM1_uc009yef.2_Nonsense_Mutation_p.W350*|STIM1_uc009yeg.2_Nonsense_Mutation_p.W177*	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	350	Cytoplasmic (Potential).|Potential.				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		TTCAGAAGTGGCTGCAGCTGA	0.517													18	41					0	0	0.012319	0	0	
STIM1	6786	broad.mit.edu	37	11	4112533	4112533	+	Silent	SNP	G	A	A	rs148209416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:4112533G>A	uc001lyv.2	+	12	2131	c.1563G>A	c.(1561-1563)TCG>TCA	p.S521S	STIM1_uc009yef.2_Missense_Mutation_p.G534R|STIM1_uc009yeg.2_Silent_p.S348S	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	521	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		ATTCCGATTCGGAGTCCTCCC	0.478													12	60					0	0	0.013537	0	0	
TRIM68	55128	broad.mit.edu	37	11	4621714	4621714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:4621714G>A	uc001lzf.1	-	7	1488	c.1250C>T	c.(1249-1251)CCG>CTG	p.P417L	TRIM68_uc001lzg.1_Missense_Mutation_p.P194L|TRIM68_uc010qyj.1_RNA	NM_018073	NP_060543	Q6AZZ1	TRI68_HUMAN	ring finger protein 137	417	B30.2/SPRY.				protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGGAGGGACCGGCAAGGACAG	0.532													13	44					0	0	0.002450	0	0	
OR51E1	143503	broad.mit.edu	37	11	4674693	4674693	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:4674693A>G	uc001lzi.3	+	2	1081	c.937A>G	c.(937-939)ACA>GCA	p.T313A		NM_152430	NP_689643	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E,	312	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(3)|pancreas(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCATGTGGCCACACACGCTTC	0.433													6	97					0	0	0.001168	0	0	
TRIM5	85363	broad.mit.edu	37	11	5699619	5699619	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:5699619G>A	uc001mbm.1	-	4	816	c.559C>T	c.(559-561)CAA>TAA	p.Q187*	TRIM5_uc001mbq.1_Nonsense_Mutation_p.Q187*|TRIM5_uc001mbl.1_RNA|TRIM5_uc001mbn.2_Nonsense_Mutation_p.Q187*|TRIM5_uc001mbo.2_Nonsense_Mutation_p.Q187*|TRIM5_uc001mbp.2_Nonsense_Mutation_p.Q187*	NM_033034	NP_149023	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform alpha	187	Potential.				interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		TCTCTCAGTTGCTCAAAATCT	0.463													22	64					0	0	0.002780	0	0	
CCKBR	887	broad.mit.edu	37	11	6291537	6291537	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:6291537G>A	uc001mcp.2	+	3	816	c.623G>A	c.(622-624)CGC>CAC	p.R208H	CCKBR_uc001mcq.2_Missense_Mutation_p.R136H|CCKBR_uc001mcr.2_Missense_Mutation_p.R208H|CCKBR_uc001mcs.2_Missense_Mutation_p.R208H|CCKBR_uc001mct.1_5'Flank	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	208	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	TGCGTGCATCGCTGGCCCAGT	0.582													4	36					0	0	0.009096	0	0	
CCKBR	887	broad.mit.edu	37	11	6292725	6292725	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:6292725G>A	uc001mcp.2	+	5	1489	c.1296G>A	c.(1294-1296)TCG>TCA	p.S432S	CCKBR_uc001mcq.2_Silent_p.S360S|CCKBR_uc001mcr.2_Silent_p.S415S|CCKBR_uc001mcs.2_Silent_p.S501S	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	432	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CCATTGCTTCGCTGTCCAGGC	0.652													11	39					0	0	0.013537	0	0	
APBB1	322	broad.mit.edu	37	11	6424925	6424925	+	Silent	SNP	G	T	T	rs139929849		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:6424925G>T	uc001mdb.1	-	3	949	c.849C>A	c.(847-849)CCC>CCA	p.P283P	APBB1_uc001mcz.1_5'Flank|APBB1_uc001mdd.3_Silent_p.P63P|APBB1_uc001mda.2_Intron|APBB1_uc001mdc.1_Silent_p.P283P|APBB1_uc010rab.1_5'Flank|APBB1_uc010rac.1_5'Flank|APBB1_uc010rad.1_5'Flank|APBB1_uc010rae.1_Silent_p.P48P|APBB1_uc010raf.1_Silent_p.P24P|APBB1_uc009yfa.2_Silent_p.P24P|APBB1_uc009yey.2_Silent_p.P24P|APBB1_uc010rag.1_Silent_p.P24P|APBB1_uc009yfb.2_Silent_p.P24P|APBB1_uc001mde.2_Silent_p.P24P|APBB1_uc010rah.1_Silent_p.P24P	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	283	WW.				apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		AGGCCCGGCCGGGGGGTTCCC	0.652													4	34					0.000602214	0.000636366	0.000602	1	0	
DCHS1	8642	broad.mit.edu	37	11	6655115	6655115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:6655115C>T	uc001mem.1	-	4	2533	c.2123G>A	c.(2122-2124)CGT>CAT	p.R708H		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	708	Cadherin 7.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTCATGGGCACGCAACCTCAG	0.557													7	61					0	0	0.001984	0	0	
DCHS1	8642	broad.mit.edu	37	11	6661810	6661810	+	Silent	SNP	C	T	T	rs143172918	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:6661810C>T	uc001mem.1	-	2	1445	c.1035G>A	c.(1033-1035)TCG>TCA	p.S345S		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	345	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACAAAGGCCGAGCCCAGCT	0.597													27	74					0	0	0.006320	0	0	
RBMXL2	27288	broad.mit.edu	37	11	7111248	7111248	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:7111248G>A	uc001mfc.2	+	1	1084	c.897G>A	c.(895-897)CCG>CCA	p.P299P		NM_014469	NP_055284	O75526	HNRGT_HUMAN	testes-specific heterogenous nuclear	299	Arg/Gly/Pro-rich.					nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GGGGGACACCGCCATCTTACG	0.662													3	11					0	0	0.009096	0	0	
CTR9	9646	broad.mit.edu	37	11	10793117	10793117	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:10793117G>T	uc001mja.2	+	19	2547	c.2398G>T	c.(2398-2400)GGA>TGA	p.G800*		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	800					histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		GAGTAAAGTGGGAGATAAAAT	0.318													12	94					5.16669e-11	5.7381e-11	0.010729	1	0	
PIK3C2A	5286	broad.mit.edu	37	11	17134211	17134211	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:17134211C>T	uc001mmq.3	-	20	3390	c.3324G>A	c.(3322-3324)TCG>TCA	p.S1108S	PIK3C2A_uc009ygu.1_Translation_Start_Site|PIK3C2A_uc010rcw.1_Silent_p.S728S|PIK3C2A_uc001mmr.3_Intron	NM_002645	NP_002636	O00443	P3C2A_HUMAN	phosphoinositide-3-kinase, class 2 alpha	1108					cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(4)|central_nervous_system(4)|stomach(1)|ovary(1)	10					Phosphatidylserine(DB00144)	AGAAGGAACACGACTGCAAAT	0.358													20	99					0	0	0.014323	0	0	
ABCC8	6833	broad.mit.edu	37	11	17483300	17483300	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:17483300G>T	uc001mnc.2	-	5	778	c.652C>A	c.(652-654)CTG>ATG	p.L218M	ABCC8_uc010rcy.1_Missense_Mutation_p.L218M	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	218	Cytoplasmic (By similarity).				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	AAGGGCTGCAGGAAGCGTACC	0.582													9	78					1.12685e-05	1.21448e-05	0.004482	1	0	
MYOD1	4654	broad.mit.edu	37	11	17741380	17741380	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:17741380C>T	uc001mni.2	+	1	271	c.51C>T	c.(49-51)GAC>GAT	p.D17D		NM_002478	NP_002469	P15172	MYOD1_HUMAN	myogenic differentiation 1	17					muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|skeletal muscle tissue development	nuclear chromatin|transcription factor complex	E-box binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription coactivator activity			breast(2)|ovary(1)	3						CGGCCCCCGACGGCTCTCTCT	0.657													8	39					0	0	0.006214	0	0	
E2F8	79733	broad.mit.edu	37	11	19256468	19256468	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:19256468C>T	uc001mpm.2	-	5	1111	c.589G>A	c.(589-591)GGG>AGG	p.G197R	E2F8_uc009yhv.2_RNA|E2F8_uc001mpn.3_Missense_Mutation_p.G197R	NM_024680	NP_078956	A0AVK6	E2F8_HUMAN	E2F family member 8	197					cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1						TTCTCCTCCCCGATGCTCTTC	0.433													6	52					0	0	0.001168	0	0	
KIF18A	81930	broad.mit.edu	37	11	28045380	28045380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:28045380G>A	uc001msc.2	-	16	2704	c.2522C>T	c.(2521-2523)TCG>TTG	p.S841L		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	841					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2						TGCAGTTAACGAACTGTTTGA	0.328													10	38					0	0	0.013537	0	0	
Unknown	0	broad.mit.edu	37	11	30926645	30926645	+	RNA	SNP	G	A	A	rs144668195		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:30926645G>A	uc001mss.1	-	9		c.1274C>T			uc009yjk.1_Missense_Mutation_p.R839W|uc009yjj.1_RNA					Homo sapiens mRNA for KIAA1493 protein, partial cds.																		GTCTTCATCCGTAAAGACAAT	0.403													9	32					0	0	0.004482	0	0	
CCDC73	493860	broad.mit.edu	37	11	32636061	32636061	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:32636061G>A	uc001mtv.2	-	16	1847	c.1803C>T	c.(1801-1803)TTC>TTT	p.F601F		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	601										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)					TGAATTGTTTGAATGGCTCAT	0.333													6	51					0	0	0.003080	0	0	
C11orf41	25758	broad.mit.edu	37	11	33566554	33566554	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:33566554A>G	uc001mup.3	+	2	2266	c.2142A>G	c.(2140-2142)CCA>CCG	p.P714P	C11orf41_uc001mun.1_Silent_p.P714P	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	708						integral to membrane				ovary(2)	2						CAGCCTTCCCATTCACACCAA	0.498													10	62					0	0	0.006214	0	0	
PDHX	8050	broad.mit.edu	37	11	35006241	35006241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:35006241C>T	uc001mvt.2	+	9	1674	c.1148C>T	c.(1147-1149)GCT>GTT	p.A383V	PDHX_uc010rep.1_Missense_Mutation_p.A368V|PDHX_uc010req.1_Missense_Mutation_p.A156V	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	383					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			GATGCTGCTGCTAAAGGTATC	0.388													21	87					0	0	0.012319	0	0	
CD44	960	broad.mit.edu	37	11	35211585	35211585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:35211585G>A	uc001mvu.2	+	5	1074	c.640G>A	c.(640-642)GAC>AAC	p.D214N	CD44_uc001mvv.2_Missense_Mutation_p.D214N|CD44_uc001mvw.2_Missense_Mutation_p.D214N|CD44_uc001mvx.2_Missense_Mutation_p.D214N|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Missense_Mutation_p.D214N|CD44_uc010rer.1_Missense_Mutation_p.D214N|CD44_uc009ykh.2_RNA|CD44_uc010res.1_5'UTR|CD44_uc010ret.1_RNA|CD44_uc010reu.1_5'UTR	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor	214	Extracellular (Potential).				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)	CTGGATCACCGACAGCACAGA	0.493													25	60					0	0	0.010818	0	0	
ACCS	84680	broad.mit.edu	37	11	44105261	44105261	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:44105261G>A	uc009yks.1	+	15	1569	c.1425G>A	c.(1423-1425)CAG>CAA	p.Q475Q	EXT2_uc010rfo.1_Intron|ACCS_uc001mxx.2_Silent_p.Q475Q	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	475							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4						AGAGGGTCCAGCAGGTGCTTG	0.617													3	22					0	0	0.004672	0	0	
EXT2	2132	broad.mit.edu	37	11	44135753	44135753	+	Silent	SNP	C	T	T	rs111364140		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:44135753C>T	uc001mxz.2	+	4	979	c.645C>T	c.(643-645)GGC>GGT	p.G215G	EXT2_uc010rfo.1_Silent_p.G243G|EXT2_uc001mxy.2_Silent_p.G228G|EXT2_uc009ykt.2_Silent_p.G215G|EXT2_uc001mya.2_Silent_p.G248G	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	215	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5						TGGCTGGTGGCGGCTTTTCTA	0.473			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				8	37					0	0	0.010729	0	0	
MADD	8567	broad.mit.edu	37	11	47298400	47298400	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:47298400G>A	uc001ner.1	+	5	1272	c.1081G>A	c.(1081-1083)GCA>ACA	p.A361T	MADD_uc001neq.2_Missense_Mutation_p.A361T|MADD_uc001nev.1_Missense_Mutation_p.A361T|MADD_uc001nes.1_Missense_Mutation_p.A361T|MADD_uc001net.1_Missense_Mutation_p.A361T|MADD_uc009yln.1_Missense_Mutation_p.A361T|MADD_uc001neu.1_Missense_Mutation_p.A361T|MADD_uc001nex.2_Missense_Mutation_p.A361T|MADD_uc001nez.2_Missense_Mutation_p.A361T|MADD_uc001new.2_Missense_Mutation_p.A361T	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	361	DENN.				activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)		CACCTGCATGGCATCAGCAGA	0.512													13	50					0	0	0.003163	0	0	
PTPRJ	5795	broad.mit.edu	37	11	48134376	48134376	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:48134376G>A	uc001ngp.3	+	3	548	c.193G>A	c.(193-195)GCA>ACA	p.A65T	PTPRJ_uc001ngo.3_Missense_Mutation_p.A65T	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	65	Extracellular (Potential).				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						CAGCAGTACAGCAGAATCCTT	0.448													11	113					0	0	0.001855	0	0	
OR4C15	81309	broad.mit.edu	37	11	55322311	55322311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:55322311G>A	uc010rig.1	+	1	529	c.529G>A	c.(529-531)GTG>ATG	p.V177M		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	123	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						TGATCGTTATGTGGCCATTTG	0.507										HNSCC(20;0.049)			8	69					0	0	0.004482	0	0	
OR5L1	219437	broad.mit.edu	37	11	55579394	55579394	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:55579394G>T	uc001nhw.1	+	1	452	c.452G>T	c.(451-453)TGT>TTT	p.C151F		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)				TGCTACTTCTGTGGGACGGTG	0.468													32	100					2.81731e-10	3.11857e-10	0.010818	1	0	
OR5D16	390144	broad.mit.edu	37	11	55606783	55606783	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:55606783C>A	uc010rio.1	+	1	556	c.556C>A	c.(556-558)CTG>ATG	p.L186M		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_epithelial(135;0.208)				GTTATCCTCCCTGATATCACT	0.418													14	73					2.61681e-11	2.91008e-11	0.002450	1	0	
OR5M8	219484	broad.mit.edu	37	11	56258583	56258583	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:56258583C>A	uc001nix.1	-	1	264	c.264G>T	c.(262-264)AAG>AAT	p.K88N		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	88	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)					AAATGCTTTTCTTCTCTGAAA	0.458													13	87					0.000219431	0.000233346	0.002450	1	0	
OR5M10	390167	broad.mit.edu	37	11	56345140	56345140	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:56345140C>T	uc001niz.1	-	1	58	c.58G>A	c.(58-60)GAC>AAC	p.D20N		NM_001004741	NP_001004741	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AGCACTGGGTCGTCTGTCAGT	0.458													24	100					0	0	0.003954	0	0	
OR9I1	219954	broad.mit.edu	37	11	57886596	57886596	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:57886596A>G	uc001nml.1	-	1	321	c.321T>C	c.(319-321)TGT>TGC	p.C107C	OR9Q1_uc001nmj.2_Intron	NM_001005211	NP_001005211	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I,	107	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Breast(21;0.0589)				CTGTGCCTGCACAGATGGTGA	0.542													8	38					0	0	0.004482	0	0	
GLYATL2	219970	broad.mit.edu	37	11	58604809	58604809	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:58604809T>C	uc001nnd.3	-	4	379	c.248A>G	c.(247-249)GAC>GGC	p.D83G	GLYATL2_uc009ymq.2_Missense_Mutation_p.D83G	NM_145016	NP_659453	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	83						mitochondrion	glycine N-acyltransferase activity			ovary(1)|skin(1)	2		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	CTCTAATTTGTCAGGAGCTTT	0.378													22	93					0	0	0.003330	0	0	
OR10V1	390201	broad.mit.edu	37	11	59480554	59480554	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:59480554G>A	uc001nof.1	-	1	765	c.765C>T	c.(763-765)TGC>TGT	p.C255C		NM_001005324	NP_001005324	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V,	255	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TAAAGCTGGTGCAGCCATACT	0.522													14	53					0	0	0.003163	0	0	
MRPL16	54948	broad.mit.edu	37	11	59574080	59574080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:59574080G>A	uc001noh.2	-	4	710	c.496C>T	c.(496-498)CGT>TGT	p.R166C		NM_017840	NP_060310	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16 precursor	166							rRNA binding			central_nervous_system(1)	1						AATTCACAACGCCCACCCATC	0.552													14	45					0	0	0.002450	0	0	
TMEM132A	54972	broad.mit.edu	37	11	60704376	60704376	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:60704376C>A	uc001nqj.2	+	11	3262	c.3069C>A	c.(3067-3069)TCC>TCA	p.S1023S	TMEM132A_uc001nqi.2_Silent_p.S1024S|TMEM132A_uc001nqm.2_Silent_p.S233S	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	1023	Cytoplasmic (Potential).|Confers cellular localization similar to full-length form (By similarity).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1						GGGGCAGCTCCTGACCCTCCA	0.647													5	15					1.23904e-05	1.33197e-05	0.000602	1	0	
SLC15A3	51296	broad.mit.edu	37	11	60707056	60707056	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:60707056T>C	uc001nqn.2	-	6	1565	c.1331A>G	c.(1330-1332)CAG>CGG	p.Q444R	SLC15A3_uc001nqo.2_Missense_Mutation_p.S388G	NM_016582	NP_057666	Q8IY34	S15A3_HUMAN	solute carrier family 15, member 3	444					oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0						CCCAATCTGCTGGGACACGGT	0.577													7	34					0	0	0.004482	0	0	
CD6	923	broad.mit.edu	37	11	60783258	60783258	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:60783258G>A	uc001nqq.2	+	9	1684	c.1461G>A	c.(1459-1461)GAG>GAA	p.E487E	CD6_uc001nqp.2_Silent_p.E487E|CD6_uc001nqr.2_Silent_p.E455E|CD6_uc001nqs.2_RNA|CD6_uc001nqt.2_Intron	NM_006725	NP_006716	P30203	CD6_HUMAN	CD6 molecule precursor	487	Cytoplasmic (Potential).				cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1						CAGACTATGAGCACTATGACT	0.627													10	36					0	0	0.006214	0	0	
DAK	26007	broad.mit.edu	37	11	61110231	61110231	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:61110231C>A	uc001nre.2	+	10	1037	c.780C>A	c.(778-780)TCC>TCA	p.S260S	DDB1_uc010rlf.1_5'Flank|DAK_uc009ynm.1_Silent_p.S190S	NM_015533	NP_056348	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2	260	DhaK.				glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding				0						CCGCAGGCTCCTCAGTTGTGA	0.622													7	22					1.26484e-09	1.39274e-09	0.003080	1	0	
AHNAK	79026	broad.mit.edu	37	11	62292451	62292451	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:62292451C>T	uc001ntl.2	-	5	9738	c.9438G>A	c.(9436-9438)TGG>TGA	p.W3146*	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	3146					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				TCTTCAGGTGCCAGTCTGGGC	0.488													51	251					0	0	0.014410	0	0	
METTL12	751071	broad.mit.edu	37	11	62433383	62433383	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:62433383C>T	uc001nug.1	+	2	291	c.32C>T	c.(31-33)CCG>CTG	p.P11L	C11orf48_uc001nue.2_Intron|C11orf48_uc001nuf.2_Intron|METTL12_uc001nuh.2_5'UTR|METTL12_uc010rmc.1_RNA	NM_001043229	NP_001036694	A8MUP2	MTL12_HUMAN	methyltransferase like 12 precursor	11						mitochondrion	methyltransferase activity				0						CTCCACTTGCCGAGCCTGATG	0.632													9	29					0	0	0.010729	0	0	
UBXN1	51035	broad.mit.edu	37	11	62446025	62446025	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:62446025A>G	uc001nul.1	-	3	294	c.162T>C	c.(160-162)ACT>ACC	p.T54T	UBXN1_uc001nuj.2_Silent_p.T54T|UBXN1_uc001num.1_Silent_p.T54T|UBXN1_uc001nuk.2_Silent_p.T19T|UBXN1_uc010rme.1_Silent_p.T54T|UBXN1_uc010rmf.1_Silent_p.T54T	NM_015853	NP_056937	Q04323	UBXN1_HUMAN	UBX domain protein 1	54	Interaction with BRCA1.				negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process	cytoplasm	ATPase binding|K6-linked polyubiquitin binding				0						GTCCAAGGGGAGTCTCTAAAG	0.612													13	51					0	0	0.008871	0	0	
PLCB3	5331	broad.mit.edu	37	11	64026040	64026040	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:64026040C>T	uc001nzb.2	+	11	1108	c.1108C>T	c.(1108-1110)CCG>TCG	p.P370S	PLCB3_uc009ypg.1_Missense_Mutation_p.P370S|PLCB3_uc009yph.1_Missense_Mutation_p.P303S|PLCB3_uc009ypi.2_Missense_Mutation_p.P370S	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	370	PI-PLC X-box.				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						GAAGGGACGGCCGCCTGAGGA	0.652													13	35					0	0	0.004007	0	0	
GPR137	56834	broad.mit.edu	37	11	64054479	64054479	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:64054479C>T	uc001nzg.1	+	3	708	c.400C>T	c.(400-402)CGA>TGA	p.R134*	BAD_uc001nzd.2_5'Flank|BAD_uc001nzc.2_5'Flank|GPR137_uc009ypj.1_Nonsense_Mutation_p.R140*|BAD_uc009ypk.2_5'Flank|GPR137_uc010rni.1_Nonsense_Mutation_p.R192*|GPR137_uc001nze.1_Nonsense_Mutation_p.R134*|GPR137_uc001nzf.2_Nonsense_Mutation_p.R134*|GPR137_uc001nzh.1_Nonsense_Mutation_p.R134*|GPR137_uc001nzi.2_Nonsense_Mutation_p.R134*|GPR137_uc010rnj.1_Nonsense_Mutation_p.R134*	NM_020155	NP_064540	Q96N19	G137A_HUMAN	G protein-coupled receptor 137	134	Cytoplasmic (Potential).					integral to membrane				central_nervous_system(1)	1						GGAGATGAGCCGAGGCTTGTA	0.532													3	10					0	0	0.004672	0	0	
SLC22A11	55867	broad.mit.edu	37	11	64329603	64329603	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:64329603G>A	uc001oai.2	+	3	999	c.625G>A	c.(625-627)GGC>AGC	p.G209S	SLC22A11_uc001oah.1_Missense_Mutation_p.R174Q|SLC22A11_uc001oaj.2_Missense_Mutation_p.G209S|SLC22A11_uc009ypq.2_Missense_Mutation_p.G209S|SLC22A11_uc001oak.1_Missense_Mutation_p.G38S	NM_018484	NP_060954	Q9NSA0	S22AB_HUMAN	solute carrier family 22 member 11	209	Helical; (Potential).				urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2					Probenecid(DB01032)	TGGGATGGCCGGCATCTTTCT	0.662											OREG0004030	type=REGULATORY REGION|Gene=SLC22A11|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	7	22					0	0	0.003080	0	0	
NRXN2	9379	broad.mit.edu	37	11	64428294	64428294	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:64428294G>A	uc001oar.2	-	11	2555	c.2116C>T	c.(2116-2118)CGA>TGA	p.R706*	NRXN2_uc001oas.2_Nonsense_Mutation_p.R675*|NRXN2_uc001oaq.2_Nonsense_Mutation_p.R373*	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	Error:Variant_position_missing_in_P58401_after_alignment					cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10						CAGCCTTCTCGACAGACGCCC	0.632													6	46					0	0	0.001984	0	0	
C11orf2	738	broad.mit.edu	37	11	64878997	64878997	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:64878997C>T	uc001ocr.1	+	10	2327	c.2287C>T	c.(2287-2289)CGC>TGC	p.R763C	TM7SF2_uc001oct.2_5'Flank|TM7SF2_uc010rny.1_5'Flank|TM7SF2_uc001ocu.2_5'Flank|TM7SF2_uc001ocv.2_5'Flank|C11orf2_uc001ocs.1_Missense_Mutation_p.R639C	NM_013265	NP_037397	Q9UID3	FFR_HUMAN	chromosome 11 open reading frame 2	763					lipid transport|protein transport	Golgi apparatus|integral to membrane					0						TGCTGCCCTGCGCTGCCCAGA	0.642													4	34					0	0	0.009096	0	0	
PELI3	246330	broad.mit.edu	37	11	66241301	66241301	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:66241301G>A	uc001oic.3	+	7	909	c.745G>A	c.(745-747)GAG>AAG	p.E249K	PELI3_uc001oib.2_Missense_Mutation_p.E249K|PELI3_uc001oid.3_Missense_Mutation_p.E225K|PELI3_uc001oie.3_Missense_Mutation_p.E100K|PELI3_uc010rpd.1_Missense_Mutation_p.E90K	NM_145065	NP_659502	Q8N2H9	PELI3_HUMAN	pellino 3 alpha isoform 1	249						cytosol	protein binding			ovary(1)	1						CGGCTTCTCCGAGGACTCAGC	0.652													9	25					0	0	0.006214	0	0	
DPP3	10072	broad.mit.edu	37	11	66262922	66262922	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:66262922C>T	uc001oig.1	+	14	1601	c.1539C>T	c.(1537-1539)AGC>AGT	p.S513S	DPP3_uc001oif.1_Silent_p.S513S|DPP3_uc010rpe.1_Silent_p.S502S|DPP3_uc001oih.1_5'Flank	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	513					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2						GGGCTGAGAGCGTGGGTCTCT	0.642													5	13					0	0	0.001168	0	0	
SPTBN2	6712	broad.mit.edu	37	11	66475139	66475139	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:66475139G>A	uc001ojd.2	-	12	1573	c.1501C>T	c.(1501-1503)CGC>TGC	p.R501C		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	501	Spectrin 2.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						GCGGCGATGCGCTTGATGTCG	0.687													4	18					0	0	0.000602	0	0	
SSH3	54961	broad.mit.edu	37	11	67076941	67076941	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:67076941C>T	uc001okj.2	+	11	1313	c.1135C>T	c.(1135-1137)CGC>TGC	p.R379C	SSH3_uc001okk.2_RNA|SSH3_uc001okl.2_Missense_Mutation_p.R233C	NM_017857	NP_060327	Q8TE77	SSH3_HUMAN	slingshot homolog 3	379	Tyrosine-protein phosphatase.				regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton|nucleus	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CCACAATGTGCGCCTCTGGGA	0.617													4	24					0	0	0.001168	0	0	
CARNS1	57571	broad.mit.edu	37	11	67191613	67191613	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:67191613C>T	uc009yrp.2	+	9	2477	c.2025C>T	c.(2023-2025)AAC>AAT	p.N675N	PPP1CA_uc001okx.1_5'Flank|CARNS1_uc001olc.3_Silent_p.N814N	NM_020811	NP_065862	A5YM72	CRNS1_HUMAN	ATP-grasp domain containing 1	675	ATP-grasp.				carnosine biosynthetic process		ATP binding|carnosine synthase activity|metal ion binding				0						GAGTCTTCAACGTGGAGCTCA	0.627													5	20					0	0	0.000602	0	0	
NUMA1	4926	broad.mit.edu	37	11	71725087	71725087	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:71725087C>T	uc001orl.1	-	15	3634	c.3462G>A	c.(3460-3462)CGG>CGA	p.R1154R	NUMA1_uc009ysw.1_Silent_p.R717R|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Silent_p.R1154R|NUMA1_uc001orn.2_Silent_p.R717R|NUMA1_uc009ysx.1_Silent_p.R1154R|NUMA1_uc001oro.1_Silent_p.R1154R	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1154	Potential.				G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8						CCCGGGAGGCCCGCTCAGCCT	0.647			T	RARA	APL								4	42					0	0	0.000602	0	0	
NUMA1	4926	broad.mit.edu	37	11	71725245	71725245	+	Missense_Mutation	SNP	C	T	T	rs140741340	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:71725245C>T	uc001orl.1	-	15	3476	c.3304G>A	c.(3304-3306)GCA>ACA	p.A1102T	NUMA1_uc009ysw.1_Missense_Mutation_p.A665T|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Missense_Mutation_p.A1102T|NUMA1_uc001orn.2_Missense_Mutation_p.A665T|NUMA1_uc009ysx.1_Missense_Mutation_p.A1102T|NUMA1_uc001oro.1_Missense_Mutation_p.A1102T	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1102	Potential.				G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8						GAGCCAGATGCGTGCTCCTTT	0.577			T	RARA	APL								20	73					0	0	0.010504	0	0	
C11orf51	25906	broad.mit.edu	37	11	71821248	71821248	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:71821248C>A	uc001orw.2	-	5	426	c.204G>T	c.(202-204)GAG>GAT	p.E68D	LRTOMT_uc010rqv.1_3'UTR|LRTOMT_uc010rqw.1_3'UTR|LRTOMT_uc001ors.3_3'UTR|C11orf51_uc009ytc.1_Missense_Mutation_p.E59D|C11orf51_uc001orv.2_Missense_Mutation_p.E68D	NM_014042	NP_054761	P60006	CK051_HUMAN	hypothetical protein LOC25906	68	Asp-rich.					intracellular					0						cttcatcatcctcttcttcct	0.348													22	145					2.89027e-11	3.21205e-11	0.014323	1	0	
RELT	84957	broad.mit.edu	37	11	73106159	73106159	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:73106159G>A	uc001otv.2	+	10	1239	c.1074G>A	c.(1072-1074)CAG>CAA	p.Q358Q	RELT_uc001otw.2_Silent_p.Q358Q|RELT_uc001otx.2_RNA	NM_152222	NP_689408	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor precursor	358	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane	binding|receptor activity			upper_aerodigestive_tract(1)	1						tTCCTGAGCAGCGGACAAGTT	0.348													12	46					0	0	0.001855	0	0	
DNAJB13	374407	broad.mit.edu	37	11	73679454	73679454	+	Missense_Mutation	SNP	G	A	A	rs147921001	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:73679454G>A	uc001ouo.2	+	6	1422	c.671G>A	c.(670-672)CGC>CAC	p.R224H		NM_153614	NP_705842	P59910	DJB13_HUMAN	testis spermatogenesis apoptosis-related protein	224					apoptosis|protein folding|spermatogenesis		heat shock protein binding|unfolded protein binding				0	Breast(11;7.42e-05)					CCTCGCTTCCGCAGGGAGAAT	0.552													7	31					0	0	0.004482	0	0	
RSF1	51773	broad.mit.edu	37	11	77386207	77386207	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:77386207G>A	uc001oyn.2	-	14	3556	c.3436C>T	c.(3436-3438)CGT>TGT	p.R1146C	RSF1_uc001oym.2_Missense_Mutation_p.R894C	NM_016578	NP_057662	Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1146	Arg-rich.				CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CTCAGTCTACGGCTACAAAAG	0.468													14	50					0	0	0.003163	0	0	
KCTD21	283219	broad.mit.edu	37	11	77884897	77884897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:77884897C>T	uc001ozb.2	-	2	779	c.704G>A	c.(703-705)GGC>GAC	p.G235D		NM_001029859	NP_001025030	Q4G0X4	KCD21_HUMAN	potassium channel tetramerisation domain	235						voltage-gated potassium channel complex	voltage-gated potassium channel activity			pancreas(1)	1	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.46e-24)			GATGCAGAAGCCATCGCTCAG	0.473													32	129					0	0	0.013726	0	0	
PRCP	5547	broad.mit.edu	37	11	82560971	82560971	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:82560971G>A	uc001ozs.2	-	5	849	c.736C>T	c.(736-738)CGA>TGA	p.R246*	PRCP_uc001ozr.2_Nonsense_Mutation_p.R267*	NM_005040	NP_005031	P42785	PCP_HUMAN	prolylcarboxypeptidase isoform 1 preproprotein	246	SKS domain.				blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1						TTTGAGAGTCGATTAATGGCA	0.353													17	71					0	0	0.008871	0	0	
CCDC83	220047	broad.mit.edu	37	11	85622403	85622403	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:85622403A>T	uc001pbh.1	+	8	1264	c.752A>T	c.(751-753)GAT>GTT	p.D251V	CCDC83_uc001pbg.1_Missense_Mutation_p.D251V|CCDC83_uc001pbi.1_RNA|CCDC83_uc001pbj.1_Missense_Mutation_p.D152V	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	251	Potential.									skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GTGCTTATTGATCAACTATCC	0.333													12	104					0	0	0.002450	0	0	
CCDC81	60494	broad.mit.edu	37	11	86123507	86123507	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:86123507C>A	uc001pbx.1	+	11	1725	c.1297C>A	c.(1297-1299)CTG>ATG	p.L433M	CCDC81_uc001pbw.1_Missense_Mutation_p.L343M|CCDC81_uc010rtq.1_Missense_Mutation_p.L216M|CCDC81_uc001pby.1_Missense_Mutation_p.L168M	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	433										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				CCGGAGTCTCCTGAAACAAAT	0.428													13	86					3.27435e-08	3.57726e-08	0.002450	1	0	
Unknown	0	broad.mit.edu	37	11	89385730	89385730	+	RNA	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:89385730T>C	uc001pcz.2	+	1		c.17T>C								Homo sapiens mRNA for hypothetical protein, partial cds, clone:Hsa11-digit35-15-11-R.																		TATTGTACCATCTTTCAGTGC	0.338													4	94					0	0	0.009096	0	0	
CEP57	9702	broad.mit.edu	37	11	95564282	95564282	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:95564282A>G	uc001pfp.1	+	11	1586	c.1365A>G	c.(1363-1365)GGA>GGG	p.G455G	CEP57_uc010ruh.1_Silent_p.G446G|CEP57_uc010rui.1_Silent_p.G429G|CEP57_uc009ywn.1_Silent_p.G303G|CEP57_uc001pfq.1_Silent_p.G429G|CEP57_uc001pfr.1_Silent_p.G303G	NM_014679	NP_055494	Q86XR8	CEP57_HUMAN	translokin	455	Mediates interaction with microtubules (By similarity).|Potential.				fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCCGTTCTGGAATCACAGGGA	0.378									Mosaic_Variegated_Aneuploidy_Syndrome				12	59					0	0	0.008871	0	0	
CNTN5	53942	broad.mit.edu	37	11	100211310	100211310	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:100211310C>T	uc001pga.2	+	22	3185	c.2846C>T	c.(2845-2847)ACA>ATA	p.T949I	CNTN5_uc001pgb.2_Missense_Mutation_p.T875I|CNTN5_uc010ruk.1_Missense_Mutation_p.T220I	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	949	Fibronectin type-III 3.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TATCACTTCACAGTGAGGGCT	0.443													5	52					0	0	0.000602	0	0	
DYNC2H1	79659	broad.mit.edu	37	11	103090682	103090682	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:103090682G>T	uc001pho.2	+	56	9015	c.8871G>T	c.(8869-8871)AAG>AAT	p.K2957N	DYNC2H1_uc001phn.1_Missense_Mutation_p.K2957N|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2957	Potential.|Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AAAGACTGAAGCACAGAATAG	0.269													5	32					0.000157383	0.000167469	0.003080	1	0	
DYNC2H1	79659	broad.mit.edu	37	11	103128425	103128425	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:103128425G>A	uc001pho.2	+	69	10694	c.10550G>A	c.(10549-10551)CGT>CAT	p.R3517H	DYNC2H1_uc001phn.1_Missense_Mutation_p.R3524H|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3517					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AACATGTACCGTTTTAGTTTG	0.428													5	14					0	0	0.000602	0	0	
NPAT	4863	broad.mit.edu	37	11	108031665	108031665	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:108031665C>T	uc001pjz.3	-	17	4250	c.4148G>A	c.(4147-4149)CGT>CAT	p.R1383H	NPAT_uc010rvv.1_Missense_Mutation_p.R439H	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	1383					positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		ACTAGAAGGACGAGAGTTTCG	0.333													7	37					0	0	0.003080	0	0	
DLAT	1737	broad.mit.edu	37	11	111922036	111922036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:111922036G>A	uc001pmo.2	+	11	2136	c.1477G>A	c.(1477-1479)GAA>AAA	p.E493K	DLAT_uc009yyk.1_Missense_Mutation_p.E388K|DLAT_uc010rwr.1_Missense_Mutation_p.E366K	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	493	Catalytic (By similarity).				glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	AAAAGTTCCCGAAGCAAATTC	0.348													13	54					0	0	0.002450	0	0	
DRD2	1813	broad.mit.edu	37	11	113286314	113286314	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:113286314A>G	uc001pnz.2	-	4	873	c.552T>C	c.(550-552)ATT>ATC	p.I184I	DRD2_uc010rwv.1_Silent_p.I183I|DRD2_uc001poa.3_Silent_p.I184I|DRD2_uc001pob.3_Silent_p.I184I|DRD2_uc009yyr.1_Silent_p.I184I	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long	184	Extracellular (By similarity).				activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)|skin(1)	2		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)	CCGGGTTGGCAATGATGCACT	0.582													3	18					0	0	0.004672	0	0	
NNMT	4837	broad.mit.edu	37	11	114168792	114168792	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:114168792C>T	uc001por.1	+	4	538	c.274C>T	c.(274-276)CAG>TAG	p.Q92*	NNMT_uc001pos.1_Nonsense_Mutation_p.Q92*	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	92					xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	CCAGAACCTGCAGGAGCTGGA	0.517													9	75					0	0	0.001855	0	0	
DSCAML1	57453	broad.mit.edu	37	11	117651330	117651330	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:117651330G>A	uc001prh.1	-	2	424	c.422C>T	c.(421-423)ACG>ATG	p.T141M	DSCAML1_uc001pri.1_Translation_Start_Site	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	81	Extracellular (Potential).|Ig-like C2-type 1.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GAGCTGCAGCGTCCCGTTGGC	0.657													12	64					0	0	0.003163	0	0	
TMPRSS4	56649	broad.mit.edu	37	11	117985906	117985906	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:117985906C>T	uc010rxo.1	+	11	1354	c.1063C>T	c.(1063-1065)CGG>TGG	p.R355W	TMPRSS4_uc010rxp.1_Missense_Mutation_p.R350W|TMPRSS4_uc010rxq.1_Missense_Mutation_p.R208W|TMPRSS4_uc010rxr.1_Missense_Mutation_p.R330W|TMPRSS4_uc010rxs.1_Missense_Mutation_p.R315W|TMPRSS4_uc009yzu.2_Intron|TMPRSS4_uc010rxt.1_Missense_Mutation_p.R330W	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	355	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TGACAGCACACGGTGCAATGC	0.577													4	13					0	0	0.000602	0	0	
CD3E	916	broad.mit.edu	37	11	118183570	118183570	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:118183570T>C	uc001psq.3	+	6	597	c.341T>C	c.(340-342)CTG>CCG	p.L114P	CD3E_uc010rya.1_Missense_Mutation_p.L114P	NM_000733	NP_000724	P07766	CD3E_HUMAN	CD3E antigen, epsilon polypeptide precursor	114	Extracellular (Potential).				G-protein coupled receptor protein signaling pathway|signal complex assembly|T cell costimulation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	external side of plasma membrane|integral to plasma membrane	protein heterodimerization activity|protein kinase binding|receptor signaling complex scaffold activity|receptor signaling protein activity|SH3 domain binding|T cell receptor binding|transmembrane receptor activity			ovary(2)	2	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)	TATCTCTACCTGAGGGCAAGA	0.473													11	52					0	0	0.010729	0	0	
OAF	220323	broad.mit.edu	37	11	120096485	120096485	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:120096485C>T	uc001pxb.2	+	2	588	c.347C>T	c.(346-348)GCC>GTC	p.A116V		NM_178507	NP_848602	Q86UD1	OAF_HUMAN	OAF homolog precursor	116											0		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		CCCAGTGAGGCCATGGCCAAG	0.672													20	65					0	0	0.002780	0	0	
GRIK4	2900	broad.mit.edu	37	11	120702613	120702613	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:120702613G>A	uc001pxn.2	+	7	851	c.564G>A	c.(562-564)ACG>ACA	p.T188T	GRIK4_uc009zav.1_Silent_p.T188T|GRIK4_uc009zaw.1_Silent_p.T188T|GRIK4_uc009zax.1_Silent_p.T188T	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	188	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	CCAAGGACACGCTGTCCGTCC	0.607													5	51					0	0	0.001168	0	0	
TBCEL	219899	broad.mit.edu	37	11	120925921	120925921	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:120925921G>A	uc009zay.2	+	5	694	c.616G>A	c.(616-618)GTC>ATC	p.V206I	TBCEL_uc001pxo.2_Missense_Mutation_p.V206I|TBCEL_uc001pxp.2_Missense_Mutation_p.V62I|TBCEL_uc001pxq.2_Intron	NM_001130047	NP_001123519	Q5QJ74	TBCEL_HUMAN	tubulin folding cofactor E-like	206	LRR 6.					cytoplasm|cytoskeleton				skin(1)	1		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)		GGATACCCTCGTCCTGGCCAA	0.428													6	51					0	0	0.001984	0	0	
KCNJ1	3758	broad.mit.edu	37	11	128709289	128709289	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:128709289A>G	uc001qeo.1	-	2	958	c.907T>C	c.(907-909)TCC>CCC	p.S303P	KCNJ1_uc001qep.1_Missense_Mutation_p.S284P|KCNJ1_uc001qeq.1_Missense_Mutation_p.S284P|KCNJ1_uc001qer.1_Missense_Mutation_p.S284P|KCNJ1_uc001qes.1_Missense_Mutation_p.S284P	NM_000220	NP_000211	P48048	IRK1_HUMAN	potassium inwardly-rectifying channel J1 isoform	303	Cytoplasmic (By similarity).				excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)	GCACTGGTGGACTCCACTGTG	0.512													12	53					0	0	0.013537	0	0	
ARHGAP32	9743	broad.mit.edu	37	11	128842510	128842510	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:128842510A>G	uc009zcp.2	-	21	3849	c.3849T>C	c.(3847-3849)GCT>GCC	p.A1283A	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Silent_p.A242A|ARHGAP32_uc001qez.2_Silent_p.A934A	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1283					cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5						TGGGTTGTTCAGCCACATCCC	0.562													8	55					0	0	0.006214	0	0	
APLP2	334	broad.mit.edu	37	11	129992333	129992333	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:129992333T>C	uc010sby.1	+	6	1004	c.847T>C	c.(847-849)TAC>CAC	p.Y283H	APLP2_uc001qfp.2_Missense_Mutation_p.Y283H|APLP2_uc001qfq.2_Missense_Mutation_p.Y283H|APLP2_uc010sbz.1_Missense_Mutation_p.Y127H|APLP2_uc001qfr.2_Missense_Mutation_p.Y105H|APLP2_uc001qfs.2_Intron|APLP2_uc001qfv.2_Missense_Mutation_p.Y230H	NM_001642	NP_001633	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	283	Extracellular (Potential).				G-protein coupled receptor protein signaling pathway	integral to membrane|nucleus|plasma membrane	DNA binding|identical protein binding|serine-type endopeptidase inhibitor activity			ovary(3)	3	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)		AGGAGATGACTACAATGAGGA	0.363													13	74					0	0	0.002450	0	0	
LRTM2	654429	broad.mit.edu	37	12	1943444	1943444	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:1943444G>A	uc001qjt.2	+	5	1476	c.670G>A	c.(670-672)GAC>AAC	p.D224N	CACNA2D4_uc001qjp.2_Intron|CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron|LRTM2_uc001qju.2_Missense_Mutation_p.D224N|LRTM2_uc010sdx.1_Missense_Mutation_p.D224N|LRTM2_uc001qjv.2_5'UTR	NM_001039029	NP_001034118	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	224	LRRCT.|Extracellular (Potential).					integral to membrane				large_intestine(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)			GGGACGCTTGGACCAGCTTGC	0.592													5	20					0	0	0.000602	0	0	
CACNA1C	775	broad.mit.edu	37	12	2566787	2566787	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:2566787C>T	uc009zdu.1	+	5	985	c.672C>T	c.(670-672)CTC>CTT	p.L224L	CACNA1C_uc009zdv.1_Silent_p.L224L|CACNA1C_uc001qkb.2_Silent_p.L224L|CACNA1C_uc001qkc.2_Silent_p.L224L|CACNA1C_uc001qke.2_Silent_p.L224L|CACNA1C_uc001qkf.2_Silent_p.L224L|CACNA1C_uc001qjz.2_Silent_p.L224L|CACNA1C_uc001qkd.2_Silent_p.L224L|CACNA1C_uc001qkg.2_Silent_p.L224L|CACNA1C_uc009zdw.1_Silent_p.L224L|CACNA1C_uc001qkh.2_Silent_p.L224L|CACNA1C_uc001qkl.2_Silent_p.L224L|CACNA1C_uc001qkn.2_Silent_p.L224L|CACNA1C_uc001qko.2_Silent_p.L224L|CACNA1C_uc001qkp.2_Silent_p.L224L|CACNA1C_uc001qkr.2_Silent_p.L224L|CACNA1C_uc001qku.2_Silent_p.L224L|CACNA1C_uc001qkq.2_Silent_p.L224L|CACNA1C_uc001qks.2_Silent_p.L224L|CACNA1C_uc001qkt.2_Silent_p.L224L|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_5'UTR|CACNA1C_uc001qkj.1_5'UTR|CACNA1C_uc001qkk.1_5'UTR|CACNA1C_uc001qkm.1_5'UTR	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	224	Extracellular (Potential).|I.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CAAACGCTCTCGGAGGGAAAG	0.552													16	93					0	0	0.006122	0	0	
CACNA1C	775	broad.mit.edu	37	12	2602496	2602496	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:2602496A>G	uc009zdu.1	+	7	1370	c.1057A>G	c.(1057-1059)ATG>GTG	p.M353V	CACNA1C_uc009zdv.1_Missense_Mutation_p.M350V|CACNA1C_uc001qkb.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkc.2_Missense_Mutation_p.M353V|CACNA1C_uc001qke.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkf.2_Missense_Mutation_p.M353V|CACNA1C_uc001qjz.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkd.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkg.2_Missense_Mutation_p.M353V|CACNA1C_uc009zdw.1_Missense_Mutation_p.M353V|CACNA1C_uc001qkh.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkl.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkn.2_Missense_Mutation_p.M353V|CACNA1C_uc001qko.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkp.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkr.2_Missense_Mutation_p.M353V|CACNA1C_uc001qku.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkq.2_Missense_Mutation_p.M353V|CACNA1C_uc001qks.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkt.2_Missense_Mutation_p.M353V|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_Missense_Mutation_p.M89V|CACNA1C_uc001qkj.1_Missense_Mutation_p.M89V|CACNA1C_uc001qkk.1_Missense_Mutation_p.M89V|CACNA1C_uc001qkm.1_Missense_Mutation_p.M89V	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	353	I.|Extracellular (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TGCCTTCGCCATGCTCACGGT	0.627													28	157					0	0	0.003271	0	0	
CCND2	894	broad.mit.edu	37	12	4385203	4385203	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:4385203C>T	uc001qmo.2	+	2	533	c.228C>T	c.(226-228)GTC>GTT	p.V76V		NM_001759	NP_001750	P30279	CCND2_HUMAN	cyclin D2	76	Cyclin N-terminal.				cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			haematopoietic_and_lymphoid_tissue(1)|breast(1)|kidney(1)	3			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			AAGAAGAGGTCTTCCCTCTGG	0.552			T	IGL@	NHL,CLL								7	63					0	0	0.003080	0	0	
ACRBP	84519	broad.mit.edu	37	12	6752705	6752705	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:6752705C>T	uc001qpu.1	-	6	1125	c.1077G>A	c.(1075-1077)TCG>TCA	p.S359S	ACRBP_uc010sfg.1_Silent_p.S326S	NM_032489	NP_115878	Q8NEB7	ACRBP_HUMAN	proacrosin binding protein sp32 precursor	359						acrosomal vesicle|extracellular region				central_nervous_system(1)	1						GCTGGCATACCGACTTCCCGA	0.542													6	39					0	0	0.006214	0	0	
MLF2	8079	broad.mit.edu	37	12	6861114	6861114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:6861114G>A	uc010sfi.1	-	3	220	c.157C>T	c.(157-159)CCT>TCT	p.P53S	MLF2_uc001qqp.2_Missense_Mutation_p.P53S|MLF2_uc009zey.1_Missense_Mutation_p.P53S	NM_005439	NP_005430	Q15773	MLF2_HUMAN	myeloid leukemia factor 2	53					defense response	cytoplasm|nucleus	protein binding			large_intestine(1)	1						CGGCTGGCAGGCCTGGTCCCT	0.507													8	39					0	0	0.003080	0	0	
TPI1	7167	broad.mit.edu	37	12	6978878	6978878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:6978878G>A	uc001qrk.2	+	5	522	c.484G>A	c.(484-486)GTC>ATC	p.V162I	TPI1_uc010sfo.1_Missense_Mutation_p.V80I	NM_000365	NP_000356	P60174	TPIS_HUMAN	triosephosphate isomerase 1 isoform 1	162					fatty acid biosynthetic process|gluconeogenesis|glycolysis|pentose-phosphate shunt	cytosol	triose-phosphate isomerase activity				0						GAGCAAGGTCGTCCTGGCCTA	0.587											OREG0021638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	20	75					0	0	0.003330	0	0	
NECAP1	25977	broad.mit.edu	37	12	8245544	8245544	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:8245544C>T	uc001qtx.2	+	6	647	c.569C>T	c.(568-570)CCG>CTG	p.P190L	NECAP1_uc001qty.2_Missense_Mutation_p.P48L	NM_015509	NP_056324	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	190					endocytosis|protein transport	clathrin coated vesicle membrane|plasma membrane				ovary(1)	1				Kidney(36;0.0915)		CTCCCACCCCCGCCAGGAGGC	0.512													44	85					0	0	0.013114	0	0	
RIMKLB	57494	broad.mit.edu	37	12	8926004	8926004	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:8926004G>A	uc001quu.2	+	6	1036	c.785G>A	c.(784-786)GGC>GAC	p.G262D	RIMKLB_uc009zgf.1_RNA|RIMKLB_uc001qux.2_Missense_Mutation_p.G262D|RIMKLB_uc010sgl.1_Missense_Mutation_p.G262D|RIMKLB_uc001quw.2_Missense_Mutation_p.G262D	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	262	ATP-grasp.				protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						GATGTGTGTGGCATTGATCTG	0.468													23	101					0	0	0.014323	0	0	
A2M	2	broad.mit.edu	37	12	9246138	9246138	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:9246138C>T	uc001qvk.1	-	18	2276	c.2163G>A	c.(2161-2163)GTG>GTA	p.V721V	A2M_uc009zgk.1_Silent_p.V571V	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	721	Bait region.|Inhibitory.				blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	CTTCAACATGCACCAGGCGTG	0.443													9	40					0	0	0.006214	0	0	
PZP	5858	broad.mit.edu	37	12	9305467	9305467	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:9305467G>A	uc001qvl.2	-	31	4103	c.4074C>T	c.(4072-4074)TGC>TGT	p.C1358C	PZP_uc009zgl.2_Silent_p.C1144C	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						TGTGTCCATCGCAAGTTTGGG	0.438													12	72					0	0	0.001855	0	0	
GABARAPL1	23710	broad.mit.edu	37	12	10374385	10374385	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:10374385G>A	uc001qxs.2	+	4	529	c.289_splice	c.e4-1	p.D97_splice	GABARAPL1_uc001qxt.2_Splice_Site|GABARAPL1_uc001qxu.2_Splice_Site	NM_031412	NP_113600	Q9H0R8	GBRL1_HUMAN	GABA(A) receptor-associated protein like 1							autophagic vacuole|endoplasmic reticulum|Golgi apparatus|membrane|microtubule	beta-tubulin binding|GABA receptor binding				0						TCTTCCCCTAGGACAATCATG	0.284													6	28					0	0	0.001984	0	0	
TAS2R50	259296	broad.mit.edu	37	12	11139175	11139175	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:11139175G>A	uc001qzl.2	-	1	337	c.285C>T	c.(283-285)AGC>AGT	p.S95S	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176890	NP_795371	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	95	Helical; Name=3; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(2)	2						CAAGCCACATGCTGAAATGGT	0.338													16	138					0	0	0.006122	0	0	
PRB1	5542	broad.mit.edu	37	12	11506766	11506766	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:11506766G>A	uc001qzw.1	-	3	308	c.271C>T	c.(271-273)CGA>TGA	p.R91*	PRB1_uc001qzu.1_Nonsense_Mutation_p.R91*|PRB1_uc001qzv.1_Nonsense_Mutation_p.R91*	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	152	5.|15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in clone CP-4).|Missing (in clone CP-5).|Missing (in allele S).|Missing (in allele M).			extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGAGGAGATCGGGGACTTCGG	0.612													50	80					0	0	0.014410	0	0	
MANSC1	54682	broad.mit.edu	37	12	12491444	12491444	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:12491444G>A	uc001rai.1	-	3	532	c.274C>T	c.(274-276)CAA>TAA	p.Q92*	MANSC1_uc010shm.1_Nonsense_Mutation_p.Q26*|MANSC1_uc001raj.1_Nonsense_Mutation_p.Q58*|MANSC1_uc009zht.1_Nonsense_Mutation_p.Q11*	NM_018050	NP_060520	Q9H8J5	MANS1_HUMAN	MANSC domain containing 1 precursor	92	MANSC.|Extracellular (Potential).					integral to membrane					0		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		CAGTTGGGTTGTCTAGCTGTT	0.393													14	80					0	0	0.004007	0	0	
ATF7IP	55729	broad.mit.edu	37	12	14650841	14650841	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:14650841T>C	uc001rbw.2	+	15	3805	c.3647T>C	c.(3646-3648)ATT>ACT	p.I1216T	ATF7IP_uc001rbx.2_Missense_Mutation_p.I1215T|ATF7IP_uc001rby.3_Missense_Mutation_p.I1216T|ATF7IP_uc001rca.2_Missense_Mutation_p.I1216T	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	1216	Interaction with MBD1.|Fibronectin type-III.				DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						TGGAAAAAGATTGGGGAAGTC	0.483													11	71					0	0	0.010729	0	0	
ABCC9	10060	broad.mit.edu	37	12	22005044	22005044	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:22005044T>C	uc001rfi.1	-	22	2776	c.2756A>G	c.(2755-2757)CAA>CGA	p.Q919R	ABCC9_uc001rfh.2_Missense_Mutation_p.Q919R|ABCC9_uc001rfj.1_Missense_Mutation_p.Q883R	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	919	Cytoplasmic (Potential).				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TTCTAATTCTTGATCTTGCCG	0.333													7	46					0	0	0.006214	0	0	
ABCC9	10060	broad.mit.edu	37	12	22015949	22015949	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:22015949A>G	uc001rfi.1	-	18	2297	c.2277T>C	c.(2275-2277)CCT>CCC	p.P759P	ABCC9_uc001rfh.2_Silent_p.P759P|ABCC9_uc001rfj.1_Silent_p.P723P	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	759	Cytoplasmic (Potential).|ABC transporter 1.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TTAATAGCCAAGGCTTTTGAG	0.338													4	42					0	0	0.000602	0	0	
SOX5	6660	broad.mit.edu	37	12	23893839	23893839	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:23893839G>A	uc001rfw.2	-	5	805	c.703C>T	c.(703-705)CGT>TGT	p.R235C	SOX5_uc001rfx.2_Missense_Mutation_p.R222C|SOX5_uc001rfy.2_Missense_Mutation_p.R222C|SOX5_uc010siv.1_Missense_Mutation_p.R222C|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Missense_Mutation_p.R187C	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	235	Potential.				transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						ATTTGCTGACGCTGTTTCTCA	0.493													8	35					0	0	0.006214	0	0	
CASC1	55259	broad.mit.edu	37	12	25267796	25267796	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:25267796A>G	uc001rgl.2	-	12	1469	c.1387T>C	c.(1387-1389)TGG>CGG	p.W463R	CASC1_uc001rgk.2_Missense_Mutation_p.W469R|CASC1_uc001rgm.3_Missense_Mutation_p.W527R|CASC1_uc001rgj.2_Missense_Mutation_p.W423R|CASC1_uc010sje.1_Missense_Mutation_p.W404R|CASC1_uc010sjf.1_Missense_Mutation_p.W351R|CASC1_uc010sjg.1_3'UTR	NM_001082973	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1 isoform b	463										ovary(2)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			TCAGTTCTCCAATGTTTACCT	0.343													6	32					0	0	0.001168	0	0	
KRAS	3845	broad.mit.edu	37	12	25398281	25398281	+	Missense_Mutation	SNP	C	T	T	rs112445441		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:25398281C>T	uc001rgp.1	-	2	219	c.38G>A	c.(37-39)GGC>GAC	p.G13D	KRAS_uc001rgq.1_Missense_Mutation_p.G13D|KRAS_uc001rgr.2_RNA	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	13	GTP.		G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway).|G -> D (in a breast carcinoma cell line and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G13D(2647)|p.G13C(182)|p.G13S(58)|p.G13R(41)|p.G13V(27)|p.G13A(24)|p.G13G(11)|p.G13E(4)|p.G12_G13insG(4)|p.G13N(3)|p.G13I(1)|p.G13_V14>DI(1)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CTTGCCTACGCCACCAGCTCC	0.338	G13D(NCIH647_LUNG)|G13D(MDAMB231_BREAST)|G13D(NCIH747_LARGE_INTESTINE)|G13D(T84_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT15_LARGE_INTESTINE)|G13D(HCT116_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			7	24					0	0	0.004482	0	0	
IFLTD1	160492	broad.mit.edu	37	12	25679780	25679780	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:25679780G>T	uc001rgs.2	-	4	688	c.538C>A	c.(538-540)CAA>AAA	p.Q180K	IFLTD1_uc001rgt.1_Missense_Mutation_p.Q83K|IFLTD1_uc010sji.1_Missense_Mutation_p.Q201K|IFLTD1_uc010sjj.1_Missense_Mutation_p.Q117K|IFLTD1_uc009zjc.2_Missense_Mutation_p.Q201K	NM_152590	NP_689803	Q8N9Z9	ILFT1_HUMAN	intermediate filament tail domain containing 1	180						intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TTCACATTTTGCTGGAGAATA	0.373													12	72					2.80697e-09	3.08473e-09	0.010729	1	0	
ARNTL2	56938	broad.mit.edu	37	12	27568857	27568857	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:27568857A>G	uc001rht.1	+	15	1660	c.1642A>G	c.(1642-1644)ACT>GCT	p.T548A	ARNTL2_uc001rhw.2_Missense_Mutation_p.T511A|ARNTL2_uc010sjp.1_Missense_Mutation_p.T511A|ARNTL2_uc001rhu.1_Missense_Mutation_p.T534A|ARNTL2_uc009zji.1_Missense_Mutation_p.T514A|ARNTL2_uc001rhv.1_Missense_Mutation_p.T500A|uc001rhx.2_Intron	NM_020183	NP_064568	Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear	548					circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)					AATGAAAGATACTCATACTGT	0.264													4	48					0	0	0.001168	0	0	
PKP2	5318	broad.mit.edu	37	12	32996207	32996207	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:32996207G>A	uc001rlj.3	-	6	1534	c.1419C>T	c.(1417-1419)GGC>GGT	p.G473G	PKP2_uc001rlk.3_Intron|PKP2_uc010skj.1_Intron	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	473					cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					gagccaccgcgcccggccAGC	0.199													7	41					0	0	0.003080	0	0	
ALG10	84920	broad.mit.edu	37	12	34179081	34179081	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:34179081A>T	uc001rlm.2	+	3	972	c.653A>T	c.(652-654)GAC>GTC	p.D218V		NM_032834	NP_116223	Q5BKT4	AG10A_HUMAN	asparagine-linked glycosylation 10 homolog	218	Cytoplasmic (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			skin(1)	1	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)				AAGAAGGAAGACAGACTTCCA	0.378													14	145					0	0	0.007413	0	0	
ADAMTS20	80070	broad.mit.edu	37	12	43846079	43846079	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:43846079T>G	uc010skx.1	-	14	2077	c.2077A>C	c.(2077-2079)ATG>CTG	p.M693L		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	693	Cys-rich.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTACTTACCATACACTGGCCT	0.313													12	51					0	0	0.013537	0	0	
PLEKHA9	51054	broad.mit.edu	37	12	45567083	45567083	+	Missense_Mutation	SNP	C	T	T	rs150051178	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:45567083C>T	uc001rom.1	-	3	1603	c.1066G>A	c.(1066-1068)GTA>ATA	p.V356I	PLEKHA9_uc009zke.2_Missense_Mutation_p.V356I	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)		CCTTCCTTTACGGTTAACGCG	0.498													24	84					0	0	0.005443	0	0	
PLEKHA9	51054	broad.mit.edu	37	12	45567160	45567160	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:45567160C>T	uc001rom.1	-	3	1526	c.989G>A	c.(988-990)GGC>GAC	p.G330D	PLEKHA9_uc009zke.2_Missense_Mutation_p.G330D	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)		AACTACCCAGCCATGGTGTTG	0.443													21	101					0	0	0.012319	0	0	
ANO6	196527	broad.mit.edu	37	12	45803165	45803165	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:45803165T>C	uc001roo.2	+	16	2241	c.1906T>C	c.(1906-1908)TTT>CTT	p.F636L	ANO6_uc010sld.1_Missense_Mutation_p.F636L|ANO6_uc010sle.1_Missense_Mutation_p.F636L|ANO6_uc010slf.1_Missense_Mutation_p.F657L|ANO6_uc010slg.1_Missense_Mutation_p.F618L	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	636	Extracellular (Potential).				activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						AATTGGGCGATTTCACAGAGT	0.373													31	112					0	0	0.012213	0	0	
SLC38A1	81539	broad.mit.edu	37	12	46622973	46622973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:46622973C>T	uc001rpa.2	-	5	535	c.277G>A	c.(277-279)GCC>ACC	p.A93T	SLC38A1_uc001rpb.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpc.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpd.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpe.2_Missense_Mutation_p.A93T|SLC38A1_uc010slh.1_Missense_Mutation_p.A66T|SLC38A1_uc009zkj.1_Missense_Mutation_p.A93T	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	93	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			AGGGCAAAGGCGAGTCCCAAA	0.408													5	34					0	0	0.001168	0	0	
FAM113B	91523	broad.mit.edu	37	12	47629502	47629502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:47629502G>A	uc001rpn.2	+	4	1387	c.656G>A	c.(655-657)CGC>CAC	p.R219H	FAM113B_uc010slj.1_Missense_Mutation_p.R99H|FAM113B_uc001rpq.2_Missense_Mutation_p.R219H	NM_138371	NP_612380	Q96HM7	F113B_HUMAN	hypothetical protein LOC91523	219							hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)					TTCCACTTCCGCCACGCGAGG	0.602													4	12					0	0	0.000602	0	0	
VDR	7421	broad.mit.edu	37	12	48238574	48238574	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:48238574C>T	uc001rqm.2	-	11	1521	c.1239G>A	c.(1237-1239)AAG>AAA	p.K413K	VDR_uc001rql.2_Silent_p.K463K|VDR_uc001rqn.2_Silent_p.K413K|VDR_uc010slq.1_Silent_p.K381K	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor	413	Ligand-binding.				decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GGGGCGTTAGCTTCATGCTGC	0.602													14	41					0	0	0.001855	0	0	
WNT10B	7480	broad.mit.edu	37	12	49361733	49361733	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:49361733C>T	uc001rss.2	-	4	1053	c.707G>A	c.(706-708)CGC>CAC	p.R236H	WNT10B_uc001rst.2_Missense_Mutation_p.A189T	NM_003394	NP_003385	O00744	WN10B_HUMAN	wingless-type MMTV integration site family,	236					axis specification|bone trabecula formation|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|chondrocyte differentiation|female gonad development|hemopoietic stem cell proliferation|midbrain-hindbrain boundary development|myoblast cell differentiation involved in skeletal muscle regeneration|negative regulation of epithelial cell proliferation|negative regulation of fat cell differentiation|neuron differentiation|positive regulation of anagen|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cell proliferation|positive regulation of epithelial cell differentiation|positive regulation of osteoblast differentiation|protein stabilization|regulation of skeletal muscle tissue development|skeletal muscle fiber development|smoothened signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			skin(4)|lung(3)	7						ACATACCTGGCGCCCCACCCT	0.512													12	27					0	0	0.013537	0	0	
MLL2	8085	broad.mit.edu	37	12	49424718	49424718	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:49424718G>A	uc001rta.3	-	40	13629	c.13629C>T	c.(13627-13629)GAC>GAT	p.D4543D		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4543					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						CCCTGACCCCGTCCTCCTTCC	0.622			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			5	29					0	0	0.000602	0	0	
MLL2	8085	broad.mit.edu	37	12	49434552	49434552	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:49434552C>T	uc001rta.3	-	31	7001	c.7001G>A	c.(7000-7002)CGG>CAG	p.R2334Q		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	2334	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						CTGAGATGCCCGAGGGGTCAG	0.637			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			6	14					0	0	0.001984	0	0	
DHH	50846	broad.mit.edu	37	12	49484980	49484980	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:49484980C>T	uc001rtf.2	-	2	803	c.496G>A	c.(496-498)GCA>ACA	p.A166T		NM_021044	NP_066382	O43323	DHH_HUMAN	desert hedgehog preproprotein	166					cell-cell signaling|proteolysis	extracellular space|plasma membrane	calcium ion binding|peptidase activity|zinc ion binding			lung(1)|breast(1)	2						GCTTCCACTGCGAGGCGCGCC	0.602													13	78					0	0	0.014323	0	0	
DNAJC22	79962	broad.mit.edu	37	12	49743155	49743155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:49743155G>A	uc001rua.2	+	2	901	c.500G>A	c.(499-501)CGC>CAC	p.R167H	DNAJC22_uc001rub.2_Missense_Mutation_p.R167H	NM_024902	NP_079178	Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	167					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)	1						CAGAGGCATCGCCGCTACAAA	0.567													13	54					0	0	0.002450	0	0	
ACCN2	41	broad.mit.edu	37	12	50452564	50452564	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:50452564C>T	uc001rvw.2	+	2	244	c.15C>T	c.(13-15)GCC>GCT	p.A5A	ACCN2_uc001rvv.2_Silent_p.A5A|ACCN2_uc009zln.2_5'UTR|ACCN2_uc009zlo.2_Silent_p.A5A	NM_001095	NP_001086	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	5	Cytoplasmic (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)	AACTGAAGGCCGAGGAGGAGG	0.617													7	31					0	0	0.001984	0	0	
SLC11A2	4891	broad.mit.edu	37	12	51393164	51393164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:51393164C>T	uc001rxe.3	-	7	668	c.571G>A	c.(571-573)GCA>ACA	p.A191T	SLC11A2_uc001rxd.3_Missense_Mutation_p.A40T|SLC11A2_uc001rxc.3_Missense_Mutation_p.A191T|SLC11A2_uc001rxf.2_RNA|SLC11A2_uc010smx.1_Missense_Mutation_p.A187T|SLC11A2_uc001rxh.1_Missense_Mutation_p.A191T|SLC11A2_uc001rxj.1_Missense_Mutation_p.A191T|SLC11A2_uc001rxi.2_Missense_Mutation_p.A191T|SLC11A2_uc001rxk.1_Missense_Mutation_p.A220T|SLC11A2_uc010smy.1_Missense_Mutation_p.A154T	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	191	Helical; (Potential).				activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1						AAAGTATCTGCAATGGTGATG	0.458													21	94					0	0	0.012319	0	0	
SLC11A2	4891	broad.mit.edu	37	12	51393180	51393180	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:51393180G>A	uc001rxe.3	-	7	652	c.555C>T	c.(553-555)GGC>GGT	p.G185G	SLC11A2_uc001rxd.3_Silent_p.G34G|SLC11A2_uc001rxc.3_Silent_p.G185G|SLC11A2_uc001rxf.2_RNA|SLC11A2_uc010smx.1_Silent_p.G181G|SLC11A2_uc001rxh.1_Silent_p.G185G|SLC11A2_uc001rxj.1_Silent_p.G185G|SLC11A2_uc001rxi.2_Silent_p.G185G|SLC11A2_uc001rxk.1_Silent_p.G214G|SLC11A2_uc010smy.1_Silent_p.G148G	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	185	Helical; (Potential).				activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1						TGATGAGAACGCCACCCCACA	0.458													16	81					0	0	0.007413	0	0	
KRT75	9119	broad.mit.edu	37	12	52826943	52826943	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:52826943G>A	uc001saj.2	-	2	614	c.592C>T	c.(592-594)CCC>TCC	p.P198S		NM_004693	NP_004684	O95678	K2C75_HUMAN	keratin 75	198	Linker 1.|Rod.					keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.192)		TCAAAGAGGGGCTCTAGGTTC	0.582													22	73					0	0	0.003954	0	0	
KRT74	121391	broad.mit.edu	37	12	52962173	52962173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:52962173G>A	uc001sap.1	-	7	1183	c.1135C>T	c.(1135-1137)CGT>TGT	p.R379C		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	379	Rod.|Coil 2.					keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)		AGGCTGGCACGCTGAAGGGCA	0.552													5	23					0	0	0.003080	0	0	
ESPL1	9700	broad.mit.edu	37	12	53680232	53680232	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:53680232C>A	uc001sck.2	+	18	3803	c.3712C>A	c.(3712-3714)CCA>ACA	p.P1238T	ESPL1_uc001scj.2_Missense_Mutation_p.P913T|ESPL1_uc010soe.1_Intron	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1238					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						CCTGAACCAGCCATCAAACGA	0.542													19	115					9.95505e-16	1.11744e-15	0.014323	1	0	
ESPL1	9700	broad.mit.edu	37	12	53681832	53681832	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:53681832G>A	uc001sck.2	+	19	4344	c.4253G>A	c.(4252-4254)CGG>CAG	p.R1418Q	ESPL1_uc001scj.2_Missense_Mutation_p.R1093Q|ESPL1_uc010soe.1_3'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1418					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						CCTAAGAGACGGGGCACTGCT	0.617											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	21					0	0	0.001984	0	0	
ESPL1	9700	broad.mit.edu	37	12	53681905	53681905	+	Silent	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:53681905A>T	uc001sck.2	+	19	4417	c.4326A>T	c.(4324-4326)CCA>CCT	p.P1442P	ESPL1_uc001scj.2_Silent_p.P1117P|ESPL1_uc010soe.1_3'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1442					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						TGGTTGCCCCAGGTAGTGCCC	0.667											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	16					0	0	0.009096	0	0	
ESPL1	9700	broad.mit.edu	37	12	53681913	53681913	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:53681913C>T	uc001sck.2	+	19	4425	c.4334C>T	c.(4333-4335)GCC>GTC	p.A1445V	ESPL1_uc001scj.2_Missense_Mutation_p.A1120V|ESPL1_uc010soe.1_3'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1445					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						CCAGGTAGTGCCCCTGGGAAC	0.667											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	14					0	0	0.009096	0	0	
AAAS	8086	broad.mit.edu	37	12	53701642	53701642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:53701642G>A	uc001scr.3	-	15	1566	c.1403C>T	c.(1402-1404)GCC>GTC	p.A468V	AAAS_uc001scs.3_Missense_Mutation_p.A435V	NM_015665	NP_056480	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency,	468					carbohydrate metabolic process|glucose transport|nucleocytoplasmic transport|regulation of glucose transport|regulation of nucleocytoplasmic transport|transmembrane transport|viral reproduction	nuclear pore				ovary(1)	1						ACTGAGCAGGGCCCCTTTGTT	0.602													11	76					0	0	0.013537	0	0	
SILV	6490	broad.mit.edu	37	12	56348059	56348059	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:56348059C>T	uc001sip.2	-	11	1956	c.1925G>A	c.(1924-1926)CGC>CAC	p.R642H	SILV_uc001siq.2_Missense_Mutation_p.R649H|SILV_uc010spx.1_Missense_Mutation_p.R556H|SILV_uc001sir.2_Missense_Mutation_p.R642H	NM_006928	NP_008859	P40967	PMEL_HUMAN	silver homolog	642	Cytoplasmic (Potential).				melanin biosynthetic process|melanosome organization	endoplasmic reticulum membrane|extracellular region|Golgi apparatus|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding				0						GCAGAAGATGCGGGGTAGACG	0.527													8	39					0	0	0.006214	0	0	
IKZF4	64375	broad.mit.edu	37	12	56429093	56429093	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:56429093G>A	uc001sjb.1	+	9	1895	c.1736G>A	c.(1735-1737)CGG>CAG	p.R579Q	IKZF4_uc010sqa.1_Missense_Mutation_p.R532Q|IKZF4_uc001sjc.1_Missense_Mutation_p.R579Q|IKZF4_uc001sjd.1_Missense_Mutation_p.R477Q|IKZF4_uc009zoi.1_Missense_Mutation_p.R534Q|IKZF4_uc001sje.1_Missense_Mutation_p.R538Q	NM_022465	NP_071910	Q9H2S9	IKZF4_HUMAN	zinc finger protein, subfamily 1A, 4	579	C2H2-type 6.				negative regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (6;0.025)|OV - Ovarian serous cystadenocarcinoma(18;0.123)			CACATTGTCCGGGGGGAGCAT	0.552													24	130					0	0	0.006320	0	0	
MIP	4284	broad.mit.edu	37	12	56847512	56847512	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:56847512C>T	uc001slh.2	-	2	420	c.388G>A	c.(388-390)GCA>ACA	p.A130T		NM_012064	NP_036196	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	130	Helical; (By similarity).				response to stimulus|visual perception	gap junction|integral to plasma membrane	structural constituent of eye lens			skin(1)	1						ACTGTGGTTGCCTGGCCCACG	0.602													3	15					0	0	0.004672	0	0	
NAB2	4665	broad.mit.edu	37	12	57486328	57486328	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:57486328G>A	uc001smz.2	+	3	1433	c.1055G>A	c.(1054-1056)CGA>CAA	p.R352Q		NM_005967	NP_005958	Q15742	NAB2_HUMAN	NGFI-A binding protein 2	352	NCD2.				cell proliferation|negative regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	transcription corepressor activity			upper_aerodigestive_tract(1)|ovary(1)	2						CAAGTAGCCCGAGAGAGCACC	0.552													5	43					0	0	0.000602	0	0	
LRP1	4035	broad.mit.edu	37	12	57574224	57574224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:57574224G>A	uc001snd.2	+	32	5814	c.5348G>A	c.(5347-5349)CGG>CAG	p.R1783Q		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	1783	Extracellular (Potential).|LDL-receptor class B 16.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GATGCCATGCGGAGCCAGCTG	0.617													6	73					0	0	0.003080	0	0	
MBD6	114785	broad.mit.edu	37	12	57921419	57921419	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:57921419C>A	uc001soj.1	+	8	2436	c.2212C>A	c.(2212-2214)CCT>ACT	p.P738T	MBD6_uc001sok.1_Missense_Mutation_p.P605T|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	738	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4						ACTCCTTAGCCCTCTGCTGGG	0.582													14	62					2.31682e-05	2.4858e-05	0.003163	1	0	
SLC26A10	65012	broad.mit.edu	37	12	58015593	58015593	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:58015593C>A	uc001spe.2	+	4	987	c.676C>A	c.(676-678)CTA>ATA	p.L226I	SLC26A10_uc001spf.2_RNA|SLC26A10_uc009zpz.1_5'Flank	NM_133489	NP_597996	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	226						integral to membrane	antiporter activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(17;0.122)					CCGAGACCGGCTACCCACGCC	0.692											OREG0021948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	1					0.000602214	0.000636366	0.000602	1	0	
AGAP2	116986	broad.mit.edu	37	12	58121846	58121846	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:58121846G>A	uc001spq.2	-	15	2640	c.2640C>T	c.(2638-2640)ATC>ATT	p.I880I	AGAP2_uc001spo.1_5'Flank|AGAP2_uc001spp.2_Silent_p.I879I|AGAP2_uc001spr.2_Silent_p.I524I|LOC100130776_uc001sps.3_3'UTR	NM_001122772	NP_001116244	Q99490	AGAP2_HUMAN	centaurin, gamma 1 isoform PIKE-L	880	PH.				axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding			central_nervous_system(3)|breast(2)	5						TGCTGGACACGATCAGGAACT	0.577													16	57					0	0	0.004007	0	0	
MON2	23041	broad.mit.edu	37	12	62979234	62979234	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:62979234T>C	uc001sre.2	+	33	5251	c.4860T>C	c.(4858-4860)CAT>CAC	p.H1620H	MON2_uc009zqj.2_Silent_p.H1620H|MON2_uc010ssl.1_Silent_p.H1548H|MON2_uc010ssm.1_Silent_p.H1591H|MON2_uc010ssn.1_Silent_p.H1614H|MON2_uc001srf.2_Silent_p.H1383H|MON2_uc001srg.2_Silent_p.H489H	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	1621					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		ATGTACTACATCGCTATATAG	0.348													8	36					0	0	0.004482	0	0	
XPOT	11260	broad.mit.edu	37	12	64812728	64812728	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:64812728A>G	uc001ssb.2	+	6	769	c.343A>G	c.(343-345)ACA>GCA	p.T115A	XPOT_uc009zqm.1_Missense_Mutation_p.T25A	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	115	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		GCTTTTTGTTACAGAGTATCT	0.433													5	84					0	0	0.004482	0	0	
XPOT	11260	broad.mit.edu	37	12	64812733	64812733	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:64812733G>A	uc001ssb.2	+	6	774	c.348G>A	c.(346-348)GAG>GAA	p.E116E	XPOT_uc009zqm.1_Silent_p.E26E	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	116	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		TTGTTACAGAGTATCTCACTA	0.438													5	85					0	0	0.006214	0	0	
XPOT	11260	broad.mit.edu	37	12	64812808	64812808	+	Silent	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:64812808C>G	uc001ssb.2	+	6	849	c.423C>G	c.(421-423)CTC>CTG	p.L141L	XPOT_uc009zqm.1_Silent_p.L51L	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	141	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		GAGTAGATCTCTACCTGCGAA	0.398													6	116					0	0	0.001984	0	0	
NUP107	57122	broad.mit.edu	37	12	69109410	69109410	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:69109410C>A	uc001suf.2	+	12	1088	c.973C>A	c.(973-975)CCT>ACT	p.P325T	NUP107_uc001sug.2_Missense_Mutation_p.P172T|NUP107_uc010stj.1_Missense_Mutation_p.P296T	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	325					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			CTTACAGGACCCTGATGCTCC	0.353													24	119					1.68575e-08	1.84651e-08	0.007291	1	0	
CCT2	10576	broad.mit.edu	37	12	69980567	69980567	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:69980567T>C	uc001svb.1	+	3	207	c.113T>C	c.(112-114)TTG>TCG	p.L38S	CCT2_uc009zrm.1_RNA|CCT2_uc009zrn.1_Missense_Mutation_p.L38S|CCT2_uc010stl.1_5'UTR	NM_006431	NP_006422	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2	38					'de novo' posttranslational protein folding	nucleus	ATP binding|unfolded protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			ATTGGAGACTTGGTAAAGAGC	0.338													19	167					0	0	0.012319	0	0	
TBC1D15	64786	broad.mit.edu	37	12	72307610	72307610	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:72307610T>C	uc001swu.2	+	13	1431	c.1422T>C	c.(1420-1422)TAT>TAC	p.Y474Y	TBC1D15_uc010stt.1_Silent_p.Y443Y|TBC1D15_uc001swv.2_Silent_p.Y457Y|TBC1D15_uc001sww.2_Silent_p.Y206Y	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1	452	Rab-GAP TBC.						protein binding|Rab GTPase activator activity				0						TTTTAGGATATGTTCAAGGAA	0.353													12	34					0	0	0.013537	0	0	
E2F7	144455	broad.mit.edu	37	12	77444494	77444494	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:77444494C>T	uc001sym.3	-	4	636	c.400G>A	c.(400-402)GAA>AAA	p.E134K	E2F7_uc001syn.2_Missense_Mutation_p.E134K	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	134					cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						TTTTCAAATTCGTCCACAGCA	0.458													15	68					0	0	0.003163	0	0	
PPP1R12A	4659	broad.mit.edu	37	12	80328667	80328667	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:80328667T>C	uc001syz.2	-	1	312	c.45A>G	c.(43-45)AAA>AAG	p.K15K	PPP1R12A_uc001sza.2_Silent_p.K15K|PPP1R12A_uc010sud.1_Silent_p.K15K|PPP1R12A_uc001szb.2_Silent_p.K15K|PPP1R12A_uc001szc.2_Silent_p.K15K	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	15						contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7						CGATCCAGCGTTTCAGCTGCT	0.547													4	4					0	0	0.009096	0	0	
DUSP6	1848	broad.mit.edu	37	12	89744647	89744647	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:89744647G>A	uc001tay.2	-	2	1036	c.556C>T	c.(556-558)CGA>TGA	p.R186*	DUSP6_uc001taz.2_Intron	NM_001946	NP_001937	Q16828	DUS6_HUMAN	dual specificity phosphatase 6 isoform a	186					dorsal/ventral pattern formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|nerve growth factor receptor signaling pathway|positive regulation of apoptosis|regulation of endodermal cell fate specification|regulation of fibroblast growth factor receptor signaling pathway|regulation of heart growth|response to nitrosative stress|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	cytosol|nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0						TTGGGGTCTCGGTCAAGGTCA	0.617													18	63					0	0	0.007413	0	0	
DCN	1634	broad.mit.edu	37	12	91552114	91552114	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:91552114C>T	uc001tbs.2	-	3	591	c.497G>A	c.(496-498)CGA>CAA	p.R166Q	DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Missense_Mutation_p.R166Q|DCN_uc001tbu.2_Missense_Mutation_p.R166Q	NM_133503	NP_598010	P07585	PGS2_HUMAN	decorin isoform a preproprotein	166	LRR 5.				organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4						AGTAACTTTTCGCACTTTGGT	0.378													18	98					0	0	0.007413	0	0	
C12orf63	374467	broad.mit.edu	37	12	97079013	97079013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:97079013C>T	uc001tet.1	+	9	1364	c.1286C>T	c.(1285-1287)GCA>GTA	p.A429V		NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467	429										skin(6)|ovary(1)	7						GCAAAGATAGCACAGTGAGTG	0.507													11	45					0	0	0.002450	0	0	
UHRF1BP1L	23074	broad.mit.edu	37	12	100452815	100452815	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:100452815A>G	uc001tgq.2	-	14	2469	c.2240T>C	c.(2239-2241)GTA>GCA	p.V747A	UHRF1BP1L_uc001tgp.2_Missense_Mutation_p.V397A	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	747										ovary(2)	2						ATTTAGAGATACCTGATTACA	0.418													19	110					0	0	0.010504	0	0	
SLC17A8	246213	broad.mit.edu	37	12	100790165	100790165	+	Silent	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:100790165A>C	uc010svi.1	+	5	959	c.646A>C	c.(646-648)AGA>CGA	p.R216R	SLC17A8_uc009ztx.2_Silent_p.R216R	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	216	Cytoplasmic (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						ACCTTTGGAGAGAAGCCGACT	0.398													5	22					0	0	0.001168	0	0	
TCP11L2	255394	broad.mit.edu	37	12	106715425	106715425	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:106715425C>T	uc001tln.2	+	5	750	c.576C>T	c.(574-576)CCC>CCT	p.P192P	TCP11L2_uc001tll.2_Silent_p.P192P|TCP11L2_uc001tlm.2_Silent_p.P192P	NM_152772	NP_689985	Q8N4U5	T11L2_HUMAN	t-complex 11 (mouse) like 2	192										ovary(3)	3						TGTGTGCTCCCGTGCGAGATA	0.488													19	92					0	0	0.008871	0	0	
BTBD11	121551	broad.mit.edu	37	12	108011205	108011205	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:108011205C>T	uc001tmk.1	+	9	2744	c.2223C>T	c.(2221-2223)CAC>CAT	p.H741H	BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Silent_p.H741H|BTBD11_uc001tml.1_Silent_p.H278H	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	741	ANK 4.					integral to membrane	DNA binding			skin(2)|ovary(1)	3						CTGCAGCCCACGGACACAGGT	0.408													5	30					0	0	0.000602	0	0	
WSCD2	9671	broad.mit.edu	37	12	108603945	108603945	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:108603945G>A	uc001tms.2	+	4	1289	c.545G>A	c.(544-546)GGC>GAC	p.G182D	WSCD2_uc001tmt.2_Missense_Mutation_p.G182D	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	182	WSC 1.					integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3						TGCTACTGCGGCCACAAGATC	0.672													9	11					0	0	0.006214	0	0	
SART3	9733	broad.mit.edu	37	12	108942899	108942899	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:108942899C>T	uc001tmz.1	-	2	639	c.404G>A	c.(403-405)CGC>CAC	p.R135H	SART3_uc009zux.1_5'UTR|SART3_uc010swx.1_Missense_Mutation_p.R135H|SART3_uc010swy.1_Missense_Mutation_p.R3H|SART3_uc010swz.1_Missense_Mutation_p.R135H|SART3_uc001tna.1_RNA	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	135	HAT 1.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1						CATCTTCTGGCGGGCCATCCT	0.458									Porokeratosis				7	58					0	0	0.003080	0	0	
SART3	9733	broad.mit.edu	37	12	108954646	108954646	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:108954646C>T	uc001tmz.1	-	1	520	c.285G>A	c.(283-285)CAG>CAA	p.Q95Q	SART3_uc009zux.1_5'UTR|SART3_uc010swx.1_Silent_p.Q95Q|SART3_uc010swz.1_Silent_p.Q95Q|SART3_uc001tna.1_RNA|SART3_uc001tnb.2_Silent_p.Q95Q|ISCU_uc010sxa.1_5'Flank|ISCU_uc010sxb.1_5'Flank|ISCU_uc001tnc.3_5'Flank|ISCU_uc010sxc.1_5'Flank|ISCU_uc009zuy.2_5'Flank|ISCU_uc010sxd.1_5'Flank	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	95	Potential.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1						CAATCTCCAGCTGGTTTTTCT	0.632									Porokeratosis				5	13					0	0	0.001984	0	0	
GPN3	51184	broad.mit.edu	37	12	110897617	110897617	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:110897617G>A	uc001tqr.2	-	3	264	c.208C>T	c.(208-210)CGA>TGA	p.R70*	GPN3_uc001tqs.2_Nonsense_Mutation_p.R80*	NM_016301	NP_057385	Q9UHW5	GPN3_HUMAN	GPN-loop GTPase 3 isoform 1	70						protein complex	GTP binding				0						GGACCGAATCGCAGAGAATCA	0.448													23	106					0	0	0.004656	0	0	
TCTN1	79600	broad.mit.edu	37	12	111085688	111085688	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:111085688G>A	uc009zvs.2	+	14	1863	c.1755G>A	c.(1753-1755)CCG>CCA	p.P585P	TCTN1_uc001trp.3_Silent_p.P571P|TCTN1_uc001trn.3_Silent_p.P590P|TCTN1_uc001trk.3_RNA|HVCN1_uc001trq.1_Intron	NM_001082537	NP_001076006	Q2MV58	TECT1_HUMAN	tectonic family member 1 isoform 2	585					multicellular organismal development	extracellular region					0						TCTTCTTCCCGTTTGTTTGAC	0.532													14	37					0	0	0.004007	0	0	
ACAD10	80724	broad.mit.edu	37	12	112171759	112171759	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:112171759C>T	uc001tsq.2	+	11	1627	c.1427C>T	c.(1426-1428)CCA>CTA	p.P476L	ACAD10_uc001tsp.2_Missense_Mutation_p.P476L|ACAD10_uc009zvx.2_Missense_Mutation_p.P507L|ACAD10_uc001tss.1_RNA	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10	476							acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2						CCAGAAGAGCCAGAGGTGCTT	0.537													18	58					0	0	0.007413	0	0	
NOS1	4842	broad.mit.edu	37	12	117723955	117723955	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:117723955C>T	uc001twm.1	-	6	1930	c.1244G>A	c.(1243-1245)CGG>CAG	p.R415Q		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	415					multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	CGAGGCATTCCGCCAGGCGTG	0.547													5	64					0	0	0.001168	0	0	
GCN1L1	10985	broad.mit.edu	37	12	120589033	120589033	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:120589033C>T	uc001txo.2	-	34	4238	c.4225G>A	c.(4225-4227)GGC>AGC	p.G1409S		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	1409					regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGAGGATGCCCAGGCCCTTC	0.597													7	15					0	0	0.001984	0	0	
SIRT4	23409	broad.mit.edu	37	12	120750802	120750802	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:120750802G>A	uc001tyc.2	+	4	928	c.908G>A	c.(907-909)CGT>CAT	p.R303H		NM_012240	NP_036372	Q9Y6E7	SIRT4_HUMAN	sirtuin 4	303	Deacetylase sirtuin-type.				chromatin silencing|negative regulation of insulin secretion|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTGAATTCTCGTTGTGGAGAG	0.488													31	70					0	0	0.010818	0	0	
C12orf43	64897	broad.mit.edu	37	12	121448638	121448638	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:121448638G>A	uc001tzh.1	-	3	303	c.280C>T	c.(280-282)CTG>TTG	p.L94L	C12orf43_uc009zxa.1_Silent_p.L125L|C12orf43_uc010szo.1_Silent_p.L52L|C12orf43_uc010szp.1_Silent_p.L94L|C12orf43_uc001tzi.1_Silent_p.L94L	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897	94											0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TACCTGTCCAGCAGGGCTCCC	0.403													14	59					0	0	0.008871	0	0	
LRRC43	254050	broad.mit.edu	37	12	122677528	122677528	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:122677528T>A	uc009zxm.2	+	7	1351	c.1326T>A	c.(1324-1326)GAT>GAA	p.D442E	LRRC43_uc001ubw.3_Missense_Mutation_p.D257E|LRRC43_uc009zxn.2_Missense_Mutation_p.D203E	NM_001098519	NP_001091989	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43 isoform 1	442											0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		TGCGTATAGATCCCCGGCTCT	0.597													6	19					0	0	0.001168	0	0	
KNTC1	9735	broad.mit.edu	37	12	123060124	123060124	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:123060124C>T	uc001ucv.2	+	28	2580	c.2417C>T	c.(2416-2418)GCG>GTG	p.A806V	KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	806					cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ATCATGTATGCGGCAGTGGTT	0.478													4	19					0	0	0.000602	0	0	
AACS	65985	broad.mit.edu	37	12	125613986	125613986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:125613986C>T	uc001uhc.2	+	14	1735	c.1529C>T	c.(1528-1530)GCG>GTG	p.A510V	AACS_uc001uhd.2_Missense_Mutation_p.A510V|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Missense_Mutation_p.A108V	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	510					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		TACAGGAAGGCGTATTTCTCC	0.567													15	149					0	0	0.004990	0	0	
TMEM132B	114795	broad.mit.edu	37	12	126004054	126004054	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:126004054G>A	uc001uhe.1	+	4	1169	c.1161G>A	c.(1159-1161)GGG>GGA	p.G387G		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	387	Extracellular (Potential).					integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		ACCTGGCTGGGGCCCAGCAGA	0.493													15	48					0	0	0.003163	0	0	
TMEM132D	121256	broad.mit.edu	37	12	130184915	130184915	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:130184915G>A	uc009zyl.1	-	2	736	c.408C>T	c.(406-408)GAC>GAT	p.D136D		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	136	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGTAGACTTTGTCCCGCAGGA	0.542													13	29					0	0	0.002450	0	0	
SFRS8	6433	broad.mit.edu	37	12	132238992	132238992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:132238992G>A	uc001uja.1	+	9	1542	c.1402G>A	c.(1402-1404)GCC>ACC	p.A468T	SFRS8_uc010tbn.1_Missense_Mutation_p.A468T|SFRS8_uc001ujb.1_Missense_Mutation_p.A261T|SFRS8_uc001uiz.1_Missense_Mutation_p.A342T	NM_004592	NP_004583	Q12872	SFSWA_HUMAN	splicing factor, arginine/serine-rich 8	468	SURP motif 2.				mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)		CGAGTATGTCGCCAGGAACGG	0.547													13	28					0	0	0.003163	0	0	
SFRS8	6433	broad.mit.edu	37	12	132281835	132281835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:132281835G>A	uc001uja.1	+	16	2787	c.2647G>A	c.(2647-2649)GCG>ACG	p.A883T	SFRS8_uc010tbn.1_Missense_Mutation_p.A935T	NM_004592	NP_004583	Q12872	SFSWA_HUMAN	splicing factor, arginine/serine-rich 8	883	Arg/Ser-rich (RS domain).				mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)		cgcggcccccgcggcccACTC	0.557													4	26					0	0	0.000602	0	0	
EP400	57634	broad.mit.edu	37	12	132514298	132514298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:132514298C>T	uc001ujn.2	+	27	5469	c.5434C>T	c.(5434-5436)CCG>TCG	p.P1812S	EP400_uc001ujl.2_Missense_Mutation_p.P1811S|EP400_uc001ujm.2_Missense_Mutation_p.P1731S|SNORA49_uc001ujo.2_5'Flank	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1848					histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCTACGGGTGCCGCGGCCGCC	0.637													3	13					0	0	0.000602	0	0	
LOC284232	284232	broad.mit.edu	37	13	19436206	19436206	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:19436206G>A	uc010tcj.1	-	1		c.9904C>T				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						TAGCAGAACAGGTGTGATGAG	0.383													2	2					0	0	0.004672	0	0	
ZMYM5	9205	broad.mit.edu	37	13	20399055	20399055	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:20399055C>T	uc010tcn.1	-	8	1837	c.1572G>A	c.(1570-1572)ACG>ACA	p.T524T	ZMYM5_uc001umm.1_Silent_p.T348T	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3	524						nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ttcggggccacgtacctggat	0													5	19					0	0	0.000602	0	0	
ZMYM5	9205	broad.mit.edu	37	13	20426142	20426142	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:20426142A>T	uc010tcn.1	-	3	444	c.179T>A	c.(178-180)GTT>GAT	p.V60D	ZMYM5_uc001umm.1_Translation_Start_Site|ZMYM5_uc001umn.2_Missense_Mutation_p.V60D|ZMYM5_uc001umo.2_Missense_Mutation_p.V60D	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3	60						nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		AATAAACACAAcatcatcatc	0.338													13	92					0	0	0.001855	0	0	
ZMYM2	7750	broad.mit.edu	37	13	20577064	20577064	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:20577064G>A	uc001umr.2	+	5	1220	c.922G>A	c.(922-924)GCC>ACC	p.A308T	ZMYM2_uc001umq.2_Missense_Mutation_p.A221T|ZMYM2_uc001ums.2_Missense_Mutation_p.A308T|ZMYM2_uc001umt.2_Missense_Mutation_p.A308T|ZMYM2_uc009zzn.1_Missense_Mutation_p.A243T	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	308					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		ATCACCAGTGGCCTCACTTCC	0.433													31	114					0	0	0.010818	0	0	
ZMYM2	7750	broad.mit.edu	37	13	20625630	20625630	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:20625630C>T	uc001umr.2	+	14	2648	c.2350C>T	c.(2350-2352)CGT>TGT	p.R784C	ZMYM2_uc001ums.2_Missense_Mutation_p.R784C|ZMYM2_uc001umt.2_Missense_Mutation_p.R784C|ZMYM2_uc010tco.1_RNA|ZMYM2_uc001umv.2_Missense_Mutation_p.R164C|ZMYM2_uc001umw.2_Missense_Mutation_p.R237C	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	784					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		AGTTCAGTGGCGTGGGGAAAT	0.378													18	54					0	0	0.004990	0	0	
ZMYM2	7750	broad.mit.edu	37	13	20641139	20641139	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:20641139T>C	uc001umr.2	+	21	3579	c.3281T>C	c.(3280-3282)GTA>GCA	p.V1094A	ZMYM2_uc001ums.2_Missense_Mutation_p.V1094A|ZMYM2_uc001umt.2_Missense_Mutation_p.V1094A|ZMYM2_uc001umv.2_Missense_Mutation_p.V474A|ZMYM2_uc001umw.2_Missense_Mutation_p.V547A	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	1094					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		GATCTTCTGGTATTAGATGAG	0.308													21	74					0	0	0.002780	0	0	
SPATA13	221178	broad.mit.edu	37	13	24858406	24858406	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:24858406T>C	uc001upg.1	+	4	830	c.423T>C	c.(421-423)AAT>AAC	p.N141N	SPATA13_uc001upd.1_Silent_p.N766N|C1QTNF9_uc001upe.2_RNA|SPATA13_uc010tcy.1_Silent_p.N87N|SPATA13_uc010tcz.1_Silent_p.N87N|SPATA13_uc010tda.1_Silent_p.N85N|SPATA13_uc001uph.2_Silent_p.N63N|SPATA13_uc010tdb.1_Silent_p.N63N	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	141	ABR (APC-binding region) domain.				cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TGGCCATCAATGAGGTACTGG	0.428													5	14					0	0	0.000602	0	0	
SPATA13	221178	broad.mit.edu	37	13	24861032	24861032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:24861032C>T	uc001upg.1	+	6	1143	c.736C>T	c.(736-738)CGG>TGG	p.R246W	SPATA13_uc001upd.1_Missense_Mutation_p.R871W|C1QTNF9_uc001upe.2_RNA|SPATA13_uc010tcy.1_Missense_Mutation_p.R192W|SPATA13_uc010tcz.1_Intron|SPATA13_uc010tda.1_Missense_Mutation_p.R190W|SPATA13_uc001uph.2_Missense_Mutation_p.R168W|SPATA13_uc010tdb.1_Intron|SPATA13_uc009zzz.1_5'Flank	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	246	DH.				cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CAACGTCATCCGGGAGATCAT	0.602													6	38					0	0	0.006214	0	0	
PAN3	255967	broad.mit.edu	37	13	28841313	28841313	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:28841313G>A	uc001urz.2	+	10	1225	c.1217G>A	c.(1216-1218)CGT>CAT	p.R406H	PAN3_uc010tdo.1_Missense_Mutation_p.R552H|PAN3_uc001ury.2_Missense_Mutation_p.R240H|PAN3_uc001urx.2_Missense_Mutation_p.R352H	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	552	Protein kinase.|Interaction with PAN2.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GTAACTTTGCGTGAAGTATTT	0.378													20	114					0	0	0.014323	0	0	
SLC7A1	6541	broad.mit.edu	37	13	30091734	30091734	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:30091734C>T	uc001uso.2	-	10	1873	c.1486G>A	c.(1486-1488)GTG>ATG	p.V496M		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	496	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GAAATGTTCACAATTAGCCCA	0.493													28	117					0	0	0.012213	0	0	
USPL1	10208	broad.mit.edu	37	13	31205139	31205139	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:31205139C>T	uc001utc.2	+	4	828	c.396C>T	c.(394-396)GAC>GAT	p.D132D	USPL1_uc001utb.2_Translation_Start_Site|USPL1_uc001utd.2_Intron	NM_005800	NP_005791	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	132					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			pancreas(2)|skin(1)	3		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		TTGCTATTGACGGTGGAAAAG	0.368													7	59					0	0	0.004482	0	0	
SOHLH2	54937	broad.mit.edu	37	13	36776105	36776105	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:36776105C>T	uc001uvj.2	-	2	263	c.174G>A	c.(172-174)GCG>GCA	p.A58A	SOHLH2_uc010tei.1_Silent_p.A135A	NM_017826	NP_060296	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic	58					cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		CATCCAAAAGCGCTGCTGCCT	0.453													6	97					0	0	0.001984	0	0	
SPG20	23111	broad.mit.edu	37	13	36888477	36888477	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:36888477C>T	uc001uvn.2	-	7	1640	c.1370G>A	c.(1369-1371)CGA>CAA	p.R457Q	SPG20_uc010ten.1_Missense_Mutation_p.R447Q|SPG20_uc001uvm.2_Missense_Mutation_p.R457Q|SPG20_uc001uvo.2_Missense_Mutation_p.R457Q|SPG20_uc001uvq.2_Missense_Mutation_p.R457Q	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	457					cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		AATCCGCTCTCGGAGTTTAGA	0.448													16	74					0	0	0.004990	0	0	
FAM48A	55578	broad.mit.edu	37	13	37598478	37598478	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:37598478T>C	uc001uwg.2	-	18	1679	c.1431A>G	c.(1429-1431)TCA>TCG	p.S477S	FAM48A_uc010abt.2_Silent_p.S478S|FAM48A_uc001uwh.2_Silent_p.S478S|FAM48A_uc001uwi.2_Silent_p.S477S|FAM48A_uc001uwj.2_Silent_p.S478S|FAM48A_uc001uwk.2_Silent_p.S477S|FAM48A_uc010tes.1_Silent_p.S441S|FAM48A_uc001uwl.1_Silent_p.S477S|FAM48A_uc001uwd.2_5'Flank|FAM48A_uc001uwe.2_5'UTR|FAM48A_uc001uwf.2_Silent_p.S55S	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A	477					autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)		ATGTAATACCTGAGGAACTAT	0.363													9	46					0	0	0.004482	0	0	
POSTN	10631	broad.mit.edu	37	13	38161966	38161966	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:38161966G>T	uc001uwo.3	-	5	717	c.599C>A	c.(598-600)CCT>CAT	p.P200H	POSTN_uc001uwp.3_Missense_Mutation_p.P200H|POSTN_uc001uwr.2_Missense_Mutation_p.P200H|POSTN_uc001uwq.2_Missense_Mutation_p.P200H|POSTN_uc010teu.1_Missense_Mutation_p.P200H|POSTN_uc010tev.1_Missense_Mutation_p.P200H|POSTN_uc010tew.1_Missense_Mutation_p.P200H|POSTN_uc010tex.1_Missense_Mutation_p.P115H	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	200	FAS1 1.				cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TACCCCATTAGGATAATGGTT	0.269													6	49					0.00116845	0.00122775	0.001168	1	0	
C13orf23	80209	broad.mit.edu	37	13	39588012	39588012	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:39588012G>A	uc001uwy.2	-	11	2250	c.1377C>T	c.(1375-1377)GCC>GCT	p.A459A	C13orf23_uc001uwz.2_Silent_p.A437A	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	459	Ser-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)		CAAGTGGACCGGCAACGCTGG	0.493													17	64					0	0	0.004990	0	0	
COG6	57511	broad.mit.edu	37	13	40268797	40268797	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:40268797T>C	uc001uxh.2	+	12	1201	c.1101T>C	c.(1099-1101)GCT>GCC	p.A367A	COG6_uc001uxi.2_Silent_p.A315A|COG6_uc010acb.2_Silent_p.A367A	NM_020751	NP_065802	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6 isoform	367					protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		TAATAGTTGCTGAACCTGGGG	0.294													9	58					0	0	0.008291	0	0	
ZC3H13	23091	broad.mit.edu	37	13	46549634	46549634	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:46549634C>T	uc010tfw.1	-	11	2258	c.2252G>A	c.(2251-2253)CGA>CAA	p.R751Q	ZC3H13_uc001vas.1_Missense_Mutation_p.R751Q|ZC3H13_uc001vat.1_Missense_Mutation_p.R751Q	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	751	Arg/Glu-rich.|Potential.						nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		ttctctttctcgttcccgttc	0.1													7	8					0	0	0.001984	0	0	
NEK5	341676	broad.mit.edu	37	13	52639603	52639603	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:52639603G>C	uc001vge.2	-	22	2207	c.2067C>G	c.(2065-2067)AGC>AGG	p.S689R		NM_199289	NP_954983	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	689							ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		GACGACTGACGCTAAGCACAG	0.552													6	64					0	0	0.001984	0	0	
MYCBP2	23077	broad.mit.edu	37	13	77663139	77663139	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:77663139G>A	uc001vkf.2	-	62	10530	c.10439C>T	c.(10438-10440)CCG>CTG	p.P3480L	MYCBP2_uc010aev.2_Missense_Mutation_p.P2884L|MYCBP2_uc001vke.2_Missense_Mutation_p.P100L	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3480					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CTCAGGAGACGGATGTCTCAA	0.333													8	47					0	0	0.006214	0	0	
UGGT2	55757	broad.mit.edu	37	13	96665657	96665657	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:96665657G>A	uc001vmt.2	-	5	734	c.564C>T	c.(562-564)GCC>GCT	p.A188A	UGGT2_uc010afo.2_RNA|UGGT2_uc001vmv.2_Silent_p.A188A|UGGT2_uc010afp.2_Silent_p.A188A	NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	188					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3						TACCCATTTCGGCATAGAGAA	0.338													7	55					0	0	0.001984	0	0	
OXGR1	27199	broad.mit.edu	37	13	97639911	97639911	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:97639911A>G	uc001vmx.1	-	4	347	c.103T>C	c.(103-105)TAC>CAC	p.Y35H	OXGR1_uc010afr.1_Missense_Mutation_p.Y35H	NM_080818	NP_543008	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	35	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)|skin(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			ACAGGGAGGTAGTGCATCTTG	0.418													5	50					0	0	0.000602	0	0	
TMTC4	84899	broad.mit.edu	37	13	101315320	101315320	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:101315320G>A	uc001vou.2	-	4	553	c.393C>T	c.(391-393)GGC>GGT	p.G131G	TMTC4_uc001vot.2_Silent_p.G150G|TMTC4_uc010tja.1_Intron	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	131	Helical; (Potential).					integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACTGCAGGCCGCCAAACAGAA	0.627													11	60					0	0	0.013537	0	0	
NALCN	259232	broad.mit.edu	37	13	101910909	101910909	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:101910909G>A	uc001vox.1	-	11	1340	c.1151C>T	c.(1150-1152)TCC>TTC	p.S384F	NALCN_uc001voy.2_Missense_Mutation_p.S99F|NALCN_uc001voz.2_Missense_Mutation_p.S384F|NALCN_uc001vpa.2_Missense_Mutation_p.S384F	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	384	Helical; Name=S1 of repeat II; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTGGAAAACGGATGACCGCAT	0.468													5	51					0	0	0.000602	0	0	
C13orf27	93081	broad.mit.edu	37	13	103418898	103418898	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:103418898T>C	uc001vpo.2	-	6	715	c.537A>G	c.(535-537)CAA>CAG	p.Q179Q	C13orf27_uc001vpn.2_Silent_p.Q138Q|C13orf27_uc001vpp.2_Silent_p.Q138Q	NM_138779	NP_620134	Q5JUR7	CM027_HUMAN	hypothetical protein LOC93081	179											0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TATGGGGAGCTTGCATTTTCT	0.373													6	42					0	0	0.003080	0	0	
ARHGEF7	8874	broad.mit.edu	37	13	111944543	111944543	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:111944543G>A	uc001vrs.2	+	20	2526	c.2276G>A	c.(2275-2277)CGC>CAC	p.R759H	ARHGEF7_uc001vrr.2_Missense_Mutation_p.R738H|ARHGEF7_uc001vrt.2_Missense_Mutation_p.R709H|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron|ARHGEF7_uc010tjp.1_Missense_Mutation_p.R503H|ARHGEF7_uc001vry.1_Missense_Mutation_p.R175H	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	759					apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CTGGGGCGTCGCAGTAGCCTT	0.532													9	87					0	0	0.008291	0	0	
F7	2155	broad.mit.edu	37	13	113771857	113771857	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:113771857C>T	uc001vsv.2	+	8	803	c.752C>T	c.(751-753)GCG>GTG	p.A251V	F7_uc001vsw.2_Missense_Mutation_p.A229V|F7_uc010tjt.1_Missense_Mutation_p.A182V	NM_000131	NP_000122	P08709	FA7_HUMAN	coagulation factor VII isoform a precursor	251	Peptidase S1.		A -> P (in FA7D).|A -> T (in FA7D).		anti-apoptosis|blood coagulation, extrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of leukocyte chemotaxis|positive regulation of platelet-derived growth factor receptor signaling pathway|positive regulation of positive chemotaxis|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|glycoprotein binding|serine-type endopeptidase activity				0	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	GTGGTCTCCGCGGCCCACTGT	0.617													16	55					0	0	0.003163	0	0	
PCID2	55795	broad.mit.edu	37	13	113854825	113854825	+	Silent	SNP	G	A	A	rs3751414		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:113854825G>A	uc010tju.1	-	2	123	c.42C>T	c.(40-42)TAC>TAT	p.Y14Y	PCID2_uc010tjv.1_Silent_p.Y14Y|PCID2_uc010tjw.1_Silent_p.Y14Y|PCID2_uc001vte.2_Translation_Start_Site|PCID2_uc001vtd.2_Translation_Start_Site|PCID2_uc001vtf.2_Translation_Start_Site|PCID2_uc001vtg.1_RNA	NM_001127203	NP_001120675	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	14					negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of mitotic cell cycle spindle assembly checkpoint|positive regulation of transcription, DNA-dependent|regulation of mRNA stability|spleen development		protein binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			CGATGGCTTCGTACACCTGAA	0.408													12	62					0	0	0.001855	0	0	
GAS6	2621	broad.mit.edu	37	13	114535359	114535359	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:114535359G>A	uc001vud.2	-	10	1209	c.1056C>T	c.(1054-1056)GCC>GCT	p.A352A	GAS6_uc001vug.2_Silent_p.A53A|GAS6_uc001vuf.2_Silent_p.A79A	NM_000820	NP_000811	Q14393	GAS6_HUMAN	growth arrest-specific 6 isoform 1 precursor	395	Laminin G-like 1.				cell proliferation|leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|post-translational protein modification|proteolysis|regulation of growth	endoplasmic reticulum lumen|extracellular space|Golgi lumen|platelet alpha granule lumen	calcium ion binding|receptor agonist activity			central_nervous_system(4)	4	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CCAGCCGGCCGGCTCTCAGGG	0.647													5	16					0	0	0.001168	0	0	
TMEM55B	90809	broad.mit.edu	37	14	20928912	20928912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:20928912C>T	uc001vxl.2	-	2	388	c.235G>A	c.(235-237)GCC>ACC	p.A79T	TMEM55B_uc001vxk.2_Missense_Mutation_p.A86T	NM_144568	NP_653169	Q86T03	TM55B_HUMAN	transmembrane protein 55B isoform 2	79	Pro-rich.					integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)		ATCATAGGGGCACTCCCACTG	0.572													13	87					0	0	0.001855	0	0	
SLC7A7	9056	broad.mit.edu	37	14	23243309	23243309	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:23243309G>A	uc001wgr.3	-	9	1400	c.1262C>T	c.(1261-1263)CCG>CTG	p.P421L	SLC7A7_uc001wgs.3_Missense_Mutation_p.P421L|SLC7A7_uc001wgt.3_Missense_Mutation_p.P421L|SLC7A7_uc001wgu.3_Missense_Mutation_p.P421L|SLC7A7_uc001wgv.3_Missense_Mutation_p.P421L	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7	421	Helical; (Potential).				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		GAAGACAATCGGGAAGAAAAC	0.493													12	55					0	0	0.010729	0	0	
EFS	10278	broad.mit.edu	37	14	23829153	23829153	+	Silent	SNP	C	T	T	rs115947674	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:23829153C>T	uc001wjo.2	-	4	1142	c.534G>A	c.(532-534)CCG>CCA	p.P178P	EFS_uc001wjp.2_Silent_p.P85P|EFS_uc010tnm.1_Silent_p.P85P	NM_005864	NP_005855	O43281	EFS_HUMAN	embryonal Fyn-associated substrate isoform 1	178	Pro-rich.				cell adhesion|intracellular signal transduction	cytoplasm	SH3 domain binding			large_intestine(1)	1	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		CAGGGGGCTGCGGGGCAACCC	0.662													10	40					0	0	0.001855	0	0	
MYH7	4625	broad.mit.edu	37	14	23886745	23886745	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:23886745T>C	uc001wjx.2	-	31	4426	c.4320A>G	c.(4318-4320)GCA>GCG	p.A1440A		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1440	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TGTCCAGGGCTGCAGCAGCAG	0.602													10	63					0	0	0.006214	0	0	
AP1G2	8906	broad.mit.edu	37	14	24032638	24032638	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:24032638G>A	uc001wkl.2	-	14	1698	c.1361C>T	c.(1360-1362)GCC>GTC	p.A454V	AP1G2_uc001wkj.2_Missense_Mutation_p.A73V|AP1G2_uc001wkk.3_Missense_Mutation_p.A382V|AP1G2_uc001wkn.2_Missense_Mutation_p.A73V|uc001wko.1_Intron|AP1G2_uc001wkp.1_RNA|AP1G2_uc010tnp.1_Missense_Mutation_p.A454V	NM_003917	NP_003908	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2	454					interspecies interaction between organisms|intracellular protein transport|vesicle-mediated transport	AP-1 adaptor complex|endosome membrane	protein binding|protein transporter activity			ovary(1)	1	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		CACAGAGTAGGCATGTAGCTC	0.627											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	7					0	0	0.004672	0	0	
CPNE6	9362	broad.mit.edu	37	14	24542713	24542713	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:24542713G>T	uc001wll.2	+	3	273	c.174G>T	c.(172-174)GAG>GAT	p.E58D	CPNE6_uc010tnv.1_Missense_Mutation_p.E113D|CPNE6_uc001wlm.2_5'UTR|CPNE6_uc001wln.2_5'Flank	NM_006032	NP_006023	O95741	CPNE6_HUMAN	copine 6	58	C2 1.				lipid metabolic process|nervous system development|synaptic transmission|vesicle-mediated transport		calcium ion binding|transporter activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0184)		CACAGGTAGAGCGCACAGAGG	0.577													16	83					1.56452e-12	1.74565e-12	0.007413	1	0	
CPNE6	9362	broad.mit.edu	37	14	24542860	24542860	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:24542860C>T	uc001wll.2	+	3	420	c.321C>T	c.(319-321)CTC>CTT	p.L107L	CPNE6_uc010tnv.1_Silent_p.L162L|CPNE6_uc001wlm.2_5'UTR|CPNE6_uc001wln.2_5'Flank	NM_006032	NP_006023	O95741	CPNE6_HUMAN	copine 6	107	C2 1.				lipid metabolic process|nervous system development|synaptic transmission|vesicle-mediated transport		calcium ion binding|transporter activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0184)		ATACCTTCCTCGGCTCTACGG	0.587													8	25					0	0	0.006214	0	0	
RNF31	55072	broad.mit.edu	37	14	24621133	24621133	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:24621133C>T	uc001wmn.1	+	11	2311	c.2062C>T	c.(2062-2064)CGG>TGG	p.R688W	RNF31_uc001wml.1_Missense_Mutation_p.R537W|RNF31_uc001wmm.1_RNA|RNF31_uc010alg.1_Missense_Mutation_p.R447W|RNF31_uc001wmo.1_Missense_Mutation_p.R155W|RNF31_uc001wmp.2_RNA	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	688					CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)		CAGCCAGGACCGGGCCTTCCT	0.647													10	40					0	0	0.010729	0	0	
TGM1	7051	broad.mit.edu	37	14	24731001	24731001	+	Silent	SNP	G	A	A	rs142338588		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:24731001G>A	uc001wod.2	-	3	532	c.408C>T	c.(406-408)TAC>TAT	p.Y136Y	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	136					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)	TCAGCTCGTCGTACTCATACT	0.577													4	36					0	0	0.006214	0	0	
NFATC4	4776	broad.mit.edu	37	14	24838782	24838782	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:24838782G>A	uc001wpc.2	+	2	499	c.178G>A	c.(178-180)GGT>AGT	p.G60S	NFATC4_uc010tok.1_Missense_Mutation_p.G123S|NFATC4_uc010tol.1_Missense_Mutation_p.G123S|NFATC4_uc010alr.2_Missense_Mutation_p.G123S|NFATC4_uc010als.2_Missense_Mutation_p.G73S|NFATC4_uc010tom.1_Missense_Mutation_p.G73S|NFATC4_uc010ton.1_Missense_Mutation_p.G73S|NFATC4_uc010too.1_Missense_Mutation_p.G73S|NFATC4_uc010alt.2_Missense_Mutation_p.G92S|NFATC4_uc010top.1_Missense_Mutation_p.G92S|NFATC4_uc010toq.1_Missense_Mutation_p.G92S|NFATC4_uc010alu.2_Missense_Mutation_p.G60S|NFATC4_uc010tor.1_Missense_Mutation_p.G60S|NFATC4_uc010tos.1_5'UTR|NFATC4_uc010tot.1_Missense_Mutation_p.G48S|NFATC4_uc010tou.1_5'UTR|NFATC4_uc010tov.1_Missense_Mutation_p.G48S|NFATC4_uc010tow.1_5'UTR|NFATC4_uc010alv.2_Missense_Mutation_p.G48S|NFATC4_uc010tox.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	60	Pro-rich.				cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)		TGCACCTATCGGTATTCCCCG	0.667													13	45					0	0	0.002450	0	0	
STRN3	29966	broad.mit.edu	37	14	31364745	31364745	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:31364745T>C	uc001wqu.2	-	18	2482	c.2266A>G	c.(2266-2268)ACA>GCA	p.T756A	STRN3_uc001wqv.2_Missense_Mutation_p.T672A|STRN3_uc010tpj.1_RNA	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	756	WD 5.				negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		TGCACACATGTCTTGCTGTCT	0.353													5	34					0	0	0.001168	0	0	
HECTD1	25831	broad.mit.edu	37	14	31588960	31588960	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:31588960C>T	uc001wrc.1	-	29	5840	c.5351G>A	c.(5350-5352)CGT>CAT	p.R1784H	HECTD1_uc001wra.1_5'UTR|HECTD1_uc001wrb.1_5'UTR|HECTD1_uc001wrd.1_Missense_Mutation_p.R1252H	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	1784					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		GACATTAGTACGACCAGGTCT	0.393													14	77					0	0	0.004007	0	0	
SSTR1	6751	broad.mit.edu	37	14	38679606	38679606	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:38679606C>A	uc001wul.1	+	3	1629	c.1012C>A	c.(1012-1014)CTA>ATA	p.L338I	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	338	Cytoplasmic (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)	CCAACGCATCCTATGCCTCAG	0.572													7	72					0.000157383	0.000167469	0.003080	1	0	
SSTR1	6751	broad.mit.edu	37	14	38679687	38679687	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:38679687G>A	uc001wul.1	+	3	1710	c.1093G>A	c.(1093-1095)GTG>ATG	p.V365M	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	365	Cytoplasmic (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)	TGCCTACAGTGTGGAAGACTT	0.632													8	45					0	0	0.010729	0	0	
SIP1	8487	broad.mit.edu	37	14	39601231	39601231	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:39601231C>T	uc001wuq.2	+	8	725	c.703C>T	c.(703-705)CGG>TGG	p.R235W	SIP1_uc001wur.2_Missense_Mutation_p.R235W|SIP1_uc001wus.2_Missense_Mutation_p.R220W|SIP1_uc010amx.2_RNA	NM_003616	NP_003607	O14893	GEMI2_HUMAN	SMN-interacting protein 1 isoform alpha	235					ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)		TTCACTGATTCGGCAGCTTGC	0.358													13	75					0	0	0.013537	0	0	
FKBP3	2287	broad.mit.edu	37	14	45603570	45603570	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:45603570C>A	uc010tqf.1	-	1	163	c.90G>T	c.(88-90)CAG>CAT	p.Q30H	FANCM_uc001wwc.2_5'Flank|FANCM_uc001wwd.3_5'Flank|FANCM_uc010anf.2_5'Flank	NM_002013	NP_002004	Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	30					protein folding	membrane|nucleus	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor activity				0						AACCGTGTTCCTGCAGAAACT	0.637													12	39					1.3612e-06	1.47464e-06	0.003163	1	0	
NIN	51199	broad.mit.edu	37	14	51208344	51208344	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:51208344C>A	uc001wym.2	-	25	5595	c.5404G>T	c.(5404-5406)GAA>TAA	p.E1802*	NIN_uc001wyi.2_Nonsense_Mutation_p.E1802*|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Nonsense_Mutation_p.E1089*|NIN_uc010tqp.1_Nonsense_Mutation_p.E1808*|NIN_uc001wyo.2_Nonsense_Mutation_p.E1802*|NIN_uc001wyn.2_5'Flank	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	1802	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)					GACATCACTTCTTGTTTTAAA	0.328			T	PDGFRB	MPD								38	119					1.32136e-16	1.48619e-16	0.008740	1	0	
PYGL	5836	broad.mit.edu	37	14	51375597	51375597	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:51375597A>G	uc001wyu.2	-	18	2381	c.2254T>C	c.(2254-2256)TCT>CCT	p.S752P	PYGL_uc010tqq.1_Missense_Mutation_p.S718P|PYGL_uc001wyv.2_Missense_Mutation_p.S426P|PYGL_uc001wyt.2_5'Flank	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	752					glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding	p.S752F(1)		skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)	TGCTTGGGAGAAAAAAAGCCA	0.443													32	115					0	0	0.009535	0	0	
NID2	22795	broad.mit.edu	37	14	52534592	52534592	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:52534592G>A	uc001wzo.2	-	2	752	c.518C>T	c.(517-519)GCG>GTG	p.A173V	NID2_uc010tqs.1_Missense_Mutation_p.A173V|NID2_uc010tqt.1_Missense_Mutation_p.A173V|NID2_uc001wzp.2_Missense_Mutation_p.A173V	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	173	NIDO.					basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					CGAGGGCAGCGCCCCGCGCTT	0.637													23	89					0	0	0.003330	0	0	
NID2	22795	broad.mit.edu	37	14	52535601	52535601	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:52535601G>A	uc001wzo.2	-	1	346	c.112C>T	c.(112-114)CCA>TCA	p.P38S	NID2_uc010tqs.1_Missense_Mutation_p.P38S|NID2_uc010tqt.1_Missense_Mutation_p.P38S|NID2_uc001wzp.2_Missense_Mutation_p.P38S	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	38						basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					TCCCCGTGTGGGAAGAGCTCG	0.672													4	24					0	0	0.009096	0	0	
PTGDR	5729	broad.mit.edu	37	14	52735263	52735263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:52735263C>T	uc001wzq.2	+	1	833	c.731C>T	c.(730-732)GCC>GTC	p.A244V		NM_000953	NP_000944	Q13258	PD2R_HUMAN	prostaglandin D2 receptor	244	Cytoplasmic (Potential).					integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	AGGGACTGTGCCGAGCCGCGC	0.687													5	21					0	0	0.004482	0	0	
DDHD1	80821	broad.mit.edu	37	14	53619158	53619158	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:53619158C>T	uc001xai.2	-	1	889	c.659G>A	c.(658-660)GGC>GAC	p.G220D	DDHD1_uc001xaj.2_Missense_Mutation_p.G220D|DDHD1_uc001xah.2_Missense_Mutation_p.G220D	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c	220					lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)					GGAGGCTGGGCCCGTGGGGGA	0.697													4	4					0	0	0.000602	0	0	
KIAA0831	22863	broad.mit.edu	37	14	55848756	55848756	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:55848756C>T	uc001xbx.1	-	6	837	c.801G>A	c.(799-801)TGG>TGA	p.W267*	FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbw.1_Nonsense_Mutation_p.W154*	NM_014924	NP_055739	Q6ZNE5	BAKOR_HUMAN	Barkor	267					autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0						GGAGGCTAATCCAAGGCCCTG	0.527													24	93					0	0	0.002780	0	0	
C14orf37	145407	broad.mit.edu	37	14	58563560	58563560	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:58563560G>T	uc001xdc.2	-	5	2082	c.1971C>A	c.(1969-1971)ACC>ACA	p.T657T	C14orf37_uc010tro.1_Silent_p.T695T|C14orf37_uc001xdd.2_Silent_p.T657T	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	657	Extracellular (Potential).					integral to membrane	binding				0						TACCAGGGAGGGTAAAACCTG	0.443													11	56					6.42651e-13	7.18484e-13	0.010729	1	0	
DACT1	51339	broad.mit.edu	37	14	59108339	59108339	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:59108339G>T	uc001xdw.2	+	3	672	c.508G>T	c.(508-510)GGA>TGA	p.G170*	DACT1_uc010trv.1_Translation_Start_Site|DACT1_uc001xdx.2_Nonsense_Mutation_p.G170*|DACT1_uc010trw.1_Translation_Start_Site	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	170					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5						TGGGGCTTCAGGATCCCTTTC	0.433													20	109					4.47668e-21	5.04868e-21	0.003954	1	0	
C14orf50	145376	broad.mit.edu	37	14	65053973	65053973	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:65053973A>G	uc001xhl.1	+	10	869	c.773A>G	c.(772-774)GAG>GGG	p.E258G	C14orf50_uc001xhm.1_5'UTR	NM_172365	NP_758953	Q96LQ0	CN050_HUMAN	hypothetical protein LOC145376	258										skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)		CACTTGACAGAGATTGAAGAA	0.423													14	60					0	0	0.004007	0	0	
FUT8	2530	broad.mit.edu	37	14	66082939	66082939	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:66082939G>A	uc001xin.2	+	5	1527	c.330G>A	c.(328-330)AAG>AAA	p.K110K	FUT8_uc001xio.2_Silent_p.K110K|FUT8_uc010tsp.1_5'UTR|FUT8_uc001xir.3_RNA|FUT8_uc001xip.2_Silent_p.K110K|FUT8_uc001xiq.2_5'UTR	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	110	Lumenal (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		GTCTGGGGAAGGATCATGAAA	0.373													10	39					0	0	0.008291	0	0	
GPHN	10243	broad.mit.edu	37	14	67431987	67431987	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:67431987C>T	uc001xiy.2	+	8	1930	c.809C>T	c.(808-810)TCG>TTG	p.S270L	GPHN_uc001xiw.2_Missense_Mutation_p.S285L|GPHN_uc001xix.2_Missense_Mutation_p.S303L|GPHN_uc010tss.1_Missense_Mutation_p.S283L|GPHN_uc010tst.1_Missense_Mutation_p.S239L|GPHN_uc010tsu.1_Missense_Mutation_p.S193L	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2	270	Interaction with GABARAP (By similarity).				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		CCTTCAGAATCGCCTCGTGCT	0.498			T	MLL	AL								11	71					0	0	0.013537	0	0	
GPHN	10243	broad.mit.edu	37	14	67576927	67576927	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:67576927A>G	uc001xiy.2	+	13	2386	c.1265A>G	c.(1264-1266)GAT>GGT	p.D422G	GPHN_uc001xix.2_Missense_Mutation_p.D455G|GPHN_uc010tss.1_Missense_Mutation_p.D468G|GPHN_uc010tst.1_Missense_Mutation_p.D391G|GPHN_uc010tsu.1_Missense_Mutation_p.D345G	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2	422	MPT adenylyltransferase.				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TGCGGTGCTGATGCAGTAGTA	0.443			T	MLL	AL								32	140					0	0	0.003271	0	0	
MAP3K9	4293	broad.mit.edu	37	14	71209080	71209080	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:71209080T>C	uc001xmm.2	-	6	1555	c.1555A>G	c.(1555-1557)AGC>GGC	p.S519G	MAP3K9_uc010ttk.1_Missense_Mutation_p.S256G|MAP3K9_uc001xmk.2_Missense_Mutation_p.S213G|MAP3K9_uc001xml.2_Missense_Mutation_p.S519G	NM_033141	NP_149132	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase	519				KLKDGNRISLPSDFQHKFTVQASPT -> AQPVLPFPHGHS RCPGGTGSSWGGQ (in Ref. 4).	activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GAAGGGAGGCTGATGCGGTTG	0.607													14	61					0	0	0.003163	0	0	
LTBP2	4053	broad.mit.edu	37	14	75022341	75022341	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:75022341G>T	uc001xqa.2	-	4	1273	c.886C>A	c.(886-888)CGC>AGC	p.R296S		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	296					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)		CGGACAGTGCGGGACAACCCC	0.657													10	35					3.07112e-06	3.32061e-06	0.010729	1	0	
VIPAR	63894	broad.mit.edu	37	14	77895366	77895366	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:77895366G>A	uc001xtt.1	-	19	1677	c.1339C>T	c.(1339-1341)CAT>TAT	p.H447Y	VIPAR_uc001xtu.1_Missense_Mutation_p.H447Y|VIPAR_uc010tvj.1_Missense_Mutation_p.H398Y|VIPAR_uc001xtv.1_Missense_Mutation_p.H447Y	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894	447					endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1						ACGACATCATGGCACTTGAAC	0.453													15	76					0	0	0.006122	0	0	
NRXN3	9369	broad.mit.edu	37	14	79933651	79933651	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:79933651G>A	uc001xun.2	+	13	2722	c.2231G>A	c.(2230-2232)CGC>CAC	p.R744H	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Missense_Mutation_p.R112H|NRXN3_uc010asw.2_Missense_Mutation_p.R112H|NRXN3_uc001xur.3_Missense_Mutation_p.R112H	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1117	Extracellular (Potential).|Laminin G-like 6.				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CGGTCTGACCGCCTTGCCGTG	0.567													4	41					0	0	0.009096	0	0	
SMEK1	55671	broad.mit.edu	37	14	91942843	91942843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:91942843G>A	uc001xzn.2	-	6	1841	c.1019C>T	c.(1018-1020)GCG>GTG	p.A340V	SMEK1_uc001xzm.2_Missense_Mutation_p.A340V|SMEK1_uc001xzo.2_Missense_Mutation_p.A340V|SMEK1_uc010atz.2_Missense_Mutation_p.A101V|SMEK1_uc001xzp.1_RNA|SMEK1_uc001xzq.1_Missense_Mutation_p.A216V	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1	340						microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		TTGGGAAAACGCACAAAATTC	0.259													11	49					0	0	0.013537	0	0	
GOLGA5	9950	broad.mit.edu	37	14	93299632	93299632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:93299632G>A	uc001yaz.1	+	10	2067	c.1885G>A	c.(1885-1887)GCC>ACC	p.A629T	GOLGA5_uc001yba.1_Missense_Mutation_p.A26T	NM_005113	NP_005104	Q8TBA6	GOGA5_HUMAN	Golgi autoantigen, golgin subfamily a, 5	629	Cytoplasmic (Potential).|Potential.				Golgi organization	cis-Golgi network|integral to membrane	ATP binding|protein homodimerization activity|protein tyrosine kinase activity|Rab GTPase binding			ovary(2)|lung(1)	3		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		GATGAACTCCGCCTCTGGAAG	0.428			T	RET	papillary thyroid								37	183					0	0	0.008740	0	0	
OTUB2	78990	broad.mit.edu	37	14	94510971	94510971	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:94510971G>A	uc001yci.2	+	5	503	c.343G>A	c.(343-345)GTG>ATG	p.V115M		NM_023112	NP_075601	Q96DC9	OTUB2_HUMAN	OTU domain, ubiquitin aldehyde binding 2	115	OTU.				cellular amino acid metabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination		omega peptidase activity|protein binding|ubiquitin-specific protease activity				0		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)		GGATGGCTCAGTGTCCAGCCT	0.612													7	40					0	0	0.001984	0	0	
VRK1	7443	broad.mit.edu	37	14	97326912	97326912	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:97326912T>C	uc001yft.2	+	11	1014	c.908T>C	c.(907-909)ATG>ACG	p.M303T		NM_003384	NP_003375	Q99986	VRK1_HUMAN	vaccinia related kinase 1	303	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity			large_intestine(1)|stomach(1)	2		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		GCCAAATACATGGAAACAGTG	0.279													8	44					0	0	0.004482	0	0	
EVL	51466	broad.mit.edu	37	14	100551127	100551127	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:100551127A>G	uc001ygt.2	+	2	348	c.109A>G	c.(109-111)AAC>GAC	p.N37D	EVL_uc001ygv.2_Missense_Mutation_p.N43D|EVL_uc001ygu.2_Missense_Mutation_p.N39D|EVL_uc010avu.2_5'UTR	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like	37	WH1.				actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				CAGCCGGATCAACATCTACCA	0.517													22	55					0	0	0.003330	0	0	
DYNC1H1	1778	broad.mit.edu	37	14	102471206	102471206	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:102471206G>A	uc001yks.2	+	25	5321	c.5157G>A	c.(5155-5157)GAG>GAA	p.E1719E		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	1719	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						TGCTTGCTGAGTCTGTTACGG	0.393													5	37					0	0	0.000602	0	0	
DYNC1H1	1778	broad.mit.edu	37	14	102494049	102494049	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:102494049G>A	uc001yks.2	+	47	9306	c.9142G>A	c.(9142-9144)GAG>AAG	p.E3048K		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3048	AAA 4 (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						GGACTCGCACGAGGAGCTCTA	0.577													9	45					0	0	0.006214	0	0	
TECPR2	9895	broad.mit.edu	37	14	102843129	102843129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:102843129C>T	uc001ylw.1	+	2	219	c.71C>T	c.(70-72)CCG>CTG	p.P24L	TECPR2_uc010txw.1_Missense_Mutation_p.P24L|TECPR2_uc010awl.2_Missense_Mutation_p.P24L|TECPR2_uc010txx.1_Nonsense_Mutation_p.R4*	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	24							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3						AATGCCATTCCGACAAAGATC	0.537													11	44					0	0	0.001855	0	0	
EIF5	1983	broad.mit.edu	37	14	103806054	103806054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:103806054C>T	uc001ymq.2	+	10	1507	c.985C>T	c.(985-987)CTT>TTT	p.L329F	EIF5_uc001ymr.2_Missense_Mutation_p.L329F|EIF5_uc001yms.2_Missense_Mutation_p.L329F|EIF5_uc001ymt.2_Missense_Mutation_p.L329F|EIF5_uc001ymu.2_Missense_Mutation_p.L329F	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	329	W2.				regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)			TCAAGCTCAGCTTATCTCCAA	0.433													7	66					0	0	0.001984	0	0	
AHNAK2	113146	broad.mit.edu	37	14	105409290	105409290	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:105409290G>A	uc010axc.1	-	7	12618	c.12498C>T	c.(12496-12498)GAC>GAT	p.D4166D	AHNAK2_uc001ypx.2_Silent_p.D4066D	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4166						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGAGGCTCACGTCGGCTTTCG	0.607													51	141					0	0	0.014410	0	0	
ADAM6	8755	broad.mit.edu	37	14	106714528	106714528	+	RNA	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:106714528A>G	uc010tyt.1	-	645		c.19077T>C								Parts of antibodies, mostly variable regions.												0						TACCCATTCCAGCCCCTTCCC	0.517													7	49					0	0	0.001984	0	0	
ADAM6	8755	broad.mit.edu	37	14	106994115	106994115	+	RNA	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:106994115A>G	uc010tyt.1	-	187		c.8332T>C								Parts of antibodies, mostly variable regions.												0						CTCACACTGGACACCTGCAAA	0.522													12	153					0	0	0.002450	0	0	
CYFIP1	23191	broad.mit.edu	37	15	22955256	22955256	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:22955256C>T	uc001yus.2	+	15	1754	c.1650C>T	c.(1648-1650)CGC>CGT	p.R550R	CYFIP1_uc001yut.2_Silent_p.R550R|CYFIP1_uc010aya.1_Silent_p.R578R|CYFIP1_uc001yuu.2_5'Flank	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform	550					axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TACCACGCCGCGCCGTGGGAC	0.667													8	17					0	0	0.004482	0	0	
MKRN3	7681	broad.mit.edu	37	15	23811639	23811639	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:23811639T>C	uc001ywh.3	+	1	1186	c.710T>C	c.(709-711)GTG>GCG	p.V237A	MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Missense_Mutation_p.V237A	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	237						ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			lung(6)|large_intestine(2)|ovary(2)	10		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		CAGATGGCTGTGGGCAGTGGG	0.567													5	28					0	0	0.001168	0	0	
MAGEL2	54551	broad.mit.edu	37	15	23889460	23889460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:23889460G>A	uc001ywj.3	-	1	1716	c.1621C>T	c.(1621-1623)CGG>TGG	p.R541W		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TTTGTCTCCCGGACATCCAAC	0.463													10	39					0	0	0.006214	0	0	
SNRPN	6638	broad.mit.edu	37	15	25222053	25222053	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:25222053A>G	uc001ywp.1	+	10	1187	c.297A>G	c.(295-297)GGA>GGG	p.G99G	SNRPN_uc001ywq.1_Silent_p.G99G|SNRPN_uc001ywr.1_Silent_p.G99G|SNRPN_uc001yws.1_Silent_p.G99G|SNRPN_uc001ywt.1_Silent_p.G99G|SNRPN_uc001ywv.1_Silent_p.G102G|SNRPN_uc001yww.1_Silent_p.G99G|SNRPN_uc001ywx.1_Silent_p.G99G|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_3'UTR	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	99					RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		CACTTGCTGGAGCTGCTGGAG	0.512									Prader-Willi_syndrome				9	68					0	0	0.001855	0	0	
HERC2	8924	broad.mit.edu	37	15	28357109	28357109	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:28357109G>A	uc001zbj.2	-	93	14411	c.14305C>T	c.(14305-14307)CCC>TCC	p.P4769S	HERC2_uc001zbi.2_Missense_Mutation_p.P458S	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	4769	HECT.				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GAATACCTGGGCAGCTTCAGC	0.498													11	63					0	0	0.013537	0	0	
HERC2	8924	broad.mit.edu	37	15	28366563	28366563	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:28366563G>A	uc001zbj.2	-	86	13307	c.13201C>T	c.(13201-13203)CGG>TGG	p.R4401W		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	4401					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ACTACTTTCCGGAAAGCCGCC	0.438													6	51					0	0	0.003080	0	0	
HERC2	8924	broad.mit.edu	37	15	28538035	28538035	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:28538035T>C	uc001zbj.2	-	4	427	c.321A>G	c.(319-321)CCA>CCG	p.P107P	HERC2_uc001zbl.1_5'UTR	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	107					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAAGATTACCTGGTTGCTTGC	0.378													5	34					0	0	0.001168	0	0	
FMN1	342184	broad.mit.edu	37	15	33192305	33192305	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:33192305C>T	uc001zhf.3	-	10	2860	c.2860G>A	c.(2860-2862)GTG>ATG	p.V954M		NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	1177	FH2.				actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		ATATCCTTCACGCTCTTCACG	0.433													16	67					0	0	0.004990	0	0	
PGBD4	161779	broad.mit.edu	37	15	34396276	34396276	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:34396276C>T	uc001zho.2	+	1	2003	c.1544C>T	c.(1543-1545)ACA>ATA	p.T515I	C15orf24_uc001zhm.2_5'Flank|C15orf24_uc001zhn.2_5'Flank	NM_152595	NP_689808	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	515											0		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)		GATGATGTCACACCTCTTCGT	0.483													11	62					0	0	0.010729	0	0	
LOC723972	723972	broad.mit.edu	37	15	35529571	35529571	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:35529571G>A	uc001ziy.2	+	1		c.45G>A				NR_003144				Homo sapiens hepatopoietin PCn127 mRNA, complete cds.												0						GGAACAGGACGCCCTCTGATG	0.507													43	137					0	0	0.011902	0	0	
SPRED1	161742	broad.mit.edu	37	15	38641674	38641674	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:38641674G>A	uc001zka.3	+	6	969	c.634G>A	c.(634-636)GTA>ATA	p.V212I		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	212					inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		TATGGAATACGTACAGCGGCA	0.328									Legius_syndrome				9	52					0	0	0.010729	0	0	
BAHD1	22893	broad.mit.edu	37	15	40758302	40758302	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:40758302C>T	uc001zlu.2	+	7	2387	c.2316C>T	c.(2314-2316)CAC>CAT	p.H772H	BAHD1_uc001zlt.2_Silent_p.H771H|BAHD1_uc010bbp.1_Silent_p.H768H|BAHD1_uc001zlv.2_Silent_p.H769H	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	772	BAH.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		ACTTCCGCCACGGGCGCATCC	0.632													5	44					0	0	0.013537	0	0	
RAD51	5888	broad.mit.edu	37	15	41021004	41021004	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:41021004C>T	uc001zmi.3	+	7	925	c.626C>T	c.(625-627)GCC>GTC	p.A209V	RAD51_uc010bbw.2_Missense_Mutation_p.A209V|RAD51_uc010bbx.2_Missense_Mutation_p.A210V|RAD51_uc001zmk.3_RNA|RAD51_uc001zml.3_Missense_Mutation_p.A210V	NM_002875	NP_002866	Q06609	RAD51_HUMAN	RAD51 homolog protein isoform 1	209	Interaction with PALB2.				DNA recombinase assembly|DNA unwinding involved in replication|mitotic recombination|positive regulation of DNA ligation|protein homooligomerization|reciprocal meiotic recombination	mitochondrial matrix|nucleus|perinuclear region of cytoplasm|PML body	ATP binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|protein C-terminus binding|single-stranded DNA binding|single-stranded DNA-dependent ATPase activity				0		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		CAAGCATCAGCCATGATGGTA	0.433								Homologous_recombination					13	158					0	0	0.001855	0	0	
RPAP1	26015	broad.mit.edu	37	15	41820101	41820101	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:41820101G>A	uc001zod.2	-	11	1509	c.1385C>T	c.(1384-1386)GCC>GTC	p.A462V		NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	462						nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AGCACGGATGGCGGTTGCAAT	0.577													10	25					0	0	0.008291	0	0	
ZFP106	64397	broad.mit.edu	37	15	42743354	42743354	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:42743354C>T	uc001zpw.2	-	2	1382	c.1047G>A	c.(1045-1047)TGG>TGA	p.W349*	ZFP106_uc001zpu.2_5'Flank|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Nonsense_Mutation_p.W132*|ZFP106_uc001zpy.1_Nonsense_Mutation_p.W372*	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	349						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)		GGTAAGGCGTCCAGCGACGAG	0.453													20	93					0	0	0.010504	0	0	
TGM5	9333	broad.mit.edu	37	15	43533132	43533132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:43533132C>T	uc001zrd.1	-	7	927	c.919G>A	c.(919-921)GAT>AAT	p.D307N	TGM5_uc001zrc.1_5'Flank|TGM5_uc001zre.1_Missense_Mutation_p.D225N	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	307					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CCATCTGTATCGTGGCCAGAG	0.453													15	75					0	0	0.003163	0	0	
TUBGCP4	27229	broad.mit.edu	37	15	43677988	43677988	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:43677988G>A	uc001zro.2	+	8	964	c.724_splice	c.e8-1	p.R242_splice	TUBGCP4_uc001zrn.2_Splice_Site_p.R242_splice|TUBGCP4_uc010bdh.2_Splice_Site	NM_014444	NP_055259	Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	structural constituent of cytoskeleton			ovary(3)	3		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		TCCTTGACTAGCGCCTGATTG	0.428													16	49					0	0	0.004007	0	0	
TP53BP1	7158	broad.mit.edu	37	15	43707815	43707815	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:43707815C>T	uc001zrs.2	-	23	5199	c.5051G>A	c.(5050-5052)CGC>CAC	p.R1684H	TP53BP1_uc010udp.1_Missense_Mutation_p.R1684H|TP53BP1_uc001zrq.3_Missense_Mutation_p.R1689H|TP53BP1_uc001zrr.3_Missense_Mutation_p.R1689H|TP53BP1_uc010udq.1_Missense_Mutation_p.R1689H|TP53BP1_uc001zrp.2_Missense_Mutation_p.R101H	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	1684					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGCAGACTTGCGACCTCGCTT	0.498								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					15	72					0	0	0.004007	0	0	
SPG11	80208	broad.mit.edu	37	15	44951445	44951445	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:44951445A>G	uc001ztx.2	-	3	530	c.499T>C	c.(499-501)TTC>CTC	p.F167L	SPG11_uc010ueh.1_Missense_Mutation_p.F167L|SPG11_uc010uei.1_Missense_Mutation_p.F167L|SPG11_uc001zua.1_Missense_Mutation_p.F167L	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	167	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTGTTGATGAACAGTAATGAT	0.348													16	52					0	0	0.007413	0	0	
DUOX2	50506	broad.mit.edu	37	15	45387642	45387642	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:45387642C>T	uc010bea.2	-	31	4435	c.4232G>A	c.(4231-4233)TGT>TAT	p.C1411Y	DUOX2_uc001zun.2_Missense_Mutation_p.C1411Y	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1411	Cytoplasmic (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CACCTTCTTACACAGCATTTG	0.552													12	70					0	0	0.002450	0	0	
SLC28A2	9153	broad.mit.edu	37	15	45556197	45556197	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:45556197G>A	uc001zva.2	+	6	630	c.565G>A	c.(565-567)GCC>ACC	p.A189T		NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled	189	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)		TATCCTCTTTGCCTGCTCCAA	0.493													14	64					0	0	0.002450	0	0	
HDC	3067	broad.mit.edu	37	15	50534934	50534934	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:50534934C>T	uc001zxz.2	-	12	1618	c.1512G>A	c.(1510-1512)ACG>ACA	p.T504T	HDC_uc001zxy.2_Silent_p.T247T|HDC_uc010uff.1_Silent_p.T471T	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	504					catecholamine biosynthetic process|histidine metabolic process		histidine decarboxylase activity			large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)	L-Histidine(DB00117)|Pyridoxal Phosphate(DB00114)	ACTGAAGGGACGTTCCACAGG	0.587													21	36					0	0	0.012319	0	0	
TRPM7	54822	broad.mit.edu	37	15	50878623	50878623	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:50878623A>G	uc001zyt.3	-	28	4716	c.4452T>C	c.(4450-4452)TGT>TGC	p.C1484C	TRPM7_uc010bew.1_Silent_p.C1484C	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,	1484	Cytoplasmic (Potential).				cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AAGTTCTGTGACAGTCAGTAA	0.303													9	38					0	0	0.006214	0	0	
VPS13C	54832	broad.mit.edu	37	15	62147068	62147068	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:62147068A>G	uc002agz.2	-	84	11234	c.11160_splice	c.e84+1	p.E3720_splice	VPS13C_uc002aha.2_Splice_Site_p.E3677_splice	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						TAAATTGTTTACCTCTGCTGT	0.373													3	20					0	0	0.009096	0	0	
TLN2	83660	broad.mit.edu	37	15	63063176	63063176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:63063176C>T	uc002alb.3	+	39	5210	c.5210C>T	c.(5209-5211)GCA>GTA	p.A1737V	TLN2_uc002alc.3_Missense_Mutation_p.A130V|TLN2_uc002ald.2_Missense_Mutation_p.A130V	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1737					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						ACACAACTGGCAAGCTATTTT	0.493													14	46					0	0	0.003163	0	0	
USP3	9960	broad.mit.edu	37	15	63824853	63824853	+	Silent	SNP	G	A	A	rs148908419		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:63824853G>A	uc002amf.2	+	2	228	c.99G>A	c.(97-99)CGG>CGA	p.R33R	USP3_uc010uii.1_RNA|USP3_uc002amg.2_5'UTR|USP3_uc002amh.2_Silent_p.R11R|USP3_uc010uij.1_Silent_p.R33R|USP3_uc010uik.1_Intron|USP3_uc010bgs.2_Silent_p.R16R	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3	33	UBP-type.				DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)		TAGTGTGCCGGTCCAACAAAA	0.358													10	61					0	0	0.010729	0	0	
USP3	9960	broad.mit.edu	37	15	63881145	63881145	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:63881145T>C	uc002amf.2	+	14	1461	c.1332T>C	c.(1330-1332)CCT>CCC	p.P444P	USP3_uc002amg.2_Silent_p.P359P|USP3_uc002amh.2_Silent_p.P422P|USP3_uc010uij.1_Silent_p.P400P|USP3_uc010uik.1_Silent_p.P195P|USP3_uc010bgs.2_Silent_p.P427P|USP3_uc002ami.2_Silent_p.P275P|uc002amj.2_RNA|uc002amk.2_RNA|uc002aml.2_RNA	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3	444					DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)		TTCTGTAGCCTGAGAACAGTG	0.527													41	180					0	0	0.011902	0	0	
HERC1	8925	broad.mit.edu	37	15	63904654	63904654	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:63904654C>A	uc002amp.2	-	77	14344	c.14196G>T	c.(14194-14196)GAG>GAT	p.E4732D	HERC1_uc002amo.2_5'Flank	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	4732	HECT.				protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						CCACAGAGATCTCGGGCATCC	0.562													10	55					2.27111e-07	2.47315e-07	0.013537	1	0	
HERC1	8925	broad.mit.edu	37	15	64067377	64067377	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:64067377C>T	uc002amp.2	-	2	594	c.446G>A	c.(445-447)CGC>CAC	p.R149H	HERC1_uc010uil.1_Missense_Mutation_p.R149H|HERC1_uc010bgt.1_Missense_Mutation_p.R149H|HERC1_uc002amq.1_Missense_Mutation_p.R149H	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	149					protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						TGACCGGGGGCGTTCACTAAC	0.453													30	187					0	0	0.012213	0	0	
ITGA11	22801	broad.mit.edu	37	15	68661610	68661610	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:68661610G>A	uc002ari.2	-	3	264	c.177C>T	c.(175-177)GGC>GGT	p.G59G	ITGA11_uc010bib.2_Silent_p.G59G	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	59	FG-GAP 1.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)	CCAGTGGGGCGCCCACGACCA	0.572													9	34					0	0	0.013537	0	0	
ODF3L1	161753	broad.mit.edu	37	15	76019571	76019571	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:76019571C>A	uc002bax.1	+	4	737	c.515C>A	c.(514-516)CCT>CAT	p.P172H		NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	172											0						CCCAACACCCCTGTCAGCCGA	0.617													17	53					2.5808e-16	2.9008e-16	0.006122	1	0	
CIB2	10518	broad.mit.edu	37	15	78398176	78398176	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:78398176G>A	uc002bdb.1	-	5	768	c.447C>T	c.(445-447)TGC>TGT	p.C149C	CIB2_uc002bdc.1_Silent_p.C106C|CIB2_uc010ums.1_Silent_p.C149C	NM_006383	NP_006374	O75838	CIB2_HUMAN	DNA-dependent protein kinase catalytic	149	EF-hand 3.						calcium ion binding				0						TGACCTTGTCGCACACAAGCA	0.567													16	43					0	0	0.004007	0	0	
AGPHD1	123688	broad.mit.edu	37	15	78807371	78807371	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:78807371C>A	uc010unc.1	+	3	512	c.399C>A	c.(397-399)CCC>CCA	p.P133P	AGPHD1_uc002bdt.2_Silent_p.P133P|AGPHD1_uc010ble.2_Silent_p.P133P	NM_001013619	NP_001013641	A2RU49	AGPD1_HUMAN	aminoglycoside phosphotransferase domain	133						cytoplasm	kinase activity				0						CAGGAAGACCCATCGCTGAGC	0.418													14	38					1.5739e-10	1.74335e-10	0.004007	1	0	
ARNT2	9915	broad.mit.edu	37	15	80872883	80872883	+	Missense_Mutation	SNP	C	T	T	rs147344883		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:80872883C>T	uc002bfr.2	+	16	1911	c.1745C>T	c.(1744-1746)CCG>CTG	p.P582L	ARNT2_uc010unm.1_Missense_Mutation_p.P571L|ARNT2_uc002bfs.2_Missense_Mutation_p.P571L	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	582					central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity	p.P582Q(1)		central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			CCGCCCTTTCCGGGACAGGTA	0.567													5	36					0	0	0.001168	0	0	
IL16	3603	broad.mit.edu	37	15	81575086	81575086	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:81575086C>T	uc002bgh.3	+	9	1564	c.1188C>T	c.(1186-1188)GAC>GAT	p.D396D	IL16_uc002bgc.2_RNA|IL16_uc010blq.1_Silent_p.D396D|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Silent_p.D438D|IL16_uc002bgg.2_Silent_p.D396D|IL16_uc002bgi.1_Translation_Start_Site	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	396	PDZ 2.|Interaction with GRIN2A.				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						CGCACCTGGACGGACGTCTCC	0.537													31	105					0	0	0.004289	0	0	
FSD2	123722	broad.mit.edu	37	15	83451613	83451613	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:83451613A>G	uc002bjd.2	-	4	1067	c.900T>C	c.(898-900)GAT>GAC	p.D300D	FSD2_uc010uol.1_Silent_p.D300D|FSD2_uc010uom.1_Silent_p.D300D	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing	300	Potential.									central_nervous_system(1)	1						CTTTGCAAGTATCTAGGTTTT	0.373													52	210					0	0	0.014410	0	0	
GOLGA6L5	374650	broad.mit.edu	37	15	85056044	85056044	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:85056044G>A	uc002bkm.2	-	6		c.516C>T				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CCTGCTGGGGGCTCTGGGGCC	0.532													4	12					0	0	0.004482	0	0	
ZNF592	9640	broad.mit.edu	37	15	85327240	85327240	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:85327240C>G	uc002bld.2	+	4	1670	c.1334C>G	c.(1333-1335)GCC>GGC	p.A445G	ZNF592_uc010upb.1_RNA	NM_014630	NP_055445	Q92610	ZN592_HUMAN	zinc finger protein 592	445					cell death|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(2)	6			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CCCCAGGGGGCCAGGAAAGGG	0.642													9	33					0	0	0.006214	0	0	
ABHD2	11057	broad.mit.edu	37	15	89738497	89738497	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:89738497G>T	uc002bnj.2	+	16	2038	c.1121G>T	c.(1120-1122)GGG>GTG	p.G374V	ABHD2_uc002bnk.2_Missense_Mutation_p.G374V	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein	374						integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					CCTCTGCATGGGGGCCACTTG	0.557													6	52					5.4927e-09	6.03226e-09	0.004482	1	0	
C15orf42	90381	broad.mit.edu	37	15	90167247	90167247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:90167247C>T	uc002boe.2	+	20	3706	c.3706C>T	c.(3706-3708)CCC>TCC	p.P1236S	C15orf42_uc010upv.1_RNA	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1	1236	Pro-rich.				cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			GACTGCCCAGCCCAGGAGAGA	0.567													12	127					0	0	0.001855	0	0	
BLM	641	broad.mit.edu	37	15	91295078	91295078	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:91295078A>G	uc002bpr.2	+	4	958	c.861A>G	c.(859-861)CCA>CCG	p.P287P	BLM_uc010uqh.1_Silent_p.P287P|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_Silent_p.P287P	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	287					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AGAAAGTTCCATGTATTGAAT	0.323			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				17	63					0	0	0.004990	0	0	
ADAMTS17	170691	broad.mit.edu	37	15	100821558	100821558	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:100821558C>T	uc002bvv.1	-	4	744	c.665G>A	c.(664-666)CGG>CAG	p.R222Q	ADAMTS17_uc002bvx.1_5'UTR	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	222					proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		AGCGTTCCTCCGCTCCCGCCA	0.617													3	9					0	0	0.009096	0	0	
ASB7	140460	broad.mit.edu	37	15	101170100	101170100	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:101170100A>G	uc002bwk.2	+	5	1439	c.670A>G	c.(670-672)AGG>GGG	p.R224G	ASB7_uc002bwj.2_Missense_Mutation_p.R224G	NM_198243	NP_937886	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box-containing protein 7	224	ANK 7.				intracellular signal transduction					skin(1)	1	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			ATCTGCCCTTAGGGATGATGT	0.458													20	76					0	0	0.012319	0	0	
LRRK1	79705	broad.mit.edu	37	15	101528988	101528988	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:101528988C>T	uc002bwr.2	+	5	902	c.583C>T	c.(583-585)CGC>TGC	p.R195C	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bwq.1_Missense_Mutation_p.R195C	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	195	ANK 4.				small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGTCATCGTGCGCTTGCCCCT	0.607													5	34					0	0	0.001168	0	0	
RHBDF1	64285	broad.mit.edu	37	16	113713	113713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:113713G>A	uc002cfl.3	-	7	482	c.334C>T	c.(334-336)CGC>TGC	p.R112C	RHBDF1_uc010uty.1_Missense_Mutation_p.R135C|RHBDF1_uc010utz.1_Missense_Mutation_p.R112C|RHBDF1_uc010bqo.1_RNA	NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	112	Cytoplasmic (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|protein transport|proteolysis|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				TTCCCGTAGCGCTGGCTGCAG	0.647													6	8					0	0	0.003080	0	0	
CACNA1H	8912	broad.mit.edu	37	16	1250513	1250513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:1250513C>T	uc002cks.2	+	7	1309	c.1061C>T	c.(1060-1062)CCC>CTC	p.P354L	CACNA1H_uc002ckt.2_Missense_Mutation_p.P354L	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	354	Extracellular (Potential).|I.				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	GACTCCAACCCCCACAACGGT	0.647													6	27					0	0	0.004482	0	0	
CACNA1H	8912	broad.mit.edu	37	16	1262117	1262117	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:1262117C>T	uc002cks.2	+	25	4986	c.4738C>T	c.(4738-4740)CGC>TGC	p.R1580C	CACNA1H_uc002ckt.2_Missense_Mutation_p.R1580C|CACNA1H_uc002cku.2_Missense_Mutation_p.R286C|CACNA1H_uc010brj.2_Missense_Mutation_p.R286C|CACNA1H_uc002ckv.2_Missense_Mutation_p.R286C	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1580	Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	GCGGCTGCGGCGCCTAGAGAG	0.711													5	17					0	0	0.001168	0	0	
E4F1	1877	broad.mit.edu	37	16	2282576	2282576	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:2282576G>A	uc002cpm.2	+	5	777	c.729G>A	c.(727-729)ACG>ACA	p.T243T	E4F1_uc010bsi.2_Silent_p.T243T|E4F1_uc010bsj.2_Silent_p.T243T	NM_004424	NP_004415	Q66K89	E4F1_HUMAN	p120E4F	243	Mediates dimerization, DNA-binding, transcription repression of CCNA2 and interaction with HMGA2.				cell division|cell proliferation|interspecies interaction between organisms|mitosis|regulation of growth	cytoplasm|nucleoplasm	DNA binding|ligase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						GGCGGCACACGGGTGAGCTGG	0.687													3	6					0	0	0.009096	0	0	
ABCA3	21	broad.mit.edu	37	16	2333210	2333210	+	Missense_Mutation	SNP	C	T	T	rs149871856		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:2333210C>T	uc002cpy.1	-	26	4724	c.4012G>A	c.(4012-4014)GCC>ACC	p.A1338T	ABCA3_uc010bsk.1_Missense_Mutation_p.A1280T	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	1338					response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				CTCCGGAGGGCGCAGAGGATG	0.657													3	11					0	0	0.000602	0	0	
PRSS27	83886	broad.mit.edu	37	16	2764112	2764112	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:2764112C>T	uc002crf.2	-	4	853	c.462G>A	c.(460-462)ACG>ACA	p.T154T	PRSS27_uc002cre.2_Silent_p.T118T|PRSS27_uc002crg.2_Silent_p.T52T|PRSS27_uc010bst.1_Silent_p.T52T	NM_031948	NP_114154	Q9BQR3	PRS27_HUMAN	marapsin precursor	154	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						AGTTCATGCCCGTCTCAAAGA	0.622													11	33					0	0	0.008871	0	0	
SRRM2	23524	broad.mit.edu	37	16	2812472	2812472	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:2812472G>A	uc002crk.2	+	11	2492	c.1943G>A	c.(1942-1944)CGC>CAC	p.R648H	SRRM2_uc002crj.1_Missense_Mutation_p.R552H|SRRM2_uc002crl.1_Missense_Mutation_p.R648H|SRRM2_uc010bsu.1_Missense_Mutation_p.R552H	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	648	Arg-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						GGCAGGTCACGCTCTAGAACC	0.607													12	39					0	0	0.003163	0	0	
C16orf90	646174	broad.mit.edu	37	16	3544554	3544554	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:3544554G>A	uc002cvi.2	-	2	370	c.370C>T	c.(370-372)CGA>TGA	p.R124*		NM_001080524	NP_001073993	A8MZG2	CP090_HUMAN	hypothetical protein LOC646174	114											0						CTGGGCAATCGGGCTTCCAGA	0.672													8	10					0	0	0.013537	0	0	
BTBD12	84464	broad.mit.edu	37	16	3632513	3632513	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:3632513G>A	uc002cvp.2	-	15	5962	c.5335C>T	c.(5335-5337)CGG>TGG	p.R1779W		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	1779	Interaction with PLK1 and TERF2-TERF2IP.|Interaction with SLX1.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						TGCAGCTCCCGCAGCTCAAAG	0.647								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				9	55					0	0	0.010729	0	0	
CREBBP	1387	broad.mit.edu	37	16	3900561	3900561	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:3900561C>T	uc002cvv.2	-	2	739	c.535G>A	c.(535-537)GCT>ACT	p.A179T	CREBBP_uc002cvw.2_Missense_Mutation_p.A179T	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	179					cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTAAAGTTAGCATTCATGCAG	0.532			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				10	40					0	0	0.008291	0	0	
ADCY9	115	broad.mit.edu	37	16	4016953	4016953	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:4016953G>A	uc002cvx.2	-	11	3424	c.2885C>T	c.(2884-2886)CCG>CTG	p.P962L		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	962	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						ACTATTGCACGGGTTCCTCTC	0.597													5	28					0	0	0.000602	0	0	
VASN	114990	broad.mit.edu	37	16	4432050	4432050	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:4432050G>A	uc002cwj.1	+	2	1327	c.1172G>A	c.(1171-1173)AGC>AAC	p.S391N	CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc002cwh.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron|CORO7_uc002cwi.1_Intron|CORO7_uc010uxj.1_Intron|CORO7_uc010btp.1_Intron	NM_138440	NP_612449	Q6EMK4	VASN_HUMAN	slit-like 2 precursor	391	Extracellular (Potential).					extracellular region|integral to membrane					0						GAGGCCCCCAGCCCGCCCTCC	0.697													5	5					0	0	0.001168	0	0	
GRIN2A	2903	broad.mit.edu	37	16	9857426	9857426	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:9857426G>A	uc002czo.3	-	13	4523	c.3975C>T	c.(3973-3975)TAC>TAT	p.Y1325Y	GRIN2A_uc010uym.1_Silent_p.Y1325Y|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1325	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	ACAGGCTGCCGTAAAAATTTC	0.527													9	64					0	0	0.013537	0	0	
TEKT5	146279	broad.mit.edu	37	16	10788514	10788514	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:10788514G>A	uc002czz.1	-	1	289	c.217C>T	c.(217-219)CGG>TGG	p.R73W		NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5	73					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2						GTGGGCGGCCGCAGGGTACTG	0.637													7	47					0	0	0.001984	0	0	
CIITA	4261	broad.mit.edu	37	16	11000846	11000846	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:11000846C>T	uc002dai.3	+	11	1630	c.1497C>T	c.(1495-1497)GAC>GAT	p.D499D	CIITA_uc002daj.3_Silent_p.D500D|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Silent_p.D499D|CIITA_uc002dah.2_Silent_p.D451D|CIITA_uc010bup.1_Intron	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	499	NACHT.				interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1						TCATCCTAGACGGCTTCGAGG	0.647			T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								10	53					0	0	0.013537	0	0	
PDXDC1	23042	broad.mit.edu	37	16	15112747	15112747	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:15112747C>T	uc002dda.3	+	12	1238	c.1014C>T	c.(1012-1014)GCC>GCT	p.A338A	PDXDC1_uc010uzl.1_Silent_p.A323A|PDXDC1_uc010uzm.1_Silent_p.A247A|PDXDC1_uc002dcz.2_Silent_p.A315A|PDXDC1_uc002ddb.3_Silent_p.A311A|PDXDC1_uc010uzn.1_Silent_p.A310A|PDXDC1_uc002ddc.2_Silent_p.A338A	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	338					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	AACTCCGTGCCCTGCCTCTGT	0.408													4	103					0	0	0.006214	0	0	
TMC5	79838	broad.mit.edu	37	16	19451526	19451526	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:19451526T>G	uc002dgc.3	+	3	915	c.166T>G	c.(166-168)TCT>GCT	p.S56A	TMC5_uc010vaq.1_Missense_Mutation_p.S56A|TMC5_uc002dgb.3_Missense_Mutation_p.S56A|TMC5_uc010var.1_Missense_Mutation_p.S56A	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	56	Extracellular (Potential).					integral to membrane				skin(1)	1						CAATCCATACTCTGTAGCCTC	0.488													22	74					0	0	0.004656	0	0	
TMC5	79838	broad.mit.edu	37	16	19498632	19498632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:19498632G>A	uc002dgc.3	+	17	3306	c.2557G>A	c.(2557-2559)GCC>ACC	p.A853T	TMC5_uc010vaq.1_Missense_Mutation_p.A801T|TMC5_uc002dgb.3_Missense_Mutation_p.A853T|TMC5_uc010var.1_Missense_Mutation_p.A853T|TMC5_uc002dgd.1_Missense_Mutation_p.A607T|TMC5_uc002dge.3_Missense_Mutation_p.A607T|TMC5_uc002dgf.3_Missense_Mutation_p.A536T|TMC5_uc002dgg.3_Missense_Mutation_p.A494T	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	853	Helical; (Potential).					integral to membrane				skin(1)	1						GTGCACCCTGGCCATCACCAT	0.468													9	25					0	0	0.006214	0	0	
GPR139	124274	broad.mit.edu	37	16	20043576	20043576	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:20043576G>A	uc002dgu.1	-	2	705	c.543C>T	c.(541-543)CAC>CAT	p.H181H	GPR139_uc010vaw.1_Silent_p.H88H	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	181	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(2)	2						AGATGAGGACGTGATGCACAG	0.493													20	49					0	0	0.010504	0	0	
OTOA	146183	broad.mit.edu	37	16	21739665	21739665	+	Missense_Mutation	SNP	C	T	T	rs145160241		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:21739665C>T	uc002djh.2	+	19	2121	c.2120C>T	c.(2119-2121)GCG>GTG	p.A707V	uc002diq.3_Intron|OTOA_uc010vbj.1_Missense_Mutation_p.A628V|OTOA_uc002dji.2_Missense_Mutation_p.A383V|OTOA_uc010vbk.1_Missense_Mutation_p.A355V	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	721					sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)		AGGGCTTGGGCGACTGCTCTA	0.597													13	41					0	0	0.013537	0	0	
VWA3A	146177	broad.mit.edu	37	16	22163922	22163922	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:22163922C>T	uc010vbq.1	+	31	3468	c.3372C>T	c.(3370-3372)CAC>CAT	p.H1124H	VWA3A_uc010bxd.2_RNA|VWA3A_uc002dkg.3_Silent_p.H202H|VWA3A_uc010bxe.1_Silent_p.H226H	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	1124	VWFA 2.					extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		CCAAAATTCACAGCCTGCTGA	0.522													4	19					0	0	0.009096	0	0	
SCNN1B	6338	broad.mit.edu	37	16	23382745	23382745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:23382745G>A	uc002dln.2	+	6	1182	c.1006G>A	c.(1006-1008)GCC>ACC	p.A336T		NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta	336	Extracellular (By similarity).		A -> P.		excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	GGGCATCTACGCCATGTCGGG	0.627													7	15					0	0	0.006214	0	0	
GGA2	23062	broad.mit.edu	37	16	23494294	23494294	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:23494294G>T	uc002dlq.2	-	9	906	c.830C>A	c.(829-831)CCC>CAC	p.P277H	GGA2_uc010bxo.1_RNA	NM_015044	NP_055859	Q9UJY4	GGA2_HUMAN	ADP-ribosylation factor binding protein 2	277	GAT.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)		GAACAGCGTGGGCCGCAGCTT	0.577													8	37					1.06961e-07	1.16628e-07	0.003080	1	0	
ARHGAP17	55114	broad.mit.edu	37	16	24946893	24946893	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:24946893C>T	uc002dnb.2	-	18	1885	c.1792G>A	c.(1792-1794)GCA>ACA	p.A598T	ARHGAP17_uc002dmy.2_Missense_Mutation_p.A43T|ARHGAP17_uc002dmz.2_Missense_Mutation_p.A122T|ARHGAP17_uc002dna.2_Missense_Mutation_p.A325T|ARHGAP17_uc002dnc.2_Missense_Mutation_p.A520T|ARHGAP17_uc010vcf.1_Missense_Mutation_p.A341T	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	598	Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)		TGGCCAGATGCTATCTGACTG	0.572													5	33					0	0	0.001984	0	0	
GTF3C1	2975	broad.mit.edu	37	16	27481632	27481632	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:27481632G>A	uc002dov.1	-	31	4651	c.4611C>T	c.(4609-4611)GAC>GAT	p.D1537D	GTF3C1_uc002dou.2_Silent_p.D1537D	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1537						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5						GATCAGGCTGGTCCAACTTGC	0.502													29	126					0	0	0.003755	0	0	
KIAA0556	23247	broad.mit.edu	37	16	27585252	27585252	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:27585252G>A	uc002dow.2	+	2	62	c.38G>A	c.(37-39)TGG>TAG	p.W13*		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	13										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						GAGAGAAGCTGGTCCTGCTCA	0.488													9	46					0	0	0.006214	0	0	
CORO1A	11151	broad.mit.edu	37	16	30199821	30199821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:30199821G>A	uc002dww.2	+	10	1327	c.1205G>A	c.(1204-1206)CGG>CAG	p.R402Q	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|CORO1A_uc010bzq.2_Missense_Mutation_p.R402Q|CORO1A_uc010bzr.2_Intron|CORO1A_uc002dwx.2_Missense_Mutation_p.R296Q|CORO1A_uc002dwy.1_3'UTR|LOC606724_uc002dwz.1_5'Flank	NM_007074	NP_009005	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	402					cell-substrate adhesion|innate immune response|leukocyte chemotaxis|negative regulation of actin nucleation|phagolysosome assembly|positive chemotaxis|regulation of cell shape|uropod organization	actin filament|cortical actin cytoskeleton|lamellipodium|phagocytic cup|phagocytic vesicle membrane	actin filament binding|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein homodimerization activity				0						CCAAAGAGCCGGGAGCTGAGG	0.701													5	12					0	0	0.000602	0	0	
PRSS36	146547	broad.mit.edu	37	16	31154679	31154679	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:31154679C>T	uc002ebd.2	-	8	1143	c.1084G>A	c.(1084-1086)GCC>ACC	p.A362T	PRSS36_uc010vff.1_Missense_Mutation_p.A137T|PRSS36_uc010vfg.1_Missense_Mutation_p.A362T|PRSS36_uc010vfh.1_Missense_Mutation_p.A362T	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	362	Peptidase S1 2.				proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1						AAGCAGCTGGCAGGTGCCAAG	0.637													4	29					0	0	0.001168	0	0	
ITGAX	3687	broad.mit.edu	37	16	31371370	31371370	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:31371370G>A	uc002ebu.1	+	7	758	c.691G>A	c.(691-693)GCC>ACC	p.A231T	ITGAX_uc002ebt.2_Missense_Mutation_p.A231T|ITGAX_uc010vfk.1_5'Flank	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	231	VWFA.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CACGGCCACCGCCATCCAAAA	0.517													11	61					0	0	0.001855	0	0	
ABCC12	94160	broad.mit.edu	37	16	48155695	48155695	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:48155695C>T	uc002efc.1	-	11	1990	c.1644G>A	c.(1642-1644)CAG>CAA	p.Q548Q	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA|ABCC12_uc002efe.1_Silent_p.Q548Q	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	548	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				TCCATGCCTGCTGTGAAACGT	0.448													13	44					0	0	0.001855	0	0	
TOX3	27324	broad.mit.edu	37	16	52473718	52473718	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:52473718C>T	uc002egw.2	-	7	1321	c.1150G>A	c.(1150-1152)GCT>ACT	p.A384T	TOX3_uc010vgt.1_Missense_Mutation_p.A379T|TOX3_uc010vgu.1_Missense_Mutation_p.A384T	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	384					apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0						GGTTTGGGAGCGATTGACCTA	0.502													43	163					0	0	0.014410	0	0	
IRX3	79191	broad.mit.edu	37	16	54317634	54317634	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:54317634G>A	uc002eht.1	-	4	1886	c.1470C>T	c.(1468-1470)GAC>GAT	p.D490D		NM_024336	NP_077312	P78415	IRX3_HUMAN	iroquois homeobox 3	490					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CCAGGGCGGCGTCCAGATGGT	0.433													4	13					0	0	0.009096	0	0	
MMP2	4313	broad.mit.edu	37	16	55518003	55518003	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:55518003C>T	uc002ehz.3	+	3	767	c.456C>T	c.(454-456)AGC>AGT	p.S152S	MMP2_uc010vhd.1_Silent_p.S76S|MMP2_uc010ccc.2_Silent_p.S102S	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	152	Collagenase-like 1.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)	AAGTCTGGAGCGATGTGACCC	0.532													19	42					0	0	0.007413	0	0	
CDH11	1009	broad.mit.edu	37	16	64984769	64984769	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:64984769C>T	uc002eoi.2	-	12	2229	c.1795G>A	c.(1795-1797)GGG>AGG	p.G599R	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Missense_Mutation_p.G599R|CDH11_uc010vin.1_Missense_Mutation_p.G473R	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	599	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		AGCAGTGCCCCGTTCACGTCG	0.612			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			10	34					0	0	0.008291	0	0	
CDH16	1014	broad.mit.edu	37	16	66947046	66947046	+	Missense_Mutation	SNP	G	A	A	rs79541908		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:66947046G>A	uc002eql.2	-	9	1115	c.1042C>T	c.(1042-1044)CTC>TTC	p.L348F	CDH16_uc010cdy.2_Missense_Mutation_p.L348F|CDH16_uc002eqm.2_Missense_Mutation_p.L251F	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	348	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|upper_aerodigestive_tract(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GGTGGACTGAGCTCAGGGATG	0.592													24	116					0	0	0.006320	0	0	
AGRP	181	broad.mit.edu	37	16	67516943	67516943	+	Silent	SNP	A	C	C	rs77812484		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:67516943A>C	uc002etg.1	-	3	501	c.201T>G	c.(199-201)GCT>GCG	p.A67A	ATP6V0D1_uc002ete.1_5'Flank|ATP6V0D1_uc010vjo.1_5'Flank	NM_001138	NP_001129	O00253	AGRP_HUMAN	agouti related protein homolog isoform 1	67					hormone-mediated signaling pathway|neuropeptide signaling pathway|regulation of feeding behavior	extracellular space|Golgi lumen	neuropeptide hormone activity				0		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)		CCAAGGCCTGAGCCTCCTGCA	0.607													22	80					0	0	0.004656	0	0	
ACD	65057	broad.mit.edu	37	16	67691889	67691889	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:67691889C>A	uc002etq.3	-	10	1801	c.1464G>T	c.(1462-1464)TGG>TGT	p.W488C	ACD_uc002etp.3_Missense_Mutation_p.W485C|ACD_uc002etr.3_Missense_Mutation_p.W485C|ACD_uc010vjt.1_3'UTR|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	488					intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CTATGCTCACCCAGACAGAGC	0.612													7	32					0.00307968	0.00322789	0.003080	1	0	
TSNAXIP1	55815	broad.mit.edu	37	16	67860079	67860079	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:67860079G>A	uc002euj.2	+	10	1401	c.1007G>A	c.(1006-1008)CGC>CAC	p.R336H	TSNAXIP1_uc010cep.2_3'UTR|TSNAXIP1_uc010vjz.1_Missense_Mutation_p.R213H|TSNAXIP1_uc002euf.3_Missense_Mutation_p.R69H|TSNAXIP1_uc010vka.1_Missense_Mutation_p.R390H|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.R321H|TSNAXIP1_uc002eug.3_Missense_Mutation_p.R44H|TSNAXIP1_uc002euh.3_Missense_Mutation_p.R44H|TSNAXIP1_uc002eui.3_Missense_Mutation_p.R44H|TSNAXIP1_uc002euk.2_Missense_Mutation_p.R69H	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	336					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)		GGCCCAGAGCGCTGGCAGATG	0.647													4	7					0	0	0.001984	0	0	
DPEP2	64174	broad.mit.edu	37	16	68026860	68026860	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:68026860C>T	uc010cey.2	-	1	420	c.256G>A	c.(256-258)GTG>ATG	p.V86M	DPEP2_uc002evd.3_Missense_Mutation_p.V86M|DPEP2_uc002eve.2_Missense_Mutation_p.V86M|DPEP2_uc002evf.2_RNA|DPEP2_uc002evg.2_Missense_Mutation_p.V86M	NM_022355	NP_071750	Q9H4A9	DPEP2_HUMAN	dipeptidase 2 precursor	86					hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis	anchored to membrane|plasma membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		CACCCGTCCACGAGCGGGAAG	0.662													4	6					0	0	0.009096	0	0	
HAS3	3038	broad.mit.edu	37	16	69143549	69143549	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:69143549G>A	uc010cfh.2	+	2	475	c.251G>A	c.(250-252)CGG>CAG	p.R84Q	HAS3_uc002ewk.2_Missense_Mutation_p.R84Q|HAS3_uc010vlk.1_Missense_Mutation_p.R84Q|HAS3_uc002ewl.2_Missense_Mutation_p.R84Q	NM_005329	NP_005320	O00219	HAS3_HUMAN	hyaluronan synthase 3 isoform a	84	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	hyaluronan synthase activity				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		TCCCCGCGGCGGGGCTCGGTG	0.662													3	17					0	0	0.009096	0	0	
WWP2	11060	broad.mit.edu	37	16	69964118	69964118	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:69964118C>T	uc002exu.1	+	14	1491	c.1402C>T	c.(1402-1404)CGC>TGC	p.R468C	WWP2_uc002exv.1_Missense_Mutation_p.R468C|WWP2_uc010vlm.1_Missense_Mutation_p.R352C|WWP2_uc010vln.1_Missense_Mutation_p.R86C|WWP2_uc002exw.1_Missense_Mutation_p.R29C|uc002exx.1_5'Flank|MIR140_hsa-mir-140|MI0000456_5'Flank	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	468	WW 4.				entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6						CCACAATACCCGCACCACCAC	0.582											OREG0023910	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	32					0	0	0.001855	0	0	
COG4	25839	broad.mit.edu	37	16	70557297	70557297	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:70557297G>A	uc002ezc.2	-	1	161	c.150C>T	c.(148-150)TAC>TAT	p.Y50Y	COG4_uc010cfu.2_RNA|COG4_uc002ezd.2_Silent_p.Y50Y|COG4_uc002eze.2_Translation_Start_Site|SF3B3_uc002ezf.2_5'Flank	NM_015386	NP_056201	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	46	Interacts with SCFD1.				Golgi organization|Golgi vesicle prefusion complex stabilization|protein transport|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0		Ovarian(137;0.0694)				AGAGCCGTTCGTATACAGCCT	0.627													5	24					0	0	0.001984	0	0	
ZFHX3	463	broad.mit.edu	37	16	72828552	72828552	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:72828552C>T	uc002fck.2	-	9	8702	c.8029G>A	c.(8029-8031)GAG>AAG	p.E2677K	ZFHX3_uc002fcl.2_Missense_Mutation_p.E1763K	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2677	Homeobox 3.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				AAGCCCACCTCGTGTGCAATG	0.502													31	178					0	0	0.004289	0	0	
LOC283922	283922	broad.mit.edu	37	16	74372644	74372644	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:74372644A>G	uc002fcr.2	-	9	1661	c.315T>C	c.(313-315)CCT>CCC	p.P105P	LOC283922_uc010vms.1_RNA					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						TACCCTTGTCAGGGGGAACAA	0.443													5	52					0	0	0.001984	0	0	
GLG1	2734	broad.mit.edu	37	16	74496466	74496466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:74496466C>T	uc002fcy.3	-	21	2904	c.2854G>A	c.(2854-2856)GGT>AGT	p.G952S	GLG1_uc002fcx.2_Missense_Mutation_p.G952S|GLG1_uc002fcw.3_Missense_Mutation_p.G941S|GLG1_uc002fcz.3_Missense_Mutation_p.G369S	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	952	Cys-rich GLG1 14.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						GTCAGGATACCGTGACAGAAT	0.443													20	58					0	0	0.008871	0	0	
MLKL	197259	broad.mit.edu	37	16	74729299	74729299	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:74729299C>T	uc002fdb.2	-	2	798	c.357G>A	c.(355-357)GAG>GAA	p.E119E	MLKL_uc002fdc.2_Silent_p.E119E	NM_152649	NP_689862	Q8NB16	MLKL_HUMAN	mixed lineage kinase domain-like isoform 1	119							ATP binding|protein binding|protein kinase activity			stomach(2)	2						GCATGCGTTGCTCAACCTGAA	0.512													16	80					0	0	0.004990	0	0	
CNTNAP4	85445	broad.mit.edu	37	16	76587778	76587778	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:76587778T>C	uc002feu.1	+	25	4092	c.3707T>C	c.(3706-3708)ATC>ACC	p.I1236T	CNTNAP4_uc002fev.1_Missense_Mutation_p.I1100T|CNTNAP4_uc010chb.1_Missense_Mutation_p.I1163T|CNTNAP4_uc002fex.1_Missense_Mutation_p.I1239T	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	1236	Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						GCTAATGCAATCAAAAGTGAC	0.363													8	35					0	0	0.006214	0	0	
ADAMTS18	170692	broad.mit.edu	37	16	77356319	77356319	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:77356319A>T	uc002ffc.3	-	14	2496	c.2077T>A	c.(2077-2079)TTT>ATT	p.F693I	ADAMTS18_uc010chc.1_Missense_Mutation_p.F281I|ADAMTS18_uc002ffe.1_Missense_Mutation_p.F389I	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	693	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						GCAAAAAAAAATTCAAAGTTC	0.388													15	90					0	0	0.004007	0	0	
BCMO1	53630	broad.mit.edu	37	16	81320986	81320986	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:81320986G>A	uc002fgn.1	+	10	1607	c.1389G>A	c.(1387-1389)GCG>GCA	p.A463A	BCMO1_uc010vnp.1_Silent_p.A394A	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase	463					retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0						TTGTGCCCGCGCCAGGTGCCA	0.517													12	36					0	0	0.010729	0	0	
CDH13	1012	broad.mit.edu	37	16	83065685	83065685	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:83065685C>T	uc002fgx.2	+	3	348	c.228C>T	c.(226-228)AAC>AAT	p.N76N	CDH13_uc010chh.2_Silent_p.N76N|CDH13_uc010vns.1_Silent_p.N123N|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Silent_p.N76N	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	76					adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TCAAGGTGAACAGCGATGGCG	0.512													8	27					0	0	0.006214	0	0	
ZC3H18	124245	broad.mit.edu	37	16	88694379	88694379	+	Missense_Mutation	SNP	C	T	T	rs139646372	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:88694379C>T	uc002fky.2	+	15	2521	c.2321C>T	c.(2320-2322)TCG>TTG	p.S774L	ZC3H18_uc010voz.1_Missense_Mutation_p.S798L|ZC3H18_uc010chw.2_Intron|ZC3H18_uc002fkz.2_Missense_Mutation_p.S44L	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	774						nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		AAAAGGGATTCGTCCACACAA	0.547													18	64					0	0	0.010504	0	0	
APRT	353	broad.mit.edu	37	16	88876887	88876887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:88876887G>A	uc002flv.2	-	3	300	c.265C>T	c.(265-267)CGG>TGG	p.R89W	APRT_uc002flw.2_Missense_Mutation_p.R89W	NM_000485	NP_000476	P07741	APT_HUMAN	adenine phosphoribosyltransferase isoform a	89					purine ribonucleoside salvage	cytosol|nucleus	adenine phosphoribosyltransferase activity|AMP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	AGCTTCCCCCGCTTTCGGATG	0.652													4	14					0	0	0.001168	0	0	
SPG7	6687	broad.mit.edu	37	16	89614458	89614458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:89614458C>T	uc002fnj.2	+	12	1621	c.1600C>T	c.(1600-1602)CGG>TGG	p.R534W	SPG7_uc002fnk.1_RNA|SPG7_uc002fnl.2_5'Flank	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	534	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GCACGCGGCGCGGGAGGGACA	0.637													22	54					0	0	0.004656	0	0	
CENPBD1	92806	broad.mit.edu	37	16	90038269	90038269	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:90038269G>A	uc002fpr.2	-	1	674	c.62C>T	c.(61-63)GCG>GTG	p.A21V	AFG3L1_uc002fps.1_5'Flank|AFG3L1_uc002fpt.1_5'Flank|AFG3L1_uc002fpu.1_5'Flank|AFG3L1_uc002fpv.1_5'Flank|AFG3L1_uc002fpw.1_5'Flank|AFG3L1_uc002fpx.1_5'Flank	NM_145039	NP_659476	B2RD01	CENP1_HUMAN	CENPB DNA-binding domains containing 1	21	HTH psq-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						AAGGGTAATCGCTTTCCGTTC	0.483													9	38					0	0	0.006214	0	0	
NXN	64359	broad.mit.edu	37	17	725610	725610	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:725610C>T	uc002fsa.2	-	4	792	c.700G>A	c.(700-702)GTT>ATT	p.V234I	NXN_uc002fsb.1_Missense_Mutation_p.V121I|NXN_uc010vqd.1_5'UTR|NXN_uc002frz.2_5'UTR|NXN_uc010vqe.1_Missense_Mutation_p.V126I	NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin	234	Thioredoxin.				cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		TCTGCACTAACGAAGATGATC	0.473													11	46					0	0	0.001855	0	0	
SLC43A2	124935	broad.mit.edu	37	17	1520058	1520058	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:1520058C>T	uc002fsv.2	-	3	255	c.166G>A	c.(166-168)GTC>ATC	p.V56I	SLC43A2_uc002fsu.2_Missense_Mutation_p.V56I|SLC43A2_uc002fsw.2_Missense_Mutation_p.V56I|SLC43A2_uc002fsx.2_Missense_Mutation_p.V56I	NM_152346	NP_689559	Q8N370	LAT4_HUMAN	solute carrier family 43, member 2	56					cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CCATTGGTGACATTCTCTGTG	0.597													8	27					0	0	0.004482	0	0	
WDR81	124997	broad.mit.edu	37	17	1640830	1640830	+	Missense_Mutation	SNP	G	A	A	rs139156426		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:1640830G>A	uc002fti.2	+	10	2257	c.1996G>A	c.(1996-1998)GTC>ATC	p.V666I	WDR81_uc002fth.2_Missense_Mutation_p.V842I|WDR81_uc010vqp.1_Missense_Mutation_p.V690I|WDR81_uc002ftj.2_Missense_Mutation_p.V1893I|WDR81_uc010vqq.1_Missense_Mutation_p.V524I	NM_001163811	NP_001157283	Q562E7	WDR81_HUMAN	WD repeat domain 81 isoform 4	666										skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CAAGATTGGCGTCTGCTCCCT	0.612													8	25					0	0	0.004482	0	0	
SERPINF1	5176	broad.mit.edu	37	17	1679914	1679914	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:1679914G>A	uc002ftl.2	+	7	1032	c.875G>A	c.(874-876)AGC>AAC	p.S292N	SERPINF1_uc010cjw.2_Missense_Mutation_p.S105N	NM_002615	NP_002606	P36955	PEDF_HUMAN	serine (or cysteine) proteinase inhibitor, clade	292					cell proliferation|negative regulation of angiogenesis|positive regulation of neurogenesis|regulation of proteolysis	extracellular space|melanosome	serine-type endopeptidase inhibitor activity			ovary(1)	1						ATAGAGGAGAGCCTCACCTCC	0.522													18	116					0	0	0.008871	0	0	
ITGAE	3682	broad.mit.edu	37	17	3655092	3655092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:3655092G>A	uc002fwo.3	-	15	1844	c.1745C>T	c.(1744-1746)GCG>GTG	p.A582V		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	582	FG-GAP 6.|Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CCCCATAGCCGCCATGGCAAA	0.572													14	36					0	0	0.003163	0	0	
MYBBP1A	10514	broad.mit.edu	37	17	4446359	4446359	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:4446359T>G	uc002fyb.3	-	20	2803	c.2741A>C	c.(2740-2742)CAG>CCG	p.Q914P	MYBBP1A_uc002fxz.3_Missense_Mutation_p.Q914P|MYBBP1A_uc002fya.3_5'Flank|MYBBP1A_uc010vsa.1_5'UTR	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	914					nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2						GGAGTCGGGCTGGCGGCCAGC	0.682													4	21					0	0	0.001168	0	0	
MYBBP1A	10514	broad.mit.edu	37	17	4448439	4448439	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:4448439C>T	uc002fyb.3	-	17	2254	c.2192G>A	c.(2191-2193)AGC>AAC	p.S731N	MYBBP1A_uc002fxz.3_Missense_Mutation_p.S731N|MYBBP1A_uc002fya.3_5'Flank|MYBBP1A_uc010vsa.1_5'Flank	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	731	Glu-rich.				nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2						actctcTGAGCTTCTGTTGTC	0.453													4	16					0	0	0.009096	0	0	
PELP1	27043	broad.mit.edu	37	17	4594694	4594694	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:4594694C>T	uc002fyi.3	-	2	519	c.293G>A	c.(292-294)CGT>CAT	p.R98H	PELP1_uc010vsf.1_5'UTR	NM_014389	NP_055204	Q8IZL8	PELP1_HUMAN	proline, glutamic acid and leucine rich protein	98					transcription, DNA-dependent	cytoplasm|MLL1 complex	protein binding			ovary(1)|central_nervous_system(1)	2						GGAACTGAGACGTGCATTACT	0.453													16	109					0	0	0.004990	0	0	
TM4SF5	9032	broad.mit.edu	37	17	4685809	4685809	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:4685809G>A	uc002fyw.1	+	3	301	c.270G>A	c.(268-270)TCG>TCA	p.S90S		NM_003963	NP_003954	O14894	T4S5_HUMAN	transmembrane 4 superfamily member 5	90	Cytoplasmic (Potential).					integral to plasma membrane				ovary(1)	1						TGCTGCGCTCGGTCTTCTCCT	0.602													15	62					0	0	0.006122	0	0	
RNF167	26001	broad.mit.edu	37	17	4848022	4848022	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:4848022G>A	uc002fzq.2	+	11	1180	c.764G>A	c.(763-765)CGC>CAC	p.R255H	RNF167_uc002fzr.2_Missense_Mutation_p.R255H|RNF167_uc002fzs.2_Missense_Mutation_p.R255H|RNF167_uc002fzt.2_Missense_Mutation_p.R255H|RNF167_uc002fzu.2_Missense_Mutation_p.R254H|RNF167_uc002fzv.2_Missense_Mutation_p.R220H|RNF167_uc002fzx.2_Missense_Mutation_p.R219H|RNF167_uc002fzy.2_Missense_Mutation_p.R54H	NM_015528	NP_056343	Q9H6Y7	RN167_HUMAN	ring finger protein 167 precursor	255	RING-type; atypical.				negative regulation of cell cycle|protein polyubiquitination	cytoplasm|endomembrane system|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						TACCACAGCCGCTGCGTGGAC	0.622													14	52					0	0	0.006122	0	0	
BCL6B	255877	broad.mit.edu	37	17	6927588	6927588	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:6927588C>T	uc002geg.2	+	3	423	c.366C>T	c.(364-366)CAC>CAT	p.H122H	BCL6B_uc010clt.1_Silent_p.H122H	NM_181844	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B (zinc finger	122						nucleus	zinc ion binding			skin(1)	1						AGATGGAGCACGTGGTCCAGG	0.602													12	52					0	0	0.013537	0	0	
ACAP1	9744	broad.mit.edu	37	17	7252342	7252342	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:7252342G>A	uc002ggd.2	+	18	1913	c.1707G>A	c.(1705-1707)CTG>CTA	p.L569L	KCTD11_uc002gge.3_5'Flank	NM_014716	NP_055531	Q15027	ACAP1_HUMAN	centaurin beta1	569	Required for interaction with GULP1.				intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity		ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding			breast(2)|large_intestine(1)	3						TGGGAAGCCTGCACCCTGGGG	0.597													4	37					0	0	0.000602	0	0	
C17orf74	201243	broad.mit.edu	37	17	7329690	7329690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:7329690G>A	uc002ggw.2	+	3	453	c.380G>A	c.(379-381)CGC>CAC	p.R127H	FGF11_uc010vtw.1_Intron	NM_175734	NP_783861	Q0P670	CQ074_HUMAN	hypothetical protein LOC201243	127	Arg-rich.					integral to membrane					0		Prostate(122;0.157)				GTTcgtcgccgccgccgccgc	0.418													4	14					0	0	0.001168	0	0	
ZBTB4	57659	broad.mit.edu	37	17	7369348	7369348	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:7369348C>T	uc002ghc.3	-	3	1023	c.773G>A	c.(772-774)CGA>CAA	p.R258Q	ZBTB4_uc002ghd.3_Missense_Mutation_p.R258Q	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	258					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		GCTGGCCCCTCGTCGGCACTG	0.706													4	5					0	0	0.000602	0	0	
KDM6B	23135	broad.mit.edu	37	17	7750871	7750871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:7750871C>T	uc002giw.1	+	11	1641	c.1265C>T	c.(1264-1266)GCT>GTT	p.A422V	KDM6B_uc002gix.2_5'UTR	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	422	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2						CAGCCCGGCGCTGACCATTAC	0.597													5	21					0	0	0.001984	0	0	
ALOXE3	59344	broad.mit.edu	37	17	7999976	7999976	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:7999976G>T	uc010cnr.2	-	16	2475	c.2105C>A	c.(2104-2106)CCT>CAT	p.P702H	ALOXE3_uc002gka.2_Missense_Mutation_p.P858H|ALOXE3_uc010vuo.1_Missense_Mutation_p.P834H	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3 isoform 2	702	Lipoxygenase.				leukotriene biosynthetic process		iron ion binding|lipoxygenase activity			skin(3)|lung(1)|central_nervous_system(1)	5						AATGAGGGGAGGGTCCAGGTA	0.592													17	73					2.39187e-15	2.68306e-15	0.008871	1	0	
PFAS	5198	broad.mit.edu	37	17	8158378	8158378	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:8158378C>T	uc002gkr.2	+	4	453	c.312C>T	c.(310-312)ATC>ATT	p.I104I	PFAS_uc010vuv.1_5'UTR	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	104					'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	CCACCAACATCGTGTCAGTGT	0.632													6	44					0	0	0.004482	0	0	
KRBA2	124751	broad.mit.edu	37	17	8272949	8272949	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:8272949C>T	uc002glf.1	-	2	988	c.982G>A	c.(982-984)GTT>ATT	p.V328I	KRBA2_uc002glg.1_Missense_Mutation_p.V245I	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	328	Integrase catalytic.				DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0						GTGAACTCAACGCCACTGTCA	0.478													12	63					0	0	0.013537	0	0	
MYH10	4628	broad.mit.edu	37	17	8396161	8396161	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:8396161G>A	uc002gll.2	-	31	4394	c.4298C>T	c.(4297-4299)ACG>ATG	p.T1433M	MYH10_uc002glm.2_Missense_Mutation_p.T1464M|MYH10_uc010cnx.2_Missense_Mutation_p.T1442M	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1433	Potential.				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2						CAGGTCCACCGTGAGGTCGTC	0.622													9	37					0	0	0.003163	0	0	
USP43	124739	broad.mit.edu	37	17	9615374	9615374	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:9615374T>G	uc010cod.2	+	14	2260	c.2260T>G	c.(2260-2262)TCT>GCT	p.S754A	USP43_uc002gma.3_Missense_Mutation_p.S443A|USP43_uc010vva.1_Missense_Mutation_p.S749A|USP43_uc010coe.2_Missense_Mutation_p.S551A|USP43_uc002gmc.3_Missense_Mutation_p.S266A	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43	754					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						GTCCTGGAGCTCTGCCCCCTG	0.587													7	17					0	0	0.001984	0	0	
DHRS7C	201140	broad.mit.edu	37	17	9674812	9674812	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:9674812T>C	uc010vvb.1	-	6	932	c.932A>G	c.(931-933)GAG>GGG	p.E311G	DHRS7C_uc010cof.2_Missense_Mutation_p.E310G	NM_001105571	NP_001099041	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	311						extracellular region	binding|oxidoreductase activity				0						CAGTTACCCCTCCTCCGGGAC	0.607													3	16					0	0	0.009096	0	0	
MYH13	8735	broad.mit.edu	37	17	10231407	10231407	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:10231407G>T	uc002gmk.1	-	22	2557	c.2467C>A	c.(2467-2469)CGC>AGC	p.R823S		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	823					muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						ATAAAAGAGCGGATGTTGTAC	0.507											OREG0024177	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	62					7.48243e-07	8.1217e-07	0.006214	1	0	
DNAH9	1770	broad.mit.edu	37	17	11778363	11778363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:11778363G>A	uc002gne.2	+	53	10408	c.10340G>A	c.(10339-10341)CGC>CAC	p.R3447H	DNAH9_uc010coo.2_Missense_Mutation_p.R2741H	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3447	AAA 5 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCAGCCGACCGCATGTCCGTG	0.557													16	47					0	0	0.004990	0	0	
DNAH9	1770	broad.mit.edu	37	17	11806149	11806149	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:11806149G>T	uc002gne.2	+	60	11588	c.11520G>T	c.(11518-11520)CAG>CAT	p.Q3840H	DNAH9_uc010coo.2_Missense_Mutation_p.Q3134H|DNAH9_uc002gnf.2_Missense_Mutation_p.Q152H|DNAH9_uc010vvh.1_Missense_Mutation_p.Q193H	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3840					cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGCTCCCACAGGAGTGGAAGA	0.532													12	56					0.00010058	0.000107298	0.013537	1	0	
MYOCD	93649	broad.mit.edu	37	17	12661453	12661453	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:12661453T>C	uc002gnn.2	+	11	2409	c.2110T>C	c.(2110-2112)TCC>CCC	p.S704P	MYOCD_uc002gno.2_Missense_Mutation_p.S752P|MYOCD_uc002gnp.1_Missense_Mutation_p.S656P|MYOCD_uc002gnq.2_Intron	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2	704					cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		TTCAATTCCATCCCCAACTTT	0.398													10	68					0	0	0.008291	0	0	
Unknown	0	broad.mit.edu	37	17	16723364	16723364	+	RNA	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:16723364C>T	uc002gqq.1	-	3		c.756G>A								full-length cDNA clone CS0DI013YN06 of Placenta Cot 25-normalized of Homo sapiens (human).																		TGGCGCATGCCATTGATGTCG	0.562													7	148					0	0	0.003080	0	0	
MPRIP	23164	broad.mit.edu	37	17	17075070	17075070	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:17075070G>A	uc002gqu.1	+	16	2258	c.2202G>A	c.(2200-2202)ACG>ACA	p.T734T	MPRIP_uc002gqv.1_Silent_p.T734T|MPRIP_uc002gqw.1_Silent_p.T489T|MPRIP_uc002gqx.1_Silent_p.T963T|MPRIP_uc002gqy.1_Silent_p.T963T|MPRIP_uc010cpl.1_5'Flank|MPRIP_uc010cpm.1_5'Flank	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	734	Interaction with RHOA.|Potential.					cytoplasm|cytoskeleton	actin binding				0						TGGAAGAAACGCACCAGAAGA	0.527													18	122					0	0	0.007413	0	0	
RAI1	10743	broad.mit.edu	37	17	17698482	17698482	+	Silent	SNP	C	T	T	rs149807469		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:17698482C>T	uc002grm.2	+	3	2689	c.2220C>T	c.(2218-2220)AGC>AGT	p.S740S	RAI1_uc002grn.1_Silent_p.S740S	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	740						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)		CAGCGGACAGCGCCAACCCCT	0.622													12	47					0	0	0.001855	0	0	
SREBF1	6720	broad.mit.edu	37	17	17720322	17720322	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:17720322C>T	uc002gru.1	-	9	1929	c.1735G>A	c.(1735-1737)GCC>ACC	p.A579T	SREBF1_uc002grp.1_Missense_Mutation_p.A198T|SREBF1_uc002grq.1_Missense_Mutation_p.A98T|SREBF1_uc002grr.1_Missense_Mutation_p.A325T|SREBF1_uc002grs.1_Missense_Mutation_p.A555T|SREBF1_uc002grt.1_Missense_Mutation_p.A609T	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	579	Cytoplasmic (Potential).				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1						AAGTACACGGCGGGGCCTGAG	0.667													5	24					0	0	0.004482	0	0	
TOM1L2	146691	broad.mit.edu	37	17	17766046	17766046	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:17766046T>C	uc002grz.3	-	11	1358	c.1201A>G	c.(1201-1203)ACG>GCG	p.T401A	TOM1L2_uc002gry.3_Missense_Mutation_p.T351A|TOM1L2_uc010vwy.1_Missense_Mutation_p.T348A|TOM1L2_uc010cpr.2_Missense_Mutation_p.T356A|TOM1L2_uc010vwz.1_Missense_Mutation_p.T253A|TOM1L2_uc010vxa.1_Missense_Mutation_p.T303A|TOM1L2_uc002grv.3_Missense_Mutation_p.T134A	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	401					intracellular protein transport	intracellular					0	all_neural(463;0.228)					CCCACATACGTCTTGCGCTGC	0.527													48	201					0	0	0.014410	0	0	
SLC5A10	125206	broad.mit.edu	37	17	18874437	18874437	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:18874437A>T	uc002guu.1	+	8	793	c.752A>T	c.(751-753)CAC>CTC	p.H251L	SLC5A10_uc002gur.1_Missense_Mutation_p.H168L|SLC5A10_uc002gut.1_Missense_Mutation_p.H251L|SLC5A10_uc002guv.1_Missense_Mutation_p.H224L|SLC5A10_uc010vyl.1_Missense_Mutation_p.H251L|FAM83G_uc002guw.2_3'UTR	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose	251	Extracellular (Potential).				sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1						GACGCCATGCACATGTTTCGA	0.627													8	23					0	0	0.004482	0	0	
ALDH3A2	224	broad.mit.edu	37	17	19568354	19568354	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:19568354G>T	uc002gwb.1	+	8	1422	c.1201G>T	c.(1201-1203)GGA>TGA	p.G401*	ALDH3A2_uc002gwa.1_Nonsense_Mutation_p.G401*|ALDH3A2_uc010cqr.1_Nonsense_Mutation_p.G208*|ALDH3A2_uc002gwc.1_Nonsense_Mutation_p.G401*|ALDH3A2_uc002gwd.1_Nonsense_Mutation_p.G208*	NM_000382	NP_000373	P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3A2 isoform 2	401	Cytoplasmic.				cellular aldehyde metabolic process|central nervous system development|epidermis development|lipid metabolic process|peripheral nervous system development	endoplasmic reticulum membrane|integral to membrane	3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(2)	2	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)				NADH(DB00157)	CCCATTTGGAGGAGTGGGTGA	0.453													16	56					3.41278e-10	3.77522e-10	0.004990	1	0	
Unknown	0	broad.mit.edu	37	17	20407328	20407328	+	RNA	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:20407328C>T	uc002gxb.2	-	1		c.467G>A								Homo sapiens similar to Keratin, type I cytoskeletal 16 (Cytokeratin-16) (CK-16) (Keratin-16) (K16), mRNA (cDNA clone IMAGE:4752428).																		CTCCAGAGCACGCACCTTGTC	0.537													19	55					0	0	0.003954	0	0	
MAP2K3	5606	broad.mit.edu	37	17	21201726	21201726	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:21201726A>G	uc002gys.2	+	2	316	c.51A>G	c.(49-51)GGA>GGG	p.G17G	MAP2K3_uc002gyt.2_5'UTR|MAP2K3_uc002gyu.2_5'UTR	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	17					activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CCATTCTAGGAAAATCCAAGA	0.577													21	165					0	0	0.012319	0	0	
KIAA0100	9703	broad.mit.edu	37	17	26943183	26943183	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:26943183C>T	uc002hbu.2	-	37	6420	c.6321G>A	c.(6319-6321)GAG>GAA	p.E2107E	SGK494_uc010waq.1_5'Flank|SGK494_uc010war.1_5'Flank|SGK494_uc002hbr.1_5'Flank|uc002hbs.1_Intron|KIAA0100_uc002hbt.2_Silent_p.E436E	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	2107						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					TGGCAGCTCGCTCTTTCATCT	0.478													4	43					0	0	0.009096	0	0	
RAB34	83871	broad.mit.edu	37	17	27042914	27042914	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:27042914C>T	uc002hce.2	-	4	842	c.218G>A	c.(217-219)TGC>TAC	p.C73Y	RAB34_uc002hcg.2_Missense_Mutation_p.C73Y|RAB34_uc002hcf.2_Missense_Mutation_p.C74Y|RAB34_uc010was.1_Missense_Mutation_p.C130Y|RAB34_uc010wat.1_Missense_Mutation_p.C130Y|RAB34_uc002hch.2_Missense_Mutation_p.C73Y|RAB34_uc010wau.1_Missense_Mutation_p.C51Y|RAB34_uc010wav.1_Missense_Mutation_p.C131Y	NM_031934	NP_114140	Q9BZG1	RAB34_HUMAN	Ras-related protein RAB34 isoform 1	73					protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	Lung NSC(42;0.00431)					GGTGTCTTTGCAGAACCTGAG	0.547													7	76					0	0	0.001984	0	0	
PHF12	57649	broad.mit.edu	37	17	27251130	27251130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:27251130G>A	uc002hdg.1	-	4	1042	c.512C>T	c.(511-513)GCC>GTC	p.A171V	PHF12_uc010wbb.1_Missense_Mutation_p.A153V|PHF12_uc002hdi.1_Missense_Mutation_p.A167V|PHF12_uc002hdj.1_Missense_Mutation_p.A171V|PHF12_uc010crw.1_Intron|uc002hdl.2_5'Flank|PHF12_uc002hdh.1_5'UTR	NM_001033561	NP_001028733	Q96QT6	PHF12_HUMAN	PHD finger protein 12 isoform 1	171	Interaction with SIN3A.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			CTCTGTGCTGGCGCTGGATGT	0.567													6	20					0	0	0.001168	0	0	
SSH2	85464	broad.mit.edu	37	17	28003848	28003848	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:28003848G>A	uc002heo.1	-	7	523	c.523C>T	c.(523-525)CAG>TAG	p.Q175*	SSH2_uc010wbh.1_Nonsense_Mutation_p.Q202*|SSH2_uc002hep.1_Nonsense_Mutation_p.Q175*|SSH2_uc002heq.2_Nonsense_Mutation_p.Q182*|SSH2_uc002her.2_Nonsense_Mutation_p.Q175*|SSH2_uc010csc.1_Nonsense_Mutation_p.Q175*	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	175					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						CACATTGCCTGCACAGATACA	0.348													17	54					0	0	0.010504	0	0	
LRRC37B	114659	broad.mit.edu	37	17	30362634	30362634	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:30362634C>T	uc002hgu.2	+	7	2110	c.2099C>T	c.(2098-2100)ACG>ATG	p.T700M	LRRC37B_uc010wbx.1_Missense_Mutation_p.T618M|LRRC37B_uc010csu.2_Missense_Mutation_p.T649M	NM_052888	NP_443120	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B precursor	700	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AACATTCTCACGATGACTGTT	0.284													35	146					0	0	0.004878	0	0	
RDM1	201299	broad.mit.edu	37	17	34257080	34257080	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:34257080C>A	uc002hkh.2	-	2	325	c.276G>T	c.(274-276)AAG>AAT	p.K92N	RDM1_uc010cty.2_RNA|RDM1_uc010ctz.2_Missense_Mutation_p.K69N|RDM1_uc010cua.2_Missense_Mutation_p.K69N|RDM1_uc002hkg.3_Missense_Mutation_p.K69N|RDM1_uc010cub.2_RNA|RDM1_uc010cud.2_Missense_Mutation_p.K92N|RDM1_uc010cuf.2_RNA|RDM1_uc010cue.2_Intron|RDM1_uc010cug.2_RNA|RDM1_uc010cuc.2_Missense_Mutation_p.K92N|RDM1_uc010wco.1_Missense_Mutation_p.K69N|RDM1_uc010wcp.1_Missense_Mutation_p.K69N|RDM1_uc002hki.2_Missense_Mutation_p.K92N	NM_145654	NP_663629	Q8NG50	RDM1_HUMAN	RAD52 motif 1 isoform 1	92	RRM.|Necessary for nuclear and nucleolar localization.|Necessary for nuclear localization and for nucleolar accumulation in response to heat shock.				DNA recombination|DNA repair	Cajal body|cytoplasm|nucleolus|PML body	DNA binding|nucleotide binding|RNA binding			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TTGGACCCACCTTGACTGGAG	0.358								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					30	124					6.53348e-20	7.36333e-20	0.003755	1	0	
GPR179	440435	broad.mit.edu	37	17	36483525	36483525	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:36483525C>T	uc002hpz.2	-	11	5948	c.5927G>A	c.(5926-5928)CGC>CAC	p.R1976H		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	1976	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TTGGTCAGGGCGCTGTCTGTC	0.552													6	29					0	0	0.003080	0	0	
Unknown	0	broad.mit.edu	37	17	37188048	37188048	+	RNA	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:37188048C>A	uc002hrd.1	+	1		c.1890C>A								Homo sapiens cDNA FLJ43826 fis, clone TESTI4002703.																		GCTCAGCATCCAACATCACCC	0.502													5	41					5.9392e-07	6.45498e-07	0.001168	1	0	
CDK12	51755	broad.mit.edu	37	17	37673788	37673788	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:37673788G>A	uc010cvv.2	+	10	3528	c.2942G>A	c.(2941-2943)CGT>CAT	p.R981H	CDK12_uc010wef.1_Missense_Mutation_p.R980H|CDK12_uc002hrw.3_Missense_Mutation_p.R981H	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	981	Protein kinase.				mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19						TATCGAAGGCGTCTACGAGAA	0.473										TCGA Ovarian(9;0.13)			9	48					0	0	0.004482	0	0	
ZPBP2	124626	broad.mit.edu	37	17	38024801	38024801	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:38024801G>A	uc002hte.2	+	2	206	c.53_splice	c.e2-1	p.V18_splice	ZPBP2_uc002htf.2_Intron	NM_199321	NP_955353	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2 isoform 2						binding of sperm to zona pellucida	extracellular region				ovary(1)	1	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			TTCCTCCGCAGTCCAATGCCC	0.547													18	122					0	0	0.014323	0	0	
KRT28	162605	broad.mit.edu	37	17	38955915	38955915	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:38955915G>A	uc002hvh.1	-	1	297	c.231C>T	c.(229-231)AGC>AGT	p.S77S		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	77	Gly-rich.|Head.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				GTCCCCCTTCGCTTCCAGCAA	0.537													14	78					0	0	0.001855	0	0	
KRT38	8687	broad.mit.edu	37	17	39593778	39593778	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:39593778C>T	uc002hwq.1	-	7	1680	c.1257G>A	c.(1255-1257)CCG>CCA	p.P419P		NM_006771	NP_006762	O76015	KRT38_HUMAN	keratin 38	419	Tail.					intermediate filament	structural molecule activity			skin(2)	2		Breast(137;0.000496)				ACGTGGAGCACGGATTGCAGG	0.637													3	8					0	0	0.004672	0	0	
JUP	3728	broad.mit.edu	37	17	39680724	39680724	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:39680724G>A	uc010wfs.1	-	7	1226	c.1218C>T	c.(1216-1218)ACC>ACT	p.T406T	KRT15_uc002hxb.1_5'Flank|uc002hxc.1_5'Flank|KRT19_uc002hxd.3_Silent_p.T243T	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin	Error:Variant_position_missing_in_P14923_after_alignment					adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		TGGCGAGATCGGTGCCCGGAG	0.572													7	64					0	0	0.006214	0	0	
PSMC3IP	29893	broad.mit.edu	37	17	40729286	40729286	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:40729286T>C	uc002iai.2	-	3	213	c.170A>G	c.(169-171)CAA>CGA	p.Q57R	PSMC3IP_uc002iaj.2_5'UTR|PSMC3IP_uc002iak.2_Missense_Mutation_p.Q57R|PSMC3IP_uc010wgn.1_5'UTR|PSMC3IP_uc010wgo.1_RNA|PSMC3IP_uc010wgp.1_RNA	NM_016556	NP_057640	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein isoform 2	57					DNA recombination|meiosis	nucleus	DNA binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)		GATCTTGCCTTGTTGCGCCAG	0.547													5	42					0	0	0.000602	0	0	
TUBG2	27175	broad.mit.edu	37	17	40818663	40818663	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:40818663C>T	uc010wgr.1	+	11	1457	c.1201C>T	c.(1201-1203)CGG>TGG	p.R401W	TUBG2_uc002iaq.2_3'UTR|TUBG2_uc002iar.2_Missense_Mutation_p.R248W|TUBG2_uc002ias.2_Missense_Mutation_p.R243W|TUBG2_uc002iap.2_Missense_Mutation_p.R248W	NM_016437	NP_057521	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	401					G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization	cytosol	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		GCTGCGGAAGCGGGATGCCTT	0.498													16	55					0	0	0.004990	0	0	
DHX8	1659	broad.mit.edu	37	17	41570275	41570275	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:41570275C>T	uc002idu.1	+	6	803	c.730C>T	c.(730-732)CGG>TGG	p.R244W	DHX8_uc010wif.1_Missense_Mutation_p.R153W|DHX8_uc010wig.1_Missense_Mutation_p.R244W	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	244						catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		ATATGGAGAGCGGAATCTGGA	0.527													18	101					0	0	0.010504	0	0	
MPP3	4356	broad.mit.edu	37	17	41879176	41879176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:41879176C>T	uc002iei.3	-	20	1817	c.1651G>A	c.(1651-1653)GCC>ACC	p.A551T	MPP3_uc002ieh.2_Missense_Mutation_p.A576T|MPP3_uc002iej.2_RNA	NM_001932	NP_001923	Q13368	MPP3_HUMAN	palmitoylated membrane protein 3	551	Guanylate kinase-like.				signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		ACCAGCACGGCGTCTACCAGG	0.562													16	64					0	0	0.008871	0	0	
HDAC5	10014	broad.mit.edu	37	17	42156018	42156018	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:42156018C>T	uc002ifd.1	-	26	3390	c.3179G>A	c.(3178-3180)TGT>TAT	p.C1060Y	HDAC5_uc002ife.1_Missense_Mutation_p.C1060Y|HDAC5_uc002iff.1_Missense_Mutation_p.C1061Y|HDAC5_uc010czp.1_Missense_Mutation_p.C975Y	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1	1060					B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CTTCTGCACACAGCTCCAGTG	0.642													25	81					0	0	0.006320	0	0	
RUNDC3A	10900	broad.mit.edu	37	17	42390862	42390862	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:42390862G>A	uc002igl.3	+	4	723	c.449G>A	c.(448-450)CGG>CAG	p.R150Q	RUNDC3A_uc002igi.2_Missense_Mutation_p.R150Q|RUNDC3A_uc002igj.2_Missense_Mutation_p.R145Q|RUNDC3A_uc002igk.2_Missense_Mutation_p.R146Q	NM_001144825	NP_001138297	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A isoform 1	150	Interaction with RAP2A (By similarity).|RUN.				small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CGTGACACCCGGACCACCAGG	0.552													7	34					0	0	0.003080	0	0	
KIAA1267	284058	broad.mit.edu	37	17	44116010	44116010	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:44116010G>A	uc002ikb.2	-	9	2520	c.2435C>T	c.(2434-2436)GCA>GTA	p.A812V	KIAA1267_uc002ikc.2_Missense_Mutation_p.A812V|KIAA1267_uc002ikd.2_Missense_Mutation_p.A812V|KIAA1267_uc010dav.2_Missense_Mutation_p.A812V|KIAA1267_uc010wkb.1_Missense_Mutation_p.A143V|KIAA1267_uc010wkc.1_Missense_Mutation_p.A80V	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	812						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				GTGGGTGGCTGCCAAGTAGCT	0.527													11	53					0	0	0.001855	0	0	
NFE2L1	4779	broad.mit.edu	37	17	46136299	46136299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:46136299G>A	uc002imz.3	+	6	2266	c.1615G>A	c.(1615-1617)GAG>AAG	p.E539K	NFE2L1_uc002ina.3_Missense_Mutation_p.E509K|NFE2L1_uc002inb.3_Missense_Mutation_p.E509K|NFE2L1_uc010wle.1_Missense_Mutation_p.E351K|NFE2L1_uc010wlf.1_Missense_Mutation_p.E383K	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	539					anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						GGAAGAGGCCGAGGGTGCTGT	0.473													15	25					0	0	0.004007	0	0	
SCPEP1	59342	broad.mit.edu	37	17	55083545	55083545	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:55083545C>T	uc002iuv.3	+	13	1361	c.1308C>T	c.(1306-1308)GAC>GAT	p.D436D	SCPEP1_uc010dcl.2_RNA|SCPEP1_uc010wnk.1_Silent_p.D386D	NM_021626	NP_067639	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1 precursor	436					proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)					TTCCTTCTGACCAAGGGGACA	0.517													10	100					0	0	0.002450	0	0	
RNF43	54894	broad.mit.edu	37	17	56437605	56437605	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:56437605C>T	uc002iwf.2	-	7	2813	c.857G>A	c.(856-858)CGG>CAG	p.R286Q	RNF43_uc010wnv.1_Missense_Mutation_p.R245Q|RNF43_uc002iwh.3_Missense_Mutation_p.R286Q|RNF43_uc002iwg.3_Missense_Mutation_p.R286Q|RNF43_uc010dcw.2_Missense_Mutation_p.R159Q	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	286	RING-type; atypical.|Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGAAATGACCCGTAGCTCCTG	0.532													6	47					0	0	0.001168	0	0	
CLTC	1213	broad.mit.edu	37	17	57744280	57744280	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:57744280T>C	uc002ixq.1	+	13	2513	c.2070T>C	c.(2068-2070)CAT>CAC	p.H690H	CLTC_uc002ixp.2_Silent_p.H690H|CLTC_uc002ixr.1_Silent_p.H694H	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	690	Heavy chain arm.|Proximal segment.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CTAAATATCATGAACAACTGT	0.373			T	ALK|TFE3	ALCL|renal 								12	52					0	0	0.001855	0	0	
CLTC	1213	broad.mit.edu	37	17	57771129	57771129	+	Silent	SNP	C	A	A	rs148633723		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:57771129C>A	uc002ixq.1	+	32	5387	c.4944C>A	c.(4942-4944)GCC>GCA	p.A1648A	CLTC_uc002ixr.1_Silent_p.A1652A	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	1648	Heavy chain arm.|Proximal segment.|Trimerization (By similarity).				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CCAGTGTTGCCGTCCCTCCCC	0.557			T	ALK|TFE3	ALCL|renal 								14	59					7.93312e-07	8.60533e-07	0.002450	1	0	
HEATR6	63897	broad.mit.edu	37	17	58134524	58134524	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:58134524C>T	uc002iyk.1	-	12	1981	c.1964G>A	c.(1963-1965)CGA>CAA	p.R655Q	HEATR6_uc010ddk.1_Missense_Mutation_p.R194Q|HEATR6_uc010wos.1_Missense_Mutation_p.R487Q	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	655							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			AATGCAGAGTCGAATGAGCCA	0.557													30	128					0	0	0.012213	0	0	
HEATR6	63897	broad.mit.edu	37	17	58147131	58147131	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:58147131C>T	uc002iyk.1	-	7	897	c.880G>A	c.(880-882)GAT>AAT	p.D294N	HEATR6_uc010wos.1_Missense_Mutation_p.D126N	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	294							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GTTCGCCCATCATACTGAGGA	0.398													19	101					0	0	0.002780	0	0	
TBC1D3P2	440452	broad.mit.edu	37	17	60344534	60344534	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:60344534G>A	uc010woz.1	-	12		c.946C>T			uc010wpb.1_5'Flank	NR_027486				Homo sapiens cDNA FLJ60189 complete cds, highly similar to TBC1 domain family member 3.												0						CGGCATGAACGCCTGTTCGCC	0.602													37	157					0	0	0.006999	0	0	
TANC2	26115	broad.mit.edu	37	17	61497887	61497887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:61497887G>A	uc002jal.3	+	25	4567	c.4544G>A	c.(4543-4545)CGT>CAT	p.R1515H	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Missense_Mutation_p.R626H	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1515							binding			ovary(2)	2						GGATCTTACCGTTTCAGCCCC	0.597													5	38					0	0	0.001984	0	0	
FTSJ3	117246	broad.mit.edu	37	17	61898993	61898993	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:61898993G>A	uc002jbz.2	-	15	1685	c.1607C>T	c.(1606-1608)GCT>GTT	p.A536V	FTSJ3_uc002jca.2_Missense_Mutation_p.A536V	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3	536					RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						CTCGATCCCAGCAAAGCTGCC	0.592													27	124					0	0	0.003271	0	0	
SMARCD2	6603	broad.mit.edu	37	17	61912092	61912092	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:61912092C>T	uc010deb.1	-	6	1109	c.792G>A	c.(790-792)CTG>CTA	p.L264L	SMARCD2_uc010wpt.1_Silent_p.L216L|SMARCD2_uc010dea.1_Silent_p.L189L|SMARCD2_uc010dec.1_Silent_p.L243L	NM_001098426	NP_001091896	Q92925	SMRD2_HUMAN	SWI/SNF-related matrix-associated	264					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	SWI/SNF complex	protein binding|transcription coactivator activity				0						CAGGCCCGTACAGCTCCTTGT	0.552											OREG0024642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	58					0	0	0.013537	0	0	
SCN4A	6329	broad.mit.edu	37	17	62020407	62020407	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:62020407T>C	uc002jds.1	-	23	4144	c.4067A>G	c.(4066-4068)GAC>GGC	p.D1356G		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	1356	Helical; Name=S1 of repeat IV; (Potential).|IV.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)	GATGGTGATGTCGAAGGCCTG	0.552													19	88					0	0	0.008871	0	0	
ARSG	22901	broad.mit.edu	37	17	66303763	66303763	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:66303763C>T	uc002jhc.2	+	2	925	c.129C>T	c.(127-129)GCC>GCT	p.A43A	ARSG_uc002jhb.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor	43					sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTATTTTGGCCGATGACATGG	0.478													12	49					0	0	0.010729	0	0	
ABCA8	10351	broad.mit.edu	37	17	66937011	66937011	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:66937011G>A	uc002jhp.2	-	3	368	c.189C>T	c.(187-189)GAC>GAT	p.D63D	ABCA8_uc002jhq.2_Silent_p.D63D|ABCA8_uc010wqq.1_Silent_p.D63D|ABCA8_uc010wqr.1_Silent_p.D2D|ABCA8_uc002jhr.2_Silent_p.D63D|ABCA8_uc002jhs.2_Silent_p.D63D|ABCA8_uc002jht.2_Silent_p.D63D	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	63						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					CCCGTCCCAGGTCCATGGTAA	0.368													5	58					0	0	0.004482	0	0	
ABCA9	10350	broad.mit.edu	37	17	66982353	66982353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:66982353G>A	uc002jhu.2	-	32	4303	c.4160C>T	c.(4159-4161)GCT>GTT	p.A1387V	ABCA9_uc010dez.2_Missense_Mutation_p.A1349V	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1387	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					TTTCACGGCAGCGTACACCTC	0.612													13	74					0	0	0.003163	0	0	
ABCA9	10350	broad.mit.edu	37	17	67016664	67016664	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:67016664A>G	uc002jhu.2	-	19	2608	c.2465T>C	c.(2464-2466)CTG>CCG	p.L822P	ABCA9_uc010dez.2_Missense_Mutation_p.L822P	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	822					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					AACTTGTTCCAGCTCAACAAG	0.408													17	67					0	0	0.004990	0	0	
ABCA9	10350	broad.mit.edu	37	17	67039677	67039677	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:67039677G>A	uc002jhu.2	-	6	896	c.753C>T	c.(751-753)TAC>TAT	p.Y251Y	ABCA9_uc010dez.2_Silent_p.Y251Y|ABCA9_uc002jhv.2_Silent_p.Y251Y	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	251					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					ATGACGTAATGTATTGTCTTT	0.323													12	58					0	0	0.013537	0	0	
ABCA6	23460	broad.mit.edu	37	17	67110969	67110969	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:67110969G>A	uc002jhw.1	-	13	1891	c.1716C>T	c.(1714-1716)ACC>ACT	p.T572T	ABCA6_uc002jhx.1_Silent_p.T25T	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	572	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					TTTCCTTCACGGTGAGTATGT	0.403													13	104					0	0	0.002450	0	0	
CDC42EP4	23580	broad.mit.edu	37	17	71282053	71282053	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:71282053G>T	uc002jjn.2	-	2	734	c.587C>A	c.(586-588)GCC>GAC	p.A196D	CDC42EP4_uc002jjo.2_Missense_Mutation_p.A196D|CDC42EP4_uc002jjp.1_Missense_Mutation_p.A126D	NM_012121	NP_036253	Q9H3Q1	BORG4_HUMAN	Cdc42 effector protein 4	196					positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|cytoplasm|endomembrane system|membrane|microtubule cytoskeleton	GTP-Rho binding				0			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			CCCGTACGTGGCCTTGGGCAC	0.632													7	35					0.00198382	0.00208189	0.001984	1	0	
MRPS7	51081	broad.mit.edu	37	17	73259534	73259534	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:73259534C>A	uc002jnm.3	+	4	686	c.453C>A	c.(451-453)AAC>AAA	p.N151K	GGA3_uc002jni.1_5'Flank|GGA3_uc002jnj.1_5'Flank|GGA3_uc010wrw.1_5'Flank|GGA3_uc002jnk.1_5'Flank|GGA3_uc010wrx.1_5'Flank|GGA3_uc010wry.1_5'Flank|GGA3_uc010wrz.1_5'Flank|MRPS7_uc002jnl.2_Missense_Mutation_p.N151K|MRPS7_uc002jnn.3_Missense_Mutation_p.N180K	NM_015971	NP_057055	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7 precursor	151					translation	cytosolic small ribosomal subunit|mitochondrion	protein binding|RNA binding|structural constituent of ribosome			central_nervous_system(1)	1	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			CACTGAAAAACTGTGAGCCTA	0.517													69	328					1.34568e-36	1.52171e-36	0.014410	1	0	
QRICH2	84074	broad.mit.edu	37	17	74288203	74288203	+	Missense_Mutation	SNP	G	A	A	rs148029652		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:74288203G>A	uc002jrd.1	-	4	2287	c.2107C>T	c.(2107-2109)CGT>TGT	p.R703C	QRICH2_uc010wsz.1_Missense_Mutation_p.R629C|QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	703	Gln-rich.						protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5						accaaaccacgctgatccact	0													11	49					0	0	0.008291	0	0	
RHBDF2	79651	broad.mit.edu	37	17	74470845	74470845	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:74470845G>T	uc002jrq.1	-	11	1649	c.1356C>A	c.(1354-1356)ATC>ATA	p.I452I	RHBDF2_uc002jrp.1_Silent_p.I423I|RHBDF2_uc002jrr.1_Silent_p.I304I|RHBDF2_uc010wtf.1_Silent_p.I423I	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	452	Lumenal (Potential).				negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						TCTCCTGCTGGATGTACTTCA	0.622													10	48					9.70103e-10	1.0696e-09	0.008291	1	0	
CYGB	114757	broad.mit.edu	37	17	74527577	74527577	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:74527577C>T	uc002jru.1	-	2	498	c.340G>A	c.(340-342)GCC>ACC	p.A114T	CYGB_uc002jrv.1_Missense_Mutation_p.A49T|PRCD_uc002jrw.1_Intron	NM_134268	NP_599030	Q8WWM9	CYGB_HUMAN	cytoglobin	114	Globin.				response to oxidative stress	cytoplasm	heme binding|oxygen binding|oxygen transporter activity|peroxidase activity				0						TGCTTGAGGGCGTGGGCTTTC	0.642													7	21					0	0	0.004482	0	0	
ENGASE	64772	broad.mit.edu	37	17	77082376	77082376	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:77082376G>T	uc002jwv.2	+	14	2185	c.2177G>T	c.(2176-2178)CGG>CTG	p.R726L	ENGASE_uc002jww.2_Missense_Mutation_p.R431L	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	726						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1						GAAGGGTTCCGGGTACCTCAG	0.647													3	22					0.004672	0.00488768	0.004672	1	0	
CARD14	79092	broad.mit.edu	37	17	78176086	78176086	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:78176086C>T	uc002jxw.1	+	15	2281	c.2086C>T	c.(2086-2088)CAG>TAG	p.Q696*	CARD14_uc002jxt.1_RNA|CARD14_uc002jxv.2_Nonsense_Mutation_p.Q696*|CARD14_uc010wud.1_RNA	NM_024110	NP_077015	Q9BXL6	CAR14_HUMAN	caspase recruitment domain protein 14 isoform 1	696					activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			AGGGGAGCTGCAGGTGCATTG	0.617													7	34					0	0	0.003080	0	0	
RNF213	57674	broad.mit.edu	37	17	78354648	78354648	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:78354648C>T	uc002jyh.1	+	31	8100	c.7877C>T	c.(7876-7878)ACG>ATG	p.T2626M	uc002jyi.1_Intron|RNF213_uc010dhw.1_Missense_Mutation_p.T1008M	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCAGACAGAACGCAGACCGGC	0.602													25	103					0	0	0.004656	0	0	
RPTOR	57521	broad.mit.edu	37	17	78599546	78599546	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:78599546C>A	uc002jyt.1	+	2	1023	c.218C>A	c.(217-219)CCC>CAC	p.P73H	RPTOR_uc002jys.2_Missense_Mutation_p.P73H|RPTOR_uc010wuf.1_5'UTR|RPTOR_uc010wug.1_Missense_Mutation_p.P73H	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	73					cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						GTGGACCCTCCCGATGTGGTG	0.498													9	84					3.86212e-05	4.1306e-05	0.008291	1	0	
GPS1	2873	broad.mit.edu	37	17	80011774	80011774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:80011774G>A	uc002kdl.1	+	3	202	c.157G>A	c.(157-159)GGC>AGC	p.G53S	RFNG_uc002kdj.2_5'Flank|GPS1_uc002kdk.1_Missense_Mutation_p.G93S|GPS1_uc010dij.1_Missense_Mutation_p.G93S|GPS1_uc002kdm.1_Missense_Mutation_p.G37S|GPS1_uc002kdn.1_Missense_Mutation_p.G53S|GPS1_uc002kdo.1_Missense_Mutation_p.G53S|GPS1_uc010wvh.1_Missense_Mutation_p.G45S	NM_004127	NP_004118	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 2	53					cell cycle|cullin deneddylation|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			CAGCTACAGCGGCCTGATGCG	0.632													5	20					0	0	0.003080	0	0	
DUS1L	64118	broad.mit.edu	37	17	80019841	80019841	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:80019841G>A	uc002kdq.2	-	5	948	c.529C>T	c.(529-531)CGC>TGC	p.R177C	DUS1L_uc002kdp.2_Missense_Mutation_p.R46C|DUS1L_uc002kdr.2_Missense_Mutation_p.R177C|DUS1L_uc002kds.2_RNA|DUS1L_uc002kdt.2_RNA|DUS1L_uc010wvi.1_Missense_Mutation_p.R160C	NM_022156	NP_071439	Q6P1R4	DUS1L_HUMAN	PP3111 protein	177					tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity			skin(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			TCCTTGGTGCGTCCGTGCACC	0.448													8	29					0	0	0.006214	0	0	
ZNF750	79755	broad.mit.edu	37	17	80788993	80788993	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:80788993G>A	uc002kga.2	-	2	1649	c.1338C>T	c.(1336-1338)TAC>TAT	p.Y446Y	TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kfz.2_Intron	NM_024702	NP_078978	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	446						intracellular	zinc ion binding			central_nervous_system(1)	1	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GCTCTGGCGGGTAGAGTCTTC	0.597													13	38					0	0	0.002450	0	0	
C18orf1	753	broad.mit.edu	37	18	13621228	13621228	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:13621228C>T	uc002ksa.2	+	5	962	c.294C>T	c.(292-294)AAC>AAT	p.N98N	C18orf1_uc002ksb.2_Silent_p.N98N|C18orf1_uc002kse.2_Silent_p.N61N|C18orf1_uc002ksf.2_Silent_p.N61N|C18orf1_uc002ksg.1_Silent_p.N21N|C18orf1_uc002ksh.1_Silent_p.N40N|C18orf1_uc002ksi.1_Silent_p.N40N	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1	98	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		CCTTCATCAACCGCCCGAACC	0.632													7	56					0	0	0.008291	0	0	
POTEC	388468	broad.mit.edu	37	18	14542858	14542858	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:14542858G>A	uc010dln.2	-	1	742	c.288C>T	c.(286-288)AGC>AGT	p.S96S	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	96										skin(3)	3						TGCCCATCTTGCTCCTGAGCG	0.612													24	163					0	0	0.006320	0	0	
LAMA3	3909	broad.mit.edu	37	18	21495282	21495282	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:21495282C>T	uc002kuq.2	+	59	7760	c.7674C>T	c.(7672-7674)TAC>TAT	p.Y2558Y	LAMA3_uc002kur.2_Silent_p.Y2502Y|LAMA3_uc002kus.3_Silent_p.Y949Y|LAMA3_uc002kut.3_Silent_p.Y893Y	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	2558	Laminin G-like 1.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCCCTCCATACAAAGGTTGTA	0.338													5	48					0	0	0.001168	0	0	
DSG3	1830	broad.mit.edu	37	18	29038474	29038474	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:29038474C>T	uc002kws.2	+	4	392	c.283C>T	c.(283-285)CCG>TCG	p.P95S		NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	95	Extracellular (Potential).|Cadherin 1.				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			skin(4)|ovary(3)|lung(1)|central_nervous_system(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AATCGATCAGCCGCCTTTTGG	0.443													4	75					0	0	0.000602	0	0	
ASXL3	80816	broad.mit.edu	37	18	31323494	31323494	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:31323494C>T	uc010dmg.1	+	12	3737	c.3682C>T	c.(3682-3684)CCC>TCC	p.P1228S	ASXL3_uc002kxq.2_Missense_Mutation_p.P935S	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1228	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						TAGCAGTGTGCCCATGCTTTT	0.373													8	67					0	0	0.003080	0	0	
ASXL3	80816	broad.mit.edu	37	18	31325001	31325001	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:31325001T>A	uc010dmg.1	+	12	5244	c.5189T>A	c.(5188-5190)GTC>GAC	p.V1730D	ASXL3_uc002kxq.2_Missense_Mutation_p.V1437D	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1730					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						CTGAAGAGAGTCCCTGGTGCA	0.532													8	35					0	0	0.013537	0	0	
ASXL3	80816	broad.mit.edu	37	18	31326157	31326157	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:31326157C>T	uc010dmg.1	+	12	6400	c.6345C>T	c.(6343-6345)TTC>TTT	p.F2115F	ASXL3_uc002kxq.2_Silent_p.F1822F	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	2115					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						TAAAAGCATTCGCGCTAAAAA	0.413													17	80					0	0	0.004007	0	0	
FHOD3	80206	broad.mit.edu	37	18	34261513	34261513	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:34261513G>T	uc002kzt.1	+	12	1522	c.1425G>T	c.(1423-1425)CGG>CGT	p.R475R	FHOD3_uc002kzr.1_Silent_p.R475R|FHOD3_uc002kzs.1_Silent_p.R475R|FHOD3_uc010dmz.1_Silent_p.R190R	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	475	Potential.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GAATAGAGCGGGAAGAAAGAA	0.403													9	37					1.12685e-05	1.21448e-05	0.004482	1	0	
BCL2	596	broad.mit.edu	37	18	60985789	60985789	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:60985789G>A	uc002lit.1	-	2	604	c.111C>T	c.(109-111)GCC>GCT	p.A37A	BCL2_uc002liu.1_Silent_p.A37A|BCL2_uc002liv.1_Silent_p.A37A	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform	37					activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)	ccgggggcgcggcgcccACAT	0.527			T	IGH@	NHL|CLL								6	35					0	0	0.001984	0	0	
RTTN	25914	broad.mit.edu	37	18	67776813	67776813	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:67776813G>A	uc002lkp.2	-	28	3892	c.3824C>T	c.(3823-3825)GCG>GTG	p.A1275V	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_Missense_Mutation_p.A363V	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1275							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)				TCCCGGAAACGCAGTGAGGTT	0.507													9	50					0	0	0.004482	0	0	
ZNF407	55628	broad.mit.edu	37	18	72343485	72343485	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:72343485G>A	uc002llw.2	+	1	567	c.510G>A	c.(508-510)CCG>CCA	p.P170P	ZNF407_uc010xfc.1_Silent_p.P170P|ZNF407_uc010dqu.1_Silent_p.P170P|ZNF407_uc002llu.2_Silent_p.P169P	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	170					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTTTCCCCCCGAAAGAAATTA	0.393													12	97					0	0	0.013537	0	0	
ZNF236	7776	broad.mit.edu	37	18	74583706	74583706	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:74583706A>G	uc002lmi.2	+	5	784	c.586A>G	c.(586-588)ACG>GCG	p.T196A	ZNF236_uc002lmj.2_RNA|ZNF236_uc002lmk.1_Missense_Mutation_p.T196A	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	196					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		AAGTGGATTCACGTATTCGTG	0.438													16	77					0	0	0.006122	0	0	
GALR1	2587	broad.mit.edu	37	18	74980856	74980856	+	Nonstop_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr18:74980856T>C	uc002lms.3	+	3	1545	c.1048T>C	c.(1048-1050)TGA>CGA	p.*350R		NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1	350					digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		TACTCATGTGTGATAAAAGAT	0.388													17	94					0	0	0.006122	0	0	
PTBP1	5725	broad.mit.edu	37	19	810550	810550	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:810550G>A	uc002lpr.2	+	13	1499	c.1393G>A	c.(1393-1395)GTC>ATC	p.V465I	PTBP1_uc002lpp.2_Missense_Mutation_p.V491I|PTBP1_uc002lpq.2_Missense_Mutation_p.V484I|PTBP1_uc002lps.2_Missense_Mutation_p.V131I|PTBP1_uc002lpt.2_RNA|PTBP1_uc002lpu.1_Missense_Mutation_p.V461I	NM_031991	NP_114368	P26599	PTBP1_HUMAN	polypyrimidine tract-binding protein 1 isoform	465	RRM 4.				negative regulation of muscle cell differentiation|nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	mRNA binding|nucleotide binding|poly-pyrimidine tract binding|protein binding			kidney(1)|skin(1)	2		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		CAGGCCCTCAGTCTCCGAGGA	0.612													4	32					0	0	0.009096	0	0	
PRTN3	5657	broad.mit.edu	37	19	847857	847857	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:847857T>C	uc002lqa.1	+	5	683	c.659T>C	c.(658-660)GTG>GCG	p.V220A		NM_002777	NP_002768	P24158	PRTN3_HUMAN	myeloblastin	220	Peptidase S1.				collagen catabolic process|positive regulation of cell proliferation|proteolysis		protein binding|serine-type endopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		GACTCCTTCGTGATCTGGGGA	0.617													4	7					0	0	0.000602	0	0	
AP3D1	8943	broad.mit.edu	37	19	2102224	2102224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:2102224G>A	uc002luz.2	-	30	3633	c.3410C>T	c.(3409-3411)ACG>ATG	p.T1137M	AP3D1_uc010dsv.2_Missense_Mutation_p.T227M|AP3D1_uc002luy.2_Missense_Mutation_p.T1096M|AP3D1_uc002lva.2_Missense_Mutation_p.T1199M	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	1137					eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCAGTAGCGTGGAGTCACT	0.507													23	95					0	0	0.004656	0	0	
AP3D1	8943	broad.mit.edu	37	19	2138638	2138638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:2138638C>T	uc002luz.2	-	2	395	c.172G>A	c.(172-174)GCG>ACG	p.A58T	AP3D1_uc002luy.2_Missense_Mutation_p.A58T|AP3D1_uc002lva.2_Missense_Mutation_p.A58T	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	58	HEAT 1.				eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGCAGACCGCGTTCGCCTTC	0.532													11	84					0	0	0.013537	0	0	
UBXN6	80700	broad.mit.edu	37	19	4453928	4453928	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:4453928C>A	uc002man.1	-	2	342	c.246G>T	c.(244-246)CAG>CAT	p.Q82H	UBXN6_uc010dty.1_Missense_Mutation_p.Q29H|UBXN6_uc002mam.1_Missense_Mutation_p.Q29H	NM_025241	NP_079517	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	82						microtubule organizing center|nucleus	protein binding				0						ATATCTCACCCTGGTTTCGGA	0.662													6	32					0.00198382	0.00208189	0.001984	1	0	
KDM4B	23030	broad.mit.edu	37	19	5047625	5047625	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:5047625G>A	uc002mbq.3	+	6	797	c.571G>A	c.(571-573)GAG>AAG	p.E191K	KDM4B_uc010xil.1_Missense_Mutation_p.E191K|KDM4B_uc010xim.1_Missense_Mutation_p.E191K	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	191	JmjC.	Iron; catalytic (By similarity).			chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						CTGGCACACCGAGGACATGGA	0.632													17	66					0	0	0.006122	0	0	
PTPRS	5802	broad.mit.edu	37	19	5219994	5219994	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:5219994G>A	uc002mbv.2	-	22	3955	c.3721C>T	c.(3721-3723)CGC>TGC	p.R1241C	PTPRS_uc002mbu.1_Missense_Mutation_p.R810C|PTPRS_uc010xin.1_Missense_Mutation_p.R810C|PTPRS_uc002mbw.2_Missense_Mutation_p.R1219C|PTPRS_uc002mbx.2_Missense_Mutation_p.R814C|PTPRS_uc002mby.2_Missense_Mutation_p.R810C	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1241	Extracellular (Potential).				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		AGGACATAGCGGTGGCCGGGC	0.597													8	36					0	0	0.003080	0	0	
ACSBG2	81616	broad.mit.edu	37	19	6183243	6183243	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:6183243C>T	uc002mef.1	+	10	1509	c.1282C>T	c.(1282-1284)CCC>TCC	p.P428S	ACSBG2_uc002mee.1_Missense_Mutation_p.P241S|ACSBG2_uc002meg.1_Missense_Mutation_p.P428S|ACSBG2_uc002meh.1_Missense_Mutation_p.P428S|ACSBG2_uc002mei.1_Missense_Mutation_p.P378S|ACSBG2_uc010xiz.1_Missense_Mutation_p.P428S	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	428					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						GAGCTCGGGACCCCACACGAT	0.552													10	40					0	0	0.010729	0	0	
GPR108	56927	broad.mit.edu	37	19	6732509	6732509	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:6732509C>T	uc002mfp.2	-	11	1031	c.985G>A	c.(985-987)GTC>ATC	p.V329I	GPR108_uc010duv.2_5'Flank|GPR108_uc002mfn.2_5'UTR|GPR108_uc002mfo.3_Missense_Mutation_p.V87I|GPR108_uc010duw.2_RNA	NM_001080452	NP_001073921	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108 isoform 1	329						integral to membrane					0						TAGTACATGACGGCAAGGCCT	0.632													5	27					0	0	0.000602	0	0	
VAV1	7409	broad.mit.edu	37	19	6821674	6821674	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:6821674C>A	uc002mfu.1	+	3	460	c.363C>A	c.(361-363)GCC>GCA	p.A121A	VAV1_uc010xjh.1_Silent_p.A121A|VAV1_uc010dva.1_Silent_p.A121A|VAV1_uc002mfv.1_Silent_p.A66A	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	121					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						CCCCGATCGCCCAGAACAGGG	0.637													10	53					3.86212e-05	4.1306e-05	0.008291	1	0	
MUC16	94025	broad.mit.edu	37	19	9011368	9011368	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:9011368T>G	uc002mkp.2	-	36	39069	c.38865A>C	c.(38863-38865)AAA>AAC	p.K12955N	MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12957	SEA 6.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGCCCAGCTCTTTGATGCCAT	0.547													53	176					0	0	0.014410	0	0	
MUC16	94025	broad.mit.edu	37	19	9087335	9087335	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:9087335T>C	uc002mkp.2	-	1	4684	c.4480A>G	c.(4480-4482)ACA>GCA	p.T1494A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1494	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGAGAAGGTGTGGACATAGGT	0.428													29	212					0	0	0.012213	0	0	
OR7D2	162998	broad.mit.edu	37	19	9296531	9296531	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:9296531C>T	uc002mkz.1	+	1	262	c.74C>T	c.(73-75)CCG>CTG	p.P25L		NM_175883	NP_787079	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D,	25	Extracellular (Potential).				regulation of transcription, DNA-dependent|sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|upper_aerodigestive_tract(1)	3						GAACTACAGCCGTTCATATTT	0.498													14	57					0	0	0.003163	0	0	
OLFM2	93145	broad.mit.edu	37	19	9965414	9965414	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:9965414G>A	uc002mmp.2	-	6	841	c.813C>T	c.(811-813)CAC>CAT	p.H271H	OLFM2_uc002mmo.2_Silent_p.H193H	NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor	271	Olfactomedin-like.					extracellular region				large_intestine(1)|skin(1)	2						TGTACACCACGTGGCCCGTGC	0.607													6	8					0	0	0.001984	0	0	
ICAM1	3383	broad.mit.edu	37	19	10394931	10394931	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:10394931G>A	uc002mnq.2	+	4	1179	c.860G>A	c.(859-861)CGG>CAG	p.R287Q	ICAM1_uc010xle.1_Missense_Mutation_p.R65Q|ICAM4_uc002mnr.1_5'Flank|ICAM4_uc002mns.1_5'Flank|ICAM4_uc002mnt.1_5'Flank	NM_000201	NP_000192	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1 precursor	287	Ig-like C2-type 3.|Extracellular (Potential).				adhesion to symbiont|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking|positive regulation of cellular extravasation|regulation of immune response|regulation of leukocyte mediated cytotoxicity|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell|virion attachment, binding of host cell surface receptor	extracellular space|integral to plasma membrane	integrin binding|transmembrane receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Natalizumab(DB00108)|Simvastatin(DB00641)	GGCACCCAGCGGCTGACGTGT	0.607													7	33					0	0	0.010729	0	0	
PDE4A	5141	broad.mit.edu	37	19	10568738	10568738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:10568738G>A	uc002moj.2	+	8	1169	c.1061G>A	c.(1060-1062)CGA>CAA	p.R354Q	PDE4A_uc002mok.2_Missense_Mutation_p.R328Q|PDE4A_uc002mol.2_Missense_Mutation_p.R293Q|PDE4A_uc002mom.2_Missense_Mutation_p.R115Q|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_5'Flank	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	354	Catalytic.				signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	AACATTCCCCGATTTGGGGTG	0.577													14	49					0	0	0.004990	0	0	
SMARCA4	6597	broad.mit.edu	37	19	11143999	11143999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:11143999G>A	uc002mqf.3	+	26	3864	c.3580G>A	c.(3580-3582)GGG>AGG	p.G1194R	SMARCA4_uc010dxp.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxo.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxq.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxr.2_Missense_Mutation_p.G1194R|SMARCA4_uc002mqj.3_Missense_Mutation_p.G1194R|SMARCA4_uc010dxs.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxt.1_Missense_Mutation_p.G414R|SMARCA4_uc002mqh.3_Missense_Mutation_p.G317R|SMARCA4_uc002mqi.1_Missense_Mutation_p.G397R	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1194	Helicase C-terminal.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCACCGCATCGGGCAGCAGAA	0.612			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				11	48					0	0	0.001855	0	0	
DOCK6	57572	broad.mit.edu	37	19	11312679	11312679	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:11312679C>T	uc002mqs.3	-	44	5615	c.5574G>A	c.(5572-5574)CCG>CCA	p.P1858P	DOCK6_uc002mqr.3_Silent_p.P258P|DOCK6_uc010xlq.1_Silent_p.P1197P	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1858	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						CGCGCCCATCCGGCGTGAACG	0.592													8	26					0	0	0.004482	0	0	
DOCK6	57572	broad.mit.edu	37	19	11312758	11312758	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:11312758T>C	uc002mqs.3	-	44	5536	c.5495A>G	c.(5494-5496)TAC>TGC	p.Y1832C	DOCK6_uc002mqr.3_Missense_Mutation_p.Y232C|DOCK6_uc010xlq.1_Missense_Mutation_p.Y1171C	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1832	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						CTTGAGCTCGTAGGTATCAAA	0.612													5	38					0	0	0.001168	0	0	
ZNF799	90576	broad.mit.edu	37	19	12501739	12501739	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:12501739A>G	uc010dyt.2	-	4	1623	c.1473T>C	c.(1471-1473)CTT>CTC	p.L491L	ZNF799_uc002mts.3_Intron	NM_001080821	NP_001074290	Q96GE5	ZN799_HUMAN	zinc finger protein 799	491	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						TATGTTGAGAAAGGTATTGGA	0.363													15	95					0	0	0.004007	0	0	
MAST1	22983	broad.mit.edu	37	19	12984811	12984811	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:12984811C>T	uc002mvm.2	+	26	3968	c.3840C>T	c.(3838-3840)GGC>GGT	p.G1280G		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	1280					cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7						ACAAGAAGGGCGCGCTGCGCA	0.677													3	9					0	0	0.009096	0	0	
RFX1	5989	broad.mit.edu	37	19	14077273	14077273	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:14077273A>G	uc002mxv.2	-	14	2193	c.1921T>C	c.(1921-1923)TAC>CAC	p.Y641H		NM_002918	NP_002909	P22670	RFX1_HUMAN	regulatory factor X1	641					immune response	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			lung(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			CTGAGGTTGTACCTCCAGAAG	0.647													4	24					0	0	0.000602	0	0	
CCDC105	126402	broad.mit.edu	37	19	15132473	15132473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:15132473C>T	uc002nae.2	+	5	1186	c.1087C>T	c.(1087-1089)CGG>TGG	p.R363W		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	363					microtubule cytoskeleton organization	microtubule				ovary(1)	1						AACTATCCTCCGGTGTACGAA	0.587													11	49					0	0	0.013537	0	0	
EPHX3	79852	broad.mit.edu	37	19	15342161	15342161	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:15342161C>T	uc002nap.2	-	3	585	c.376G>A	c.(376-378)GTT>ATT	p.V126I	EPHX3_uc002naq.2_Missense_Mutation_p.V126I	NM_024794	NP_079070	Q9H6B9	EPHX3_HUMAN	abhydrolase domain containing 9 precursor	126						extracellular region	hydrolase activity				0						ACAGCCACAACATGGAAGCGG	0.617													5	24					0	0	0.004482	0	0	
WIZ	58525	broad.mit.edu	37	19	15538021	15538021	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:15538021G>A	uc002nbc.2	-	4	1398	c.1375C>T	c.(1375-1377)CCA>TCA	p.P459S	WIZ_uc002nba.3_Missense_Mutation_p.P326S|WIZ_uc002nbb.3_Missense_Mutation_p.P285S	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	1142	Pro-rich.					nucleus	zinc ion binding				0						CCCGGTGGTGGTGGCAACTTC	0.652													7	23					0	0	0.001984	0	0	
C19orf44	84167	broad.mit.edu	37	19	16612314	16612314	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:16612314C>A	uc002neh.1	+	2	784	c.711C>A	c.(709-711)GGC>GGA	p.G237G	MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Silent_p.G237G|C19orf44_uc002neg.2_Silent_p.G237G|C19orf44_uc010eai.1_RNA	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167	237											0						CGAATCAAGGCTTCAGCAGCG	0.318													8	91					7.48243e-07	8.1217e-07	0.006214	1	0	
SLC35E1	79939	broad.mit.edu	37	19	16677452	16677452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:16677452C>T	uc010xph.1	-	4	665	c.647G>A	c.(646-648)CGG>CAG	p.R216Q	MED26_uc002nee.2_RNA|SLC35E1_uc002nem.1_Missense_Mutation_p.R216Q	NM_024881	NP_079157	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	216					transport	integral to membrane				ovary(1)|central_nervous_system(1)	2						ATGGTGGATCCGTGAATCTCG	0.542													20	51					0	0	0.007413	0	0	
JAK3	3718	broad.mit.edu	37	19	17943458	17943458	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:17943458G>A	uc002nhn.3	-	19	2650	c.2550C>T	c.(2548-2550)GCC>GCT	p.A850A	JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Silent_p.A850A	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	850	Protein kinase 2.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56						CGGCCACCAGGGCACCTGTAT	0.592		2	Mis		acute megakaryocytic leukemia|								9	48					0	0	0.010729	0	0	
KLHL26	55295	broad.mit.edu	37	19	18779089	18779089	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:18779089G>A	uc002njz.1	+	3	909	c.882G>A	c.(880-882)CAG>CAA	p.Q294Q		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	294										ovary(1)	1						CCTTCCGGCAGCACGAGATGC	0.662													5	26					0	0	0.006214	0	0	
ARMC6	93436	broad.mit.edu	37	19	19165124	19165124	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:19165124C>T	uc002nld.2	+	6	1365	c.1017C>T	c.(1015-1017)GGC>GGT	p.G339G	ARMC6_uc002nlc.2_Silent_p.G314G|ARMC6_uc010xql.1_Silent_p.G246G|ARMC6_uc002nle.2_Silent_p.G314G|ARMC6_uc010xqm.1_Silent_p.G339G	NM_033415	NP_219483	Q6NXE6	ARMC6_HUMAN	armadillo repeat containing 6	339	ARM 3.						protein binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)			ACCAGAGCGGCGTTCAGGTAT	0.612											OREG0025376	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	26					0	0	0.001168	0	0	
GMIP	51291	broad.mit.edu	37	19	19747568	19747568	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:19747568G>A	uc002nnd.2	-	13	1392	c.1275C>T	c.(1273-1275)AGC>AGT	p.S425S	GMIP_uc010xrb.1_Silent_p.S425S|GMIP_uc010xrc.1_Silent_p.S422S	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	425					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1						CGCCACCCACGCTGTCCACAT	0.637													4	20					0	0	0.003080	0	0	
Unknown	0	broad.mit.edu	37	19	24102971	24102971	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:24102971G>A	uc002nrp.1	-	3		c.497C>T			uc010eda.1_RNA					Homo sapiens cDNA FLJ43698 fis, clone TCERX2000998.																		TTGGAAAGCTGCATTCCAAAG	0.398													6	26					0	0	0.001984	0	0	
ZNF536	9745	broad.mit.edu	37	19	31039431	31039431	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:31039431G>A	uc002nsu.1	+	4	3043	c.2905G>A	c.(2905-2907)GAG>AAG	p.E969K	ZNF536_uc010edd.1_Missense_Mutation_p.E969K	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	969					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					GAGGAAGTCCGAGAAATCTCA	0.592													31	137					0	0	0.012213	0	0	
TSHZ3	57616	broad.mit.edu	37	19	31769889	31769889	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:31769889G>A	uc002nsy.3	-	2	875	c.810C>T	c.(808-810)GAC>GAT	p.D270D		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	270					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					CCTTCTGGGCGTCTTCCTTCC	0.512													33	123					0	0	0.003755	0	0	
GPATCH1	55094	broad.mit.edu	37	19	33621034	33621034	+	Splice_Site	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:33621034A>C	uc002nug.1	+	20	3080	c.2766_splice	c.e20-2	p.R922_splice	GPATCH1_uc002nuh.1_Splice_Site_p.R299_splice|WDR88_uc002nui.2_5'Flank	NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					TTTCTTTTCCAGGCTGAAAAG	0.458													12	84					0	0	0.010729	0	0	
LRP3	4037	broad.mit.edu	37	19	33697607	33697607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:33697607G>A	uc010edh.2	+	6	1786	c.1693G>A	c.(1693-1695)GTG>ATG	p.V565M	LRP3_uc010xrp.1_3'UTR|LRP3_uc002nuk.3_Missense_Mutation_p.V439M	NM_002333	NP_002324	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein	565	Cytoplasmic (Potential).				receptor-mediated endocytosis	coated pit|integral to membrane	receptor activity			pancreas(2)|ovary(1)	3	Esophageal squamous(110;0.137)					CATTCCACCCGTGGAGGACTT	0.677													7	38					0	0	0.001984	0	0	
GRAMD1A	57655	broad.mit.edu	37	19	35514416	35514416	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:35514416C>T	uc010xse.1	+	19	2184	c.2047C>T	c.(2047-2049)CAG>TAG	p.Q683*	GRAMD1A_uc002nxk.2_Nonsense_Mutation_p.Q672*|GRAMD1A_uc002nxl.2_Nonsense_Mutation_p.Q445*|GRAMD1A_uc010xsf.1_Nonsense_Mutation_p.Q684*|GRAMD1A_uc002nxm.1_RNA|GRAMD1A_uc002nxn.1_Nonsense_Mutation_p.Q294*	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	683						integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CAAGTGGAGGCAGATCCTGCG	0.667													4	14					0	0	0.009096	0	0	
KRTDAP	388533	broad.mit.edu	37	19	35981334	35981334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:35981334G>A	uc002nzh.2	-	1	23	c.11C>T	c.(10-12)CCG>CTG	p.P4L		NM_207392	NP_997275	P60985	KTDAP_HUMAN	keratinocyte differentiation-associated protein	4					cell differentiation	extracellular region					0	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGAAGGACCGGGATCTTCAT	0.597													6	70					0	0	0.004482	0	0	
PRODH2	58510	broad.mit.edu	37	19	36290978	36290978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:36290978G>A	uc002obx.1	-	11	1591	c.1573C>T	c.(1573-1575)CGG>TGG	p.R525W	uc002obw.1_5'Flank	NM_021232	NP_067055	Q9UF12	PROD2_HUMAN	kidney and liver proline oxidase 1	525					glutamate biosynthetic process|proline catabolic process		proline dehydrogenase activity	p.R525W(1)		ovary(2)	2	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGCAGCCGCCGCCACAGTTCT	0.617													4	9					0	0	0.001168	0	0	
ZNF527	84503	broad.mit.edu	37	19	37879513	37879513	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:37879513C>T	uc010efk.1	+	5	673	c.562C>T	c.(562-564)CAG>TAG	p.Q188*	ZNF527_uc002ogf.3_Nonsense_Mutation_p.Q156*|ZNF527_uc010xtq.1_RNA	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	188					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCCTACCATACAGCAAGTACA	0.338													14	79					0	0	0.002450	0	0	
SIPA1L3	23094	broad.mit.edu	37	19	38673271	38673271	+	Missense_Mutation	SNP	G	A	A	rs139858184	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:38673271G>A	uc002ohk.2	+	16	4830	c.4321G>A	c.(4321-4323)GTC>ATC	p.V1441I		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1441					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTCCGCCTCCGTCCCCAAGTC	0.622													15	52					0	0	0.006122	0	0	
RYR1	6261	broad.mit.edu	37	19	38959976	38959976	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:38959976C>T	uc002oit.2	+	27	3718	c.3588C>T	c.(3586-3588)GGC>GGT	p.G1196G	RYR1_uc002oiu.2_Silent_p.G1196G	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1196	6 X approximate repeats.|Cytoplasmic.|B30.2/SPRY 2.				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)	TGGGACCTGGCCAGGTGGGTC	0.408													13	74					0	0	0.002450	0	0	
RYR1	6261	broad.mit.edu	37	19	38976392	38976392	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:38976392C>T	uc002oit.2	+	34	5227	c.5097C>T	c.(5095-5097)GAC>GAT	p.D1699D	RYR1_uc002oiu.2_Silent_p.D1699D	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1699	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)	CCCTGGAGGACGCGCACCTGC	0.657													8	35					0	0	0.003080	0	0	
RYR1	6261	broad.mit.edu	37	19	38993326	38993326	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:38993326G>A	uc002oit.2	+	48	7924	c.7794G>A	c.(7792-7794)GCG>GCA	p.A2598A	RYR1_uc002oiu.2_Silent_p.A2598A|RYR1_uc002oiv.1_5'UTR	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	2598	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)	TCACCAAGGCGCAGCGTGACG	0.512													5	11					0	0	0.003080	0	0	
FCGBP	8857	broad.mit.edu	37	19	40368650	40368650	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:40368650C>T	uc002omp.3	-	28	12706	c.12698G>A	c.(12697-12699)GGC>GAC	p.G4233D		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4233	VWFD 10.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGCCAGTGTGCCATTAGGGAA	0.642													6	55					0	0	0.004482	0	0	
SPTBN4	57731	broad.mit.edu	37	19	40996007	40996007	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:40996007G>A	uc002ony.2	+	4	433	c.347G>A	c.(346-348)CGG>CAG	p.R116Q	SPTBN4_uc002onx.2_Missense_Mutation_p.R116Q|SPTBN4_uc002onz.2_Missense_Mutation_p.R116Q	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	116	CH 1.|Actin-binding.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGCCGCATGCGGATCCACTCA	0.662													6	22					0	0	0.001984	0	0	
CEACAM7	1087	broad.mit.edu	37	19	42190985	42190985	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:42190985G>A	uc002ori.1	-	2	234	c.232C>T	c.(232-234)CGA>TGA	p.R78*	CEACAM7_uc010ehx.2_Nonsense_Mutation_p.R78*|CEACAM7_uc010ehy.1_Nonsense_Mutation_p.R78*	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion	78	Ig-like V-type.					anchored to membrane|integral to membrane|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		CCTATAATTCGATAGTTGGCA	0.458													17	86					0	0	0.004007	0	0	
CIC	23152	broad.mit.edu	37	19	42797150	42797150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:42797150G>A	uc002otf.1	+	15	3552	c.3512G>A	c.(3511-3513)CGG>CAG	p.R1171Q		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	1171	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)				AAGGCCCAGCGGCCCAGCCCG	0.652			T	DUX4	soft tissue sarcoma								6	29					0	0	0.003080	0	0	
LIPE	3991	broad.mit.edu	37	19	42909697	42909697	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:42909697G>A	uc002otr.2	-	8	2659	c.2382C>T	c.(2380-2382)GAC>GAT	p.D794D	uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	794					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				AGTTGGAGTGGTCCTCCGTCT	0.587													6	37					0	0	0.001168	0	0	
PSG1	5669	broad.mit.edu	37	19	43375950	43375950	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:43375950G>A	uc002ovb.2	-	3	816	c.678C>T	c.(676-678)AGC>AGT	p.S226S	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Silent_p.S226S|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Silent_p.S226S|PSG1_uc010eio.1_Silent_p.S226S|PSG1_uc002oux.1_Silent_p.S155S|PSG1_uc002ouy.1_Silent_p.S226S|PSG1_uc002ouz.1_Silent_p.S226S|PSG1_uc002ova.1_Intron|PSG1_uc002ovc.2_Intron|PSG1_uc002ovd.1_Silent_p.S226S	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	226	Ig-like C2-type 1.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				GGTCACTGCGGCTGGCACTCA	0.537													54	250					0	0	0.014410	0	0	
BCAM	4059	broad.mit.edu	37	19	45315631	45315631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:45315631C>T	uc002ozu.2	+	3	460	c.416C>T	c.(415-417)GCG>GTG	p.A139V	BCAM_uc002ozt.1_Missense_Mutation_p.A139V	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	139	Extracellular (Potential).|Ig-like V-type 1.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GAGGCCACTGCGCGGCTCAAC	0.682													3	7					0	0	0.004672	0	0	
BCAM	4059	broad.mit.edu	37	19	45321843	45321843	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:45321843C>T	uc002ozu.2	+	9	1187	c.1143C>T	c.(1141-1143)GTC>GTT	p.V381V	BCAM_uc002ozt.1_Silent_p.V381V	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	381	Extracellular (Potential).|Ig-like C2-type 2.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GCAGTGCAGTCGTGAACTGCT	0.647													6	26					0	0	0.001984	0	0	
PNMAL1	55228	broad.mit.edu	37	19	46974273	46974273	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:46974273A>G	uc002peq.3	-	2	326	c.20T>C	c.(19-21)ATG>ACG	p.M7T	PNMAL1_uc002per.3_Missense_Mutation_p.M7T	NM_018215	NP_060685	Q86V59	PNML1_HUMAN	PNMA-like 1 isoform a	7											0		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		cagaaggttcatcgccatggt	0													12	55					0	0	0.003163	0	0	
PRR12	57479	broad.mit.edu	37	19	50118249	50118249	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50118249G>A	uc002poo.3	+	8	5007	c.5007G>A	c.(5005-5007)CGG>CGA	p.R1669R		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	848	Pro-rich.						DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CCTGGCATCGGCCCCCAGTGC	0.517													5	32					0	0	0.000602	0	0	
PRR12	57479	broad.mit.edu	37	19	50123625	50123625	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50123625G>A	uc002poo.3	+	10	5514	c.5514G>A	c.(5512-5514)GGG>GGA	p.G1838G		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	1017							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CAGTACCTGGGCGTCTGCTCA	0.458													6	16					0	0	0.003080	0	0	
PRR12	57479	broad.mit.edu	37	19	50124783	50124783	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50124783C>T	uc002poo.3	+	11	5625	c.5625C>T	c.(5623-5625)GAC>GAT	p.D1875D		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	1054							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GTCCATCAGACGAGCTGTACC	0.512													4	13					0	0	0.009096	0	0	
VRK3	51231	broad.mit.edu	37	19	50482461	50482461	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50482461T>C	uc002prg.2	-	14	1413	c.1315A>G	c.(1315-1317)ACG>GCG	p.T439A	VRK3_uc002prh.1_Missense_Mutation_p.T439A|VRK3_uc002pri.1_Missense_Mutation_p.T389A|VRK3_uc010ens.2_Missense_Mutation_p.T439A|VRK3_uc010ybl.1_Missense_Mutation_p.T389A|VRK3_uc010ybm.1_Missense_Mutation_p.T208A	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1	439	Protein kinase.					nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		TCCTCATACGTGAGGGCCATC	0.582													6	34					0	0	0.003080	0	0	
MYH14	79784	broad.mit.edu	37	19	50726368	50726368	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50726368G>A	uc002prr.1	+	4	637	c.590_splice	c.e4+1	p.T197_splice	MYH14_uc010enu.1_Splice_Site_p.T197_splice|MYH14_uc002prq.1_Splice_Site_p.T197_splice	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TTCTCTGCACGTGAGTAATCT	0.572													5	131					0	0	0.000602	0	0	
NAPSA	9476	broad.mit.edu	37	19	50864954	50864954	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50864954C>T	uc002prx.2	-	4	487	c.434G>A	c.(433-435)CGG>CAG	p.R145Q	NR1H2_uc002prv.3_Intron	NM_004851	NP_004842	O96009	NAPSA_HUMAN	napsin A preproprotein	145					proteolysis	extracellular region	aspartic-type endopeptidase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		TCCATCTACCCGCCCAGTTCC	0.517													13	81					0	0	0.013537	0	0	
SPIB	6689	broad.mit.edu	37	19	50926203	50926203	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:50926203A>G	uc002psd.2	+	4	273	c.248A>G	c.(247-249)TAC>TGC	p.Y83C	SPIB_uc002pse.2_Missense_Mutation_p.Y83C|SPIB_uc010ycc.1_Intron	NM_003121	NP_003112	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	83					regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	sequence-specific DNA binding			lung(1)|kidney(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		CCCCCCACCTACAGCCCTGCA	0.682													3	15					0	0	0.001168	0	0	
LIM2	3982	broad.mit.edu	37	19	51883795	51883795	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:51883795G>T	uc002pwm.2	-	4	468	c.424C>A	c.(424-426)CTG>ATG	p.L142M	LIM2_uc002pwl.2_Missense_Mutation_p.L184M	NM_001161748	NP_001155220	P55344	LMIP_HUMAN	lens intrinsic membrane protein 2, 19kDa isoform	142	Helical; (Potential).				cell-cell junction assembly	cell junction|integral to membrane	structural constituent of eye lens				0		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000214)|OV - Ovarian serous cystadenocarcinoma(262;0.00985)		ACCCAGCCCAGGATGTAGGAC	0.612													24	117					2.08973e-25	2.36151e-25	0.005443	1	0	
FPR3	2359	broad.mit.edu	37	19	52328045	52328045	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:52328045G>A	uc002pxt.1	+	2	1228	c.1044G>A	c.(1042-1044)ACG>ACA	p.T348T		NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2	348	Cytoplasmic (Potential).				cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity	p.T348M(1)		lung(4)|breast(1)|skin(1)	6						CTGAGGAGACGGAGTTACAAG	0.458													5	31					0	0	0.001168	0	0	
ZNF350	59348	broad.mit.edu	37	19	52471832	52471832	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:52471832T>C	uc002pyd.2	-	4	465	c.237A>G	c.(235-237)TCA>TCG	p.S79S	uc002pyb.2_Intron|uc002pyc.2_Intron	NM_021632	NP_067645	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	79	KRAB.				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)		TTCTCTCACCTGAACAGGCTC	0.478													12	52					0	0	0.002450	0	0	
PPP2R1A	5518	broad.mit.edu	37	19	52719049	52719049	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:52719049G>A	uc002pyp.2	+	7	984	c.825G>A	c.(823-825)GGG>GGA	p.G275G	PPP2R1A_uc010ydk.1_Silent_p.G220G|PPP2R1A_uc010epm.1_Silent_p.G315G|PPP2R1A_uc002pyq.2_Silent_p.G96G	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein	275	HEAT 7.|PP2A subunit B binding.|Polyoma small and medium T antigens Binding.				ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		AAGCAGTGGGGCCTGAGATCA	0.483			Mis		clear cell ovarian carcinoma								6	54					0	0	0.001984	0	0	
ZNF331	55422	broad.mit.edu	37	19	54080491	54080491	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:54080491G>A	uc002qbx.1	+	7	2111	c.677G>A	c.(676-678)CGT>CAT	p.R226H	ZNF331_uc002qby.1_Missense_Mutation_p.R226H|ZNF331_uc002qbz.1_Missense_Mutation_p.R226H|ZNF331_uc002qca.1_Missense_Mutation_p.R226H|ZNF331_uc010eqr.1_Missense_Mutation_p.R226H|ZNF331_uc002qcb.1_Missense_Mutation_p.R226H|ZNF331_uc002qcc.1_Missense_Mutation_p.R226H|ZNF331_uc002qcd.1_Missense_Mutation_p.R226H	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	226	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)		GCCTTTCGGCGTGGTGATGAG	0.463			T	?	follicular thyroid adenoma								23	81					0	0	0.002780	0	0	
MIR371	442916	broad.mit.edu	37	19	54290948	54290948	+	RNA	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:54290948G>T	hsa-mir-371|MI0000779	+			c.20G>T			uc010yec.1_RNA|uc010yed.1_5'Flank|MIR372_hsa-mir-372|MI0000780_5'Flank|uc010yee.1_5'Flank|MIR373_hsa-mir-373|MI0000781_5'Flank																	0						AAACTGTGGGGGCACTTTCTG	0.537													4	31					0.00909568	0.00949188	0.009096	1	0	
VSTM1	284415	broad.mit.edu	37	19	54567029	54567029	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:54567029C>T	uc002qcw.3	-	1	179	c.3G>A	c.(1-3)ATG>ATA	p.M1I	VSTM1_uc010erb.2_RNA|VSTM1_uc002qcx.3_Missense_Mutation_p.M1I	NM_198481	NP_940883	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	1						integral to membrane					0	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		ATTCTGCGGTCATAGCGTCCC	0.622													15	84					0	0	0.004990	0	0	
LILRB4	11006	broad.mit.edu	37	19	55177749	55177749	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:55177749C>T	uc002qgp.2	+	8	1295	c.933C>T	c.(931-933)GAC>GAT	p.D311D	LILRB4_uc002qgq.2_Silent_p.D311D|LILRB4_uc002qgr.2_Silent_p.D352D|LILRB4_uc010ert.2_Silent_p.D352D|LILRB4_uc010eru.2_Silent_p.D340D	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,	311	Cytoplasmic (Potential).					integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)		AGCCCAAGGACGGGGGCCTAC	0.602													8	28					0	0	0.008291	0	0	
KIR3DP1	768329	broad.mit.edu	37	19	55301539	55301539	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:55301539G>A	uc010yfi.1	+	5	719	c.718G>A	c.(718-720)GTG>ATG	p.V240M	KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL4_uc010yfl.1_Intron	NM_001015070	NP_001015070			killer-cell Ig-like receptor												0				GBM - Glioblastoma multiforme(193;0.0192)		AGGAGAGAGCGTGACCTTGTC	0.562													6	27					0	0	0.002450	0	0	
NLRP2	55655	broad.mit.edu	37	19	55481397	55481397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:55481397C>T	uc002qij.2	+	2	100	c.14C>T	c.(13-15)GCG>GTG	p.A5V	NLRP2_uc010yfp.1_Missense_Mutation_p.A5V|NLRP2_uc010esn.2_Missense_Mutation_p.A5V|NLRP2_uc010eso.2_Missense_Mutation_p.A5V|NLRP2_uc010esp.2_Missense_Mutation_p.A5V	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	5	DAPIN.				apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GTGTCTTCGGCGCAGATGGGC	0.547													9	51					0	0	0.006214	0	0	
ZNF835	90485	broad.mit.edu	37	19	57176390	57176390	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:57176390T>C	uc010ygo.1	-	2	243	c.243A>G	c.(241-243)CGA>CGG	p.R81R	ZNF835_uc010ygn.1_Silent_p.R59R	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4						TTCTTGGGATTCGGCTGAATT	0.622													4	16					0	0	0.009096	0	0	
ZIM2	23619	broad.mit.edu	37	19	57286130	57286130	+	Missense_Mutation	SNP	C	T	T	rs138640675		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:57286130C>T	uc002qnr.2	-	11	1892	c.1510G>A	c.(1510-1512)GGC>AGC	p.G504S	uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_Missense_Mutation_p.G300S|ZIM2_uc010ygr.1_Missense_Mutation_p.G300S|ZIM2_uc002qnq.2_Missense_Mutation_p.G504S|ZIM2_uc010etp.2_Missense_Mutation_p.G504S|ZIM2_uc010ygs.1_Missense_Mutation_p.G504S	NM_015363	NP_056178	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	504	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		GAGGGTCGGCCGAAACATTTC	0.443													13	68					0	0	0.002450	0	0	
ZNF805	390980	broad.mit.edu	37	19	57765977	57765977	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:57765977T>C	uc010ygt.1	+	4	1997	c.1790T>C	c.(1789-1791)GTC>GCC	p.V597A	ZNF805_uc010ygu.1_Missense_Mutation_p.V464A	NM_001023563	NP_001018857	Q5CZA5	ZN805_HUMAN	zinc finger protein 805 isoform 1	597					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTTTTGAATGTCACCACTGAG	0.408													7	41					0	0	0.001984	0	0	
ZNF543	125919	broad.mit.edu	37	19	57839233	57839233	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:57839233T>C	uc002qoi.1	+	4	748	c.403T>C	c.(403-405)TTG>CTG	p.L135L		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	135					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AGAAGTCCACTTGAAAATAGG	0.478													12	51					0	0	0.010729	0	0	
ZNF749	388567	broad.mit.edu	37	19	57956447	57956447	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:57956447A>G	uc002qoq.2	+	3	2185	c.1931A>G	c.(1930-1932)GAA>GGA	p.E644G	ZNF547_uc002qpm.3_Intron	NM_001023561	NP_001018855	O43361	ZN749_HUMAN	zinc finger protein 749	644	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		GAGTGTAGTGAATGTGGGAAA	0.373													7	70					0	0	0.001984	0	0	
ZNF772	400720	broad.mit.edu	37	19	57985255	57985255	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:57985255C>A	uc002qot.2	-	5	1118	c.857G>T	c.(856-858)AGA>ATA	p.R286I	ZNF547_uc002qpm.3_Intron|ZNF772_uc010ygy.1_Missense_Mutation_p.R245I|ZNF772_uc010ygz.1_Missense_Mutation_p.R174I|ZNF772_uc010yha.1_Missense_Mutation_p.R232I|ZNF772_uc002qou.2_Missense_Mutation_p.R174I	NM_001024596	NP_001019767	Q68DY9	ZN772_HUMAN	zinc finger protein 772 isoform 1	286	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		AGTGTGGACTCTCTGGTGTTG	0.488													25	84					3.99451e-17	4.49583e-17	0.009535	1	0	
ZNF552	79818	broad.mit.edu	37	19	58319993	58319993	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:58319993G>T	uc002qqg.2	-	3	809	c.639C>A	c.(637-639)AGC>AGA	p.S213R	ZNF587_uc002qqb.2_Intron|ZNF552_uc010yhg.1_Missense_Mutation_p.S209R	NM_024762	NP_079038	Q9H707	ZN552_HUMAN	zinc finger protein 552	213	C2H2-type 3; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		ATCCTCCACAGCTGTAATGGC	0.473													15	62					9.16793e-09	1.00619e-08	0.004990	1	0	
ZNF606	80095	broad.mit.edu	37	19	58490096	58490096	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:58490096G>A	uc002qqw.2	-	7	2570	c.1952C>T	c.(1951-1953)CCC>CTC	p.P651L	ZNF606_uc010yhp.1_Missense_Mutation_p.P561L	NM_025027	NP_079303	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	651					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		GCATTCATAGGGTTTTTCTCC	0.398													10	81					0	0	0.008291	0	0	
ZSCAN1	284312	broad.mit.edu	37	19	58564966	58564966	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:58564966C>T	uc002qrc.1	+	6	1021	c.774C>T	c.(772-774)AGC>AGT	p.S258S		NM_182572	NP_872378	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	258					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CTGACCAGAGCGGCCGCCACC	0.632													5	16					0	0	0.000602	0	0	
ZNF274	10782	broad.mit.edu	37	19	58724502	58724502	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:58724502C>T	uc002qrq.1	+	10	2414	c.1955C>T	c.(1954-1956)ACC>ATC	p.T652I	ZNF274_uc002qrr.1_Missense_Mutation_p.T620I|ZNF274_uc002qrs.1_Missense_Mutation_p.T547I|ZNF274_uc010eum.1_Missense_Mutation_p.T411I	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	652					viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		AAACAGCCTACCTCATAGCTC	0.463													19	68					0	0	0.002780	0	0	
ZBTB45	84878	broad.mit.edu	37	19	59028801	59028801	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:59028801C>T	uc002qtd.2	-	2	532	c.240G>A	c.(238-240)GTG>GTA	p.V80V	ZBTB45_uc002qte.2_Silent_p.V80V|ZBTB45_uc002qtf.2_Silent_p.V80V	NM_032792	NP_116181	Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	80	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		CCAGCTGTCGCACTGTCTGCG	0.647											OREG0025700	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	26					0	0	0.004482	0	0	
CPSF3	51692	broad.mit.edu	37	2	9611523	9611523	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:9611523C>T	uc002qzo.1	+	17	1943	c.1908C>T	c.(1906-1908)AGC>AGT	p.S636S	CPSF3_uc002qzp.1_Silent_p.S599S|CPSF3_uc002qzq.1_Silent_p.S213S	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,	636					histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		CTATTCTTAGCGTCACAGTGG	0.418													12	85					0	0	0.003163	0	0	
NOL10	79954	broad.mit.edu	37	2	10729712	10729712	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:10729712G>A	uc002raq.2	-	18	1713	c.1588C>T	c.(1588-1590)CGT>TGT	p.R530C	NOL10_uc010yje.1_Missense_Mutation_p.R504C|NOL10_uc010yjf.1_Missense_Mutation_p.R480C|NOL10_uc002rap.2_Missense_Mutation_p.R480C	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	530	Potential.					nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		ACTTTTTCACGAAGTTCTTGT	0.308													5	22					0	0	0.001168	0	0	
GREB1	9687	broad.mit.edu	37	2	11758537	11758537	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:11758537C>T	uc002rbk.1	+	22	3836	c.3536C>T	c.(3535-3537)CCC>CTC	p.P1179L	GREB1_uc002rbp.1_Missense_Mutation_p.P177L	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1179	Ser-rich.					integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		AAACAGAGGCCCCGGGCAAGT	0.721													3	10					0	0	0.004672	0	0	
GREB1	9687	broad.mit.edu	37	2	11773069	11773069	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:11773069G>A	uc002rbk.1	+	28	5171	c.4871G>A	c.(4870-4872)CGG>CAG	p.R1624Q	GREB1_uc002rbp.1_Missense_Mutation_p.R622Q	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1624						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GAGCTCGAGCGGAACCGGCAG	0.562													9	18					0	0	0.013537	0	0	
NBAS	51594	broad.mit.edu	37	2	15614225	15614225	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:15614225C>T	uc002rcc.1	-	15	1591	c.1565G>A	c.(1564-1566)CGC>CAC	p.R522H	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	522										ovary(2)|liver(1)|skin(1)	4						TGTCGTGGAGCGCAAACTCAC	0.433													14	77					0	0	0.002450	0	0	
NBAS	51594	broad.mit.edu	37	2	15614424	15614424	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:15614424G>A	uc002rcc.1	-	15	1392	c.1366C>T	c.(1366-1368)CGA>TGA	p.R456*	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	456										ovary(2)|liver(1)|skin(1)	4						AAACGAGATCGTTTGGGGGCA	0.333													5	20					0	0	0.000602	0	0	
NT5C1B	93034	broad.mit.edu	37	2	18765854	18765854	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:18765854C>T	uc002rcz.2	-	5	933	c.829G>A	c.(829-831)GAC>AAC	p.D277N	NT5C1B_uc002rcy.2_Missense_Mutation_p.D277N|NT5C1B_uc010exr.2_Missense_Mutation_p.D219N|NT5C1B_uc010yju.1_Missense_Mutation_p.D217N|NT5C1B_uc002rda.2_Missense_Mutation_p.D217N|NT5C1B_uc010yjv.1_Missense_Mutation_p.D294N|NT5C1B_uc010yjw.1_Missense_Mutation_p.D260N|NT5C1B_uc010exs.2_Missense_Mutation_p.D279N|NT5C1B_uc002rdb.1_Missense_Mutation_p.D69N	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	277					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GCCTCGTAGTCGTCCTCGTCC	0.682													4	9					0	0	0.009096	0	0	
NCOA1	8648	broad.mit.edu	37	2	24927973	24927973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:24927973C>T	uc002rfk.2	+	10	1226	c.968C>T	c.(967-969)GCC>GTC	p.A323V	NCOA1_uc010eye.2_Missense_Mutation_p.A323V|NCOA1_uc002rfi.2_Missense_Mutation_p.A172V|NCOA1_uc002rfj.2_Missense_Mutation_p.A323V|NCOA1_uc002rfl.2_Missense_Mutation_p.A323V	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	323									PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTGGCACTGCCTCCAGCCCC	0.423			T	PAX3	alveolar rhadomyosarcoma								13	57					0	0	0.013537	0	0	
ASXL2	55252	broad.mit.edu	37	2	25966041	25966041	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:25966041G>A	uc002rgs.2	-	12	3386	c.3165C>T	c.(3163-3165)CAC>CAT	p.H1055H	ASXL2_uc002rgt.1_Intron	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	1055					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTAGTCCTTCGTGGTATTGGT	0.507													7	43					0	0	0.003080	0	0	
KIF3C	3797	broad.mit.edu	37	2	26203385	26203385	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:26203385G>A	uc002rgu.2	-	1	2059	c.1402C>T	c.(1402-1404)CTG>TTG	p.L468L	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Silent_p.L468L	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	468	Potential.				blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCTCCTCCAGCCGCTCCTTC	0.592													9	44					0	0	0.006214	0	0	
GTF3C2	2976	broad.mit.edu	37	2	27566374	27566374	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:27566374G>A	uc002rjv.1	-	3	411	c.48C>T	c.(46-48)CCC>CCT	p.P16P	GTF3C2_uc002rju.1_Silent_p.P27P|GTF3C2_uc002rjw.1_Silent_p.P16P|GTF3C2_uc010eyz.1_Silent_p.P16P	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	16						transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTCCCCACGGGGCCGGCCT	0.557													15	89					0	0	0.003163	0	0	
PPM1G	5496	broad.mit.edu	37	2	27607889	27607889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:27607889C>T	uc002rkl.2	-	6	583	c.476G>A	c.(475-477)CGC>CAC	p.R159H	PPM1G_uc002rkm.2_Missense_Mutation_p.R9H	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G	159					cell cycle arrest|protein dephosphorylation	cytoplasm|nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					CTGCCCGTAGCGTGTCAGCAG	0.592													17	77					0	0	0.007413	0	0	
FAM98A	25940	broad.mit.edu	37	2	33810305	33810305	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:33810305G>A	uc002rpa.1	-	8	1169	c.1095C>T	c.(1093-1095)GGC>GGT	p.G365G	FAM98A_uc010yne.1_Silent_p.G170G|FAM98A_uc010ynd.1_Silent_p.G196G|FAM98A_uc002roz.1_Silent_p.G203G	NM_015475	NP_056290	Q8NCA5	FA98A_HUMAN	hypothetical protein LOC25940	366	Gly-rich.									ovary(1)	1	all_hematologic(175;0.115)					CATGGTCATAGCCACCACGTC	0.577													13	60					0	0	0.002450	0	0	
CRIM1	51232	broad.mit.edu	37	2	36749338	36749338	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:36749338C>T	uc002rpd.2	+	13	2349	c.2310C>T	c.(2308-2310)GAC>GAT	p.D770D		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor	770	Extracellular (Potential).|VWFC 5.				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				GGAAGCCTGACGTTTGTACCA	0.468													28	78					0	0	0.007291	0	0	
FSHR	2492	broad.mit.edu	37	2	49190038	49190038	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:49190038A>G	uc002rww.2	-	10	1996	c.1922T>C	c.(1921-1923)CTG>CCG	p.L641P	FSHR_uc002rwx.2_Missense_Mutation_p.L579P|FSHR_uc010fbn.2_Missense_Mutation_p.L615P	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	641	Cytoplasmic (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	ACACTTGCTCAGCAGAATGAA	0.458									Gonadal_Dysgenesis_46_XX				12	48					0	0	0.013537	0	0	
USP34	9736	broad.mit.edu	37	2	61415812	61415812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:61415812G>A	uc002sbe.2	-	80	10088	c.10066C>T	c.(10066-10068)CGT>TGT	p.R3356C	USP34_uc002sbd.2_Missense_Mutation_p.R158C	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3356					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.R3356P(1)		ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CTGCTAACACGCCGCCTTTTA	0.478													9	50					0	0	0.004482	0	0	
USP34	9736	broad.mit.edu	37	2	61508298	61508298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:61508298C>T	uc002sbe.2	-	38	5100	c.5078G>A	c.(5077-5079)CGT>CAT	p.R1693H	USP34_uc002sbf.2_5'Flank	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	1693					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CAGAAAAGAACGATTGATTGA	0.408													10	21					0	0	0.010729	0	0	
FAM161A	84140	broad.mit.edu	37	2	62066719	62066719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:62066719C>T	uc010ypo.1	-	3	1522	c.1420G>A	c.(1420-1422)GCA>ACA	p.A474T	FAM161A_uc002sbm.3_Missense_Mutation_p.A474T|FAM161A_uc002sbn.3_Missense_Mutation_p.A284T|FAM161A_uc010fcm.1_RNA|FAM161A_uc010fcn.1_Missense_Mutation_p.A365T	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140	474					response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3						TCGATGTCTGCCAAAATTTTT	0.388													13	41					0	0	0.013537	0	0	
CCT4	10575	broad.mit.edu	37	2	62099411	62099411	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:62099411C>T	uc002sbo.2	-	12	1446	c.1297G>A	c.(1297-1299)GCC>ACC	p.A433T	CCT4_uc010ypp.1_Missense_Mutation_p.A377T|CCT4_uc010ypq.1_Missense_Mutation_p.A283T|CCT4_uc010ypr.1_Missense_Mutation_p.A377T|CCT4_uc010yps.1_Missense_Mutation_p.A403T	NM_006430	NP_006421	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	433					'de novo' posttranslational protein folding	melanosome|microtubule organizing center|nucleus	ATP binding|unfolded protein binding			ovary(2)	2	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			AATCGTAGGGCCAACTCTATT	0.373													5	45					0	0	0.001168	0	0	
SPRED2	200734	broad.mit.edu	37	2	65571870	65571870	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:65571870G>A	uc002sdr.3	-	2	722	c.187C>T	c.(187-189)CGA>TGA	p.R63*	SPRED2_uc010fcw.2_Nonsense_Mutation_p.R60*|SPRED2_uc010fcx.1_RNA	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2	63	WH1.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3						TCTTTCTGTCGTTCACCATGG	0.478													4	28					0	0	0.009096	0	0	
ARHGAP25	9938	broad.mit.edu	37	2	69015041	69015041	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:69015041A>G	uc002seu.2	+	4	783	c.419A>G	c.(418-420)GAG>GGG	p.E140G	ARHGAP25_uc010yqk.1_Missense_Mutation_p.E114G|ARHGAP25_uc010fdg.2_Missense_Mutation_p.E140G|ARHGAP25_uc010yql.1_Intron|ARHGAP25_uc002sev.2_Missense_Mutation_p.E133G|ARHGAP25_uc002sew.2_Missense_Mutation_p.E133G|ARHGAP25_uc002sex.2_Missense_Mutation_p.E133G|ARHGAP25_uc010fdh.1_RNA	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	140	PH.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4						GCGGAGATGGAGGAGTGGGTT	0.547													10	53					0	0	0.010729	0	0	
DYSF	8291	broad.mit.edu	37	2	71755438	71755438	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:71755438C>T	uc002sie.2	+	13	1567	c.1191C>T	c.(1189-1191)GCC>GCT	p.A397A	DYSF_uc010feg.2_Silent_p.A428A|DYSF_uc010feh.2_Silent_p.A397A|DYSF_uc002sig.3_Silent_p.A397A|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Silent_p.A397A|DYSF_uc010fef.2_Silent_p.A428A|DYSF_uc010fei.2_Silent_p.A428A|DYSF_uc010fek.2_Silent_p.A429A|DYSF_uc010fej.2_Silent_p.A398A|DYSF_uc010fel.2_Silent_p.A398A|DYSF_uc010feo.2_Silent_p.A429A|DYSF_uc010fem.2_Silent_p.A398A|DYSF_uc010fen.2_Silent_p.A429A|DYSF_uc002sif.2_Silent_p.A398A	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	397	Cytoplasmic (Potential).|C2 3.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						TGGACGATGCCGTGATGGACA	0.542													6	31					0	0	0.001984	0	0	
ALMS1	7840	broad.mit.edu	37	2	73717248	73717248	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:73717248G>A	uc002sje.1	+	12	8276	c.8165G>A	c.(8164-8166)CGA>CAA	p.R2722Q	ALMS1_uc002sjf.1_Missense_Mutation_p.R2678Q|ALMS1_uc002sjg.2_Missense_Mutation_p.R2108Q|ALMS1_uc002sjh.1_Missense_Mutation_p.R2108Q	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2720					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						TCATCTCACCGACATTCTAAA	0.408													23	106					0	0	0.005443	0	0	
DNAH6	1768	broad.mit.edu	37	2	84745152	84745152	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:84745152C>T	uc010fgb.2	+	2	339	c.202C>T	c.(202-204)CAG>TAG	p.Q68*	DNAH6_uc002soo.2_5'UTR|DNAH6_uc002sop.2_5'UTR	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	68	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						AAAACGACAGCAGCCTATAAA	0.383													3	12					0	0	0.009096	0	0	
C2orf89	129293	broad.mit.edu	37	2	85097639	85097639	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:85097639G>T	uc010ysl.1	-	2	468	c.379C>A	c.(379-381)CTG>ATG	p.L127M	C2orf89_uc002sou.3_Missense_Mutation_p.L127M|C2orf89_uc010fgc.1_Missense_Mutation_p.L127M	NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293 precursor	127	Extracellular (Potential).					integral to membrane				ovary(1)	1						ACATACTCCAGGTGGCGCTTG	0.572													12	38					4.14922e-12	4.62034e-12	0.004007	1	0	
C2orf68	388969	broad.mit.edu	37	2	85836566	85836566	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:85836566C>T	uc002sqc.2	-	3	442	c.370G>A	c.(370-372)GTC>ATC	p.V124I	USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_5'Flank|USP39_uc010ysv.1_5'Flank	NM_001013649	NP_001013671	Q2NKX9	CB068_HUMAN	hypothetical protein LOC388969	124										central_nervous_system(1)	1						ACCTGATAGACGATAACTGAT	0.542													28	233					0	0	0.010818	0	0	
KDM3A	55818	broad.mit.edu	37	2	86705121	86705121	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:86705121C>T	uc002sri.3	+	13	2388	c.2061C>T	c.(2059-2061)TGC>TGT	p.C687C	KDM3A_uc010ytj.1_Silent_p.C687C|KDM3A_uc010ytk.1_Silent_p.C635C	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	687	C6-type (Potential).				androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						GTGTGGACTGCTACCGGATGA	0.473													24	118					0	0	0.003330	0	0	
GGT8P	645367	broad.mit.edu	37	2	91968882	91968882	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:91968882G>A	uc010fho.1	+	2		c.1213G>A				NR_003503				Homo sapiens cDNA FLJ31276 fis, clone KIDNE2006376, weakly similar to GAMMA-GLUTAMYLTRANSPEPTIDASE 1 PRECURSOR (EC 2.3.2.2).												0						CTAGGAGGACGAGCGCTGAGT	0.622													3	3					0	0	0.009096	0	0	
GGT8P	645367	broad.mit.edu	37	2	91968886	91968886	+	RNA	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:91968886G>A	uc010fho.1	+	2		c.1217G>A				NR_003503				Homo sapiens cDNA FLJ31276 fis, clone KIDNE2006376, weakly similar to GAMMA-GLUTAMYLTRANSPEPTIDASE 1 PRECURSOR (EC 2.3.2.2).												0						GAGGACGAGCGCTGAGTGACA	0.632													3	4					0	0	0.000602	0	0	
TEKT4	150483	broad.mit.edu	37	2	95542378	95542378	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:95542378G>A	uc002stw.1	+	6	1265	c.1172G>A	c.(1171-1173)CGC>CAC	p.R391H	uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4	391	Potential.				cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3						CAGTCCCTGCGCAACCTCGAG	0.592													5	20					0	0	0.000602	0	0	
CNNM4	26504	broad.mit.edu	37	2	97475139	97475139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:97475139C>T	uc002swx.2	+	7	2311	c.2213C>T	c.(2212-2214)ACC>ATC	p.T738I	CNNM4_uc010yuy.1_Silent_p.H254H	NM_020184	NP_064569	Q6P4Q7	CNNM4_HUMAN	cyclin M4	738					biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3						GGGTGCACCACCCACATGGAG	0.572													9	21					0	0	0.006214	0	0	
VWA3B	200403	broad.mit.edu	37	2	98928714	98928714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:98928714G>A	uc002syo.2	+	28	4051	c.3787G>A	c.(3787-3789)GCC>ACC	p.A1263T	VWA3B_uc002syr.1_3'UTR|VWA3B_uc002sys.2_RNA	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1263										ovary(3)|large_intestine(2)|skin(1)	6						CAGCAGCCACGCCATCATTGC	0.597													8	29					0	0	0.010729	0	0	
CNGA3	1261	broad.mit.edu	37	2	98994199	98994199	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:98994199G>A	uc002syt.2	+	3	568	c.151G>A	c.(151-153)GCC>ACC	p.A51T	CNGA3_uc002syu.2_Missense_Mutation_p.A51T|CNGA3_uc010fij.2_5'UTR	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	51					signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)|upper_aerodigestive_tract(1)	6						GCCGGGGATCGCCATGGAGAC	0.587													4	13					0	0	0.000602	0	0	
FHL2	2274	broad.mit.edu	37	2	106002900	106002900	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:106002900C>A	uc002tcu.2	-	2	411	c.74G>T	c.(73-75)AGC>ATC	p.S25I	FHL2_uc002tdc.2_5'UTR|FHL2_uc002tdd.2_Missense_Mutation_p.S25I|FHL2_uc002tcv.2_Missense_Mutation_p.S25I|FHL2_uc002tcw.2_Missense_Mutation_p.S25I|FHL2_uc002tcx.2_Missense_Mutation_p.S25I|FHL2_uc010fje.2_5'UTR|FHL2_uc002tcy.2_Missense_Mutation_p.S25I|FHL2_uc002tcz.2_Missense_Mutation_p.S135I|FHL2_uc002tda.2_RNA|FHL2_uc002tdb.2_Missense_Mutation_p.S141I|FHL2_uc002tde.1_Missense_Mutation_p.S118I	NM_201557	NP_963851	Q14192	FHL2_HUMAN	four and a half LIM domains 2	25	C4-type (Potential).				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent	actin cytoskeleton|focal adhesion|nucleus	androgen receptor binding|identical protein binding|transcription coactivator activity|zinc ion binding			ovary(1)	1						GCAGTAGGGGCTCTCCTCCCG	0.562													17	70					0.000566183	0.000600562	0.004990	1	0	
RGPD3	653489	broad.mit.edu	37	2	107049681	107049681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:107049681T>C	uc010ywi.1	-	16	2323	c.2266A>G	c.(2266-2268)AAC>GAC	p.N756D		NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	756					intracellular transport		binding			ovary(1)	1						TCACTATAGTTTTCGAGTTCC	0.373													6	331					0	0	0.001168	0	0	
GCC2	9648	broad.mit.edu	37	2	109088540	109088540	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:109088540C>T	uc002tec.2	+	6	2909	c.2755C>T	c.(2755-2757)CGA>TGA	p.R919*	GCC2_uc002ted.2_Nonsense_Mutation_p.R818*	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	919	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						AAAAGAATTACGAGATAGGAG	0.279													18	80					0	0	0.012319	0	0	
BUB1	699	broad.mit.edu	37	2	111430296	111430296	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:111430296G>T	uc002tgc.2	-	4	476	c.364C>A	c.(364-366)CTT>ATT	p.L122I	BUB1_uc010yxh.1_Missense_Mutation_p.L102I|BUB1_uc010fkb.2_Missense_Mutation_p.L122I|BUB1_uc002tgd.2_Missense_Mutation_p.L122I	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	122	BUB1 N-terminal.|Necessary for interaction with CASC5.|Necessary for kinetochore localization.			L->G: Loss of interaction with CASC5.	apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		CCTCTCTGAAGGACAGCACTG	0.498													14	67					2.61681e-11	2.91008e-11	0.002450	1	0	
ZC3H6	376940	broad.mit.edu	37	2	113080379	113080379	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:113080379G>A	uc002thq.1	+	9	1634	c.1240G>A	c.(1240-1242)GAT>AAT	p.D414N		NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	414	Pro-rich.						nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						TCCTGAAGACGATTTTCAGAC	0.423													26	121					0	0	0.004656	0	0	
SLC20A1	6574	broad.mit.edu	37	2	113414767	113414767	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:113414767G>A	uc002tib.2	+	6	1173	c.727G>A	c.(727-729)GCC>ACC	p.A243T	SLC20A1_uc002tic.1_Missense_Mutation_p.A55T	NM_005415	NP_005406	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate	243	Helical; (Potential).				phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			ovary(2)	2						AGTTTTCTGTGCCCTTATCGT	0.413													21	79					0	0	0.014323	0	0	
DPP10	57628	broad.mit.edu	37	2	116525877	116525877	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:116525877A>G	uc002tla.1	+	13	1575	c.1118A>G	c.(1117-1119)GAG>GGG	p.E373G	DPP10_uc002tlb.1_Missense_Mutation_p.E323G|DPP10_uc002tlc.1_Missense_Mutation_p.E369G|DPP10_uc002tle.2_Missense_Mutation_p.E377G|DPP10_uc002tlf.1_Missense_Mutation_p.E366G	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	373	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						TTTTAGAATGAGGAGCCCGTG	0.438													8	26					0	0	0.006214	0	0	
GLI2	2736	broad.mit.edu	37	2	121747438	121747438	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:121747438C>T	uc010flp.2	+	13	3978	c.3948C>T	c.(3946-3948)CAC>CAT	p.H1316H	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Silent_p.H988H|GLI2_uc002tmu.3_Silent_p.H971H	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1316					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				CACCACCTCACCCAGTCCAGA	0.652													3	17					0	0	0.004672	0	0	
CNTNAP5	129684	broad.mit.edu	37	2	125405387	125405387	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:125405387G>A	uc002tno.2	+	13	2290	c.1926G>A	c.(1924-1926)GTG>GTA	p.V642V	CNTNAP5_uc010flu.2_Silent_p.V643V	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	642	Extracellular (Potential).|Fibrinogen C-terminal.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGACCCGAGTGCGGGGCGCTA	0.562													4	21					0	0	0.001168	0	0	
WDR33	55339	broad.mit.edu	37	2	128466300	128466300	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:128466300G>A	uc002tpg.1	-	21	3915	c.3732C>T	c.(3730-3732)CAC>CAT	p.H1244H		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	1244					postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CCATCTCTCTGTGCTCAGAAG	0.607													11	77					0	0	0.013537	0	0	
NCRNA00164	554226	broad.mit.edu	37	2	132914967	132914967	+	RNA	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:132914967C>T	uc002tti.3	-	2		c.495G>A			NCRNA00164_uc002ttj.3_Intron	NR_027019				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						TTCTGCATGGCCATTGGCACA	0.418													5	15					0	0	0.001168	0	0	
LRP1B	53353	broad.mit.edu	37	2	141200145	141200145	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:141200145G>A	uc002tvj.1	-	66	11314	c.10342C>T	c.(10342-10344)CAT>TAT	p.H3448Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3448	Extracellular (Potential).|LDL-receptor class A 24.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAAATGCAATGCTTCGTAGTC	0.433										TSP Lung(27;0.18)			14	102					0	0	0.003163	0	0	
LYPD6B	130576	broad.mit.edu	37	2	150069635	150069635	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:150069635C>T	uc002twv.1	+	6	859	c.458C>T	c.(457-459)ACG>ATG	p.T153M	LYPD6B_uc002tww.1_Missense_Mutation_p.T115M|LYPD6B_uc002twx.1_Missense_Mutation_p.T115M	NM_177964	NP_808879	Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	129	UPAR/Ly6.					anchored to membrane|plasma membrane					0						TCTGAACATACGGTAAGGATC	0.443													16	109					0	0	0.006122	0	0	
NEB	4703	broad.mit.edu	37	2	152501056	152501056	+	Silent	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:152501056T>G	uc010fnx.2	-	56	7761	c.7570A>C	c.(7570-7572)AGA>CGA	p.R2524R		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	2524					muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TAACCTTTTCTCTTCAGCTCC	0.383													19	73					0	0	0.010504	0	0	
KCNJ3	3760	broad.mit.edu	37	2	155555583	155555583	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:155555583C>T	uc002tyv.1	+	1	491	c.296C>T	c.(295-297)GCG>GTG	p.A99V	KCNJ3_uc010zce.1_Missense_Mutation_p.A99V	NM_002239	NP_002230	P48549	IRK3_HUMAN	potassium inwardly-rectifying channel J3	99	Helical; Name=M1; (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)	CTTTTCATGGCGTCCATGTGG	0.567													10	56					0	0	0.013537	0	0	
GPD2	2820	broad.mit.edu	37	2	157407127	157407127	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:157407127C>T	uc002tzf.3	+	8	1200	c.840C>T	c.(838-840)GAC>GAT	p.D280D	GPD2_uc010zch.1_Silent_p.D53D|GPD2_uc002tzd.3_Silent_p.D280D|GPD2_uc002tze.1_RNA	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,	280					cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						AGGAATTTGACGTGAGAGCCA	0.438													12	69					0	0	0.010729	0	0	
CCDC148	130940	broad.mit.edu	37	2	159201729	159201729	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:159201729G>A	uc002tzq.2	-	3	512	c.249C>T	c.(247-249)GTC>GTT	p.V83V	CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron|CCDC148_uc010foi.1_Silent_p.V30V|CCDC148_uc010foj.1_Intron|CCDC148_uc010fok.1_Intron|CCDC148_uc002tzs.1_Silent_p.V83V	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	83										ovary(2)	2						GTTCTTACCTGACTTCATTCA	0.368													6	139					0	0	0.003080	0	0	
ITGB6	3694	broad.mit.edu	37	2	160993949	160993949	+	Silent	SNP	G	A	A	rs139038668		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:160993949G>A	uc002ubh.2	-	10	1672	c.1656C>T	c.(1654-1656)TGC>TGT	p.C552C	ITGB6_uc010fou.2_Silent_p.C552C|ITGB6_uc010zcq.1_Silent_p.C510C|ITGB6_uc010fov.1_Silent_p.C552C	NM_000888	NP_000879	P18564	ITB6_HUMAN	integrin, beta 6 precursor	552	Extracellular (Potential).|III.|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3						GCCTACCTCCGCAGAGCAGCC	0.413													12	58					0	0	0.013537	0	0	
FIGN	55137	broad.mit.edu	37	2	164466900	164466900	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:164466900G>T	uc002uck.1	-	3	1753	c.1442C>A	c.(1441-1443)CCT>CAT	p.P481H		NM_018086	NP_060556	Q5HY92	FIGN_HUMAN	fidgetin	481						nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4						GTCCACTGGAGGTCCTTGGGT	0.512													5	70					0.000602214	0.000636366	0.000602	1	0	
COBLL1	22837	broad.mit.edu	37	2	165557205	165557205	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:165557205C>T	uc010zcw.1	-	13	1726	c.1602G>A	c.(1600-1602)GTG>GTA	p.V534V	COBLL1_uc002ucp.2_Silent_p.V468V|COBLL1_uc002ucq.2_Silent_p.V429V|COBLL1_uc010zcx.1_Silent_p.V475V|COBLL1_uc002ucs.1_RNA|COBLL1_uc002ucn.2_5'Flank|COBLL1_uc002uco.2_Silent_p.V198V	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	506										ovary(2)|pancreas(1)	3						CAACTTTAGGCACTTCACTCA	0.333													17	113					0	0	0.004990	0	0	
SCN2A	6326	broad.mit.edu	37	2	166223735	166223735	+	Missense_Mutation	SNP	C	T	T	rs115231482	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:166223735C>T	uc002udc.2	+	19	3819	c.3529C>T	c.(3529-3531)CGG>TGG	p.R1177W	SCN2A_uc002udd.2_Missense_Mutation_p.R1177W|SCN2A_uc002ude.2_Missense_Mutation_p.R1177W	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1177					myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	AGACTGTGTACGGAAGTTCAA	0.348													7	47					0	0	0.006214	0	0	
UBR3	130507	broad.mit.edu	37	2	170806482	170806482	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:170806482G>A	uc010zdi.1	+	23	3452	c.3452G>A	c.(3451-3453)CGC>CAC	p.R1151H	UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_5'UTR|UBR3_uc002uft.3_Missense_Mutation_p.R4H	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1151					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						ATGAACAAACGCATCATTGAA	0.373													18	87					0	0	0.012319	0	0	
MYO3B	140469	broad.mit.edu	37	2	171243767	171243767	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:171243767C>T	uc002ufy.2	+	14	1669	c.1526C>T	c.(1525-1527)GCA>GTA	p.A509V	MYO3B_uc002ufv.2_Missense_Mutation_p.A496V|MYO3B_uc010fqb.1_Missense_Mutation_p.A496V|MYO3B_uc002ufz.2_Missense_Mutation_p.A509V|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	509	Myosin head-like.				response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						GTGATGGGGGCAAGAATCTCT	0.433													19	84					0	0	0.010504	0	0	
TTN	7273	broad.mit.edu	37	2	179398768	179398768	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:179398768C>T	uc010zfg.1	-	307	95094	c.94870G>A	c.(94870-94872)GCC>ACC	p.A31624T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A25319T|TTN_uc010zfi.1_Missense_Mutation_p.A25252T|TTN_uc010zfj.1_Missense_Mutation_p.A25127T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32551							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)			TAGAGGATGGCCACTCCATCT	0.408													7	51					0	0	0.003080	0	0	
TTN	7273	broad.mit.edu	37	2	179424439	179424439	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:179424439C>T	uc010zfg.1	-	275	78940	c.78716G>A	c.(78715-78717)CGT>CAT	p.R26239H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R19934H|TTN_uc010zfi.1_Missense_Mutation_p.R19867H|TTN_uc010zfj.1_Missense_Mutation_p.R19742H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27166							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)			CAGTGATGTACGAGAGTCTGT	0.438													36	122					0	0	0.004289	0	0	
TTN	7273	broad.mit.edu	37	2	179453540	179453540	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:179453540T>C	uc010zfg.1	-	253	55432	c.55208A>G	c.(55207-55209)GAA>GGA	p.E18403G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E12098G|TTN_uc010zfi.1_Missense_Mutation_p.E12031G|TTN_uc010zfj.1_Missense_Mutation_p.E11906G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19330							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)			TTTAGTGACTTCTGGGGGATC	0.423													11	47					0	0	0.001855	0	0	
TTN	7273	broad.mit.edu	37	2	179454027	179454027	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:179454027C>T	uc010zfg.1	-	253	54945	c.54721G>A	c.(54721-54723)GCT>ACT	p.A18241T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A11936T|TTN_uc010zfi.1_Missense_Mutation_p.A11869T|TTN_uc010zfj.1_Missense_Mutation_p.A11744T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19168							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)			AAGTCTGTAGCGTCTTTGTCC	0.458													33	120					0	0	0.003755	0	0	
TTN	7273	broad.mit.edu	37	2	179587174	179587174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:179587174G>A	uc010zfg.1	-	74	18832	c.18608C>T	c.(18607-18609)CCC>CTC	p.P6203L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P2864L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7130							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)			CACTTGGATGGGTGCAGAGCC	0.398													19	86					0	0	0.008871	0	0	
ITGA4	3676	broad.mit.edu	37	2	182339944	182339944	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:182339944C>T	uc002unu.2	+	4	1248	c.485C>T	c.(484-486)ACT>ATT	p.T162I	ITGA4_uc010zfl.1_Missense_Mutation_p.T162I	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	162	FG-GAP 2.|Extracellular (Potential).				blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	AAGCTCCCCACTGGTGGTTGC	0.368													27	112					0	0	0.005443	0	0	
ITGA4	3676	broad.mit.edu	37	2	182399098	182399098	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:182399098G>A	uc002unu.2	+	26	3646	c.2883_splice	c.e26+1	p.H961_splice	ITGA4_uc002unv.2_Splice_Site_p.H206_splice	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor						blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	TGTTGCGCATGTAAGATTACC	0.368													6	38					0	0	0.003080	0	0	
PDE1A	5136	broad.mit.edu	37	2	183129093	183129093	+	Silent	SNP	G	A	A	rs148985621		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:183129093G>A	uc002uos.2	-	3	234	c.150C>T	c.(148-150)GTC>GTT	p.V50V	PDE1A_uc010zfp.1_5'UTR|PDE1A_uc002uoq.1_Silent_p.V50V|PDE1A_uc010zfq.1_Silent_p.V50V|PDE1A_uc002uor.2_Silent_p.V34V|PDE1A_uc002uov.1_RNA	NM_001003683	NP_001003683	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 2	50					activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)			TCTTTAAGTCGACGACGTTAA	0.363													11	74					0	0	0.010729	0	0	
DNAH7	56171	broad.mit.edu	37	2	196636411	196636411	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:196636411C>T	uc002utj.3	-	61	11507	c.11406G>A	c.(11404-11406)TCG>TCA	p.S3802S	DNAH7_uc002uti.3_Silent_p.S285S	NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3802					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TATTTACGCACGAATCTCTTA	0.328													21	135					0	0	0.012319	0	0	
FZD7	8324	broad.mit.edu	37	2	202899989	202899989	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:202899989C>A	uc002uyw.1	+	1	680	c.619C>A	c.(619-621)CCC>ACC	p.P207T		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7 precursor	207	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)|breast(1)	4						TCCCGCCTTCCCCTTCTCATG	0.731											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	8					1.23904e-05	1.33197e-05	0.000602	1	0	
FZD7	8324	broad.mit.edu	37	2	202900525	202900525	+	Silent	SNP	G	A	A	rs140334850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:202900525G>A	uc002uyw.1	+	1	1216	c.1155G>A	c.(1153-1155)GCG>GCA	p.A385A		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7 precursor	385	Helical; Name=4; (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)|breast(1)	4						ACCTGGCCGCGTGGGCCGTGC	0.647											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	30					0	0	0.008291	0	0	
WDR12	55759	broad.mit.edu	37	2	203772679	203772679	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:203772679A>G	uc002uzl.2	-	2	795	c.45T>C	c.(43-45)TAT>TAC	p.Y15Y	WDR12_uc010ftt.2_Silent_p.Y15Y	NM_018256	NP_060726	Q9GZL7	WDR12_HUMAN	WD repeat domain 12 protein	15					cell proliferation|maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	nucleoplasm|PeBoW complex|preribosome, large subunit precursor	protein binding				0						CATCTACGGCATATCTATAAA	0.343													10	43					0	0	0.010729	0	0	
RAPH1	65059	broad.mit.edu	37	2	204354422	204354422	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:204354422T>A	uc002vad.2	-	4	842	c.617A>T	c.(616-618)AAT>ATT	p.N206I	RAPH1_uc002vae.2_Missense_Mutation_p.N206I|RAPH1_uc002vaf.2_Missense_Mutation_p.N206I	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	206					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						ATGGGAGGAATTACTAATAGA	0.453													18	105					0	0	0.007413	0	0	
PARD3B	117583	broad.mit.edu	37	2	205978267	205978267	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:205978267C>G	uc002var.1	+	6	853	c.646C>G	c.(646-648)CAT>GAT	p.H216D	PARD3B_uc010fub.1_Missense_Mutation_p.H216D|PARD3B_uc002vao.1_Missense_Mutation_p.H216D|PARD3B_uc002vap.1_Missense_Mutation_p.H216D|PARD3B_uc002vaq.1_Missense_Mutation_p.H216D	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	216	PDZ 1.				cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ATTGGGAATACATGTAGTGCC	0.423													10	43					0	0	0.013537	0	0	
PARD3B	117583	broad.mit.edu	37	2	205983711	205983711	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:205983711C>T	uc002var.1	+	7	954	c.747C>T	c.(745-747)CAC>CAT	p.H249H	PARD3B_uc010fub.1_Silent_p.H249H|PARD3B_uc002vao.1_Silent_p.H249H|PARD3B_uc002vap.1_Silent_p.H249H|PARD3B_uc002vaq.1_Silent_p.H249H	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	249	PDZ 1.				cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		GACTATTTCACGAAAATGAAT	0.348													15	68					0	0	0.007413	0	0	
NRP2	8828	broad.mit.edu	37	2	206587398	206587398	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:206587398C>T	uc002vaw.2	+	4	1421	c.630C>T	c.(628-630)TAC>TAT	p.Y210Y	NRP2_uc002vat.2_Silent_p.Y210Y|NRP2_uc002vau.2_Silent_p.Y210Y|NRP2_uc002vav.2_Silent_p.Y210Y|NRP2_uc002vax.2_Silent_p.Y210Y|NRP2_uc002vay.2_Silent_p.Y210Y|NRP2_uc010fud.2_Silent_p.Y210Y	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	210	Extracellular (Potential).|CUB 2.				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						ACTGCAAGTACGATTGGCTGG	0.502													4	50					0	0	0.000602	0	0	
INO80D	54891	broad.mit.edu	37	2	206870106	206870106	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:206870106T>C	uc002vaz.3	-	11	2475	c.2070A>G	c.(2068-2070)ATA>ATG	p.I690M		NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	690					DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						AGAACACCCCTATTCCTCTAT	0.527													6	96					0	0	0.001168	0	0	
CRYGC	1420	broad.mit.edu	37	2	208993108	208993108	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:208993108C>T	uc002vco.3	-	3	382	c.344G>A	c.(343-345)CGC>CAC	p.R115H		NM_020989	NP_066269	P07315	CRGC_HUMAN	crystallin, gamma C	115	Beta/gamma crystallin 'Greek key' 3.				visual perception	cytoplasm|nucleus	protein binding|structural constituent of eye lens				0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GAGGTGGAAGCGGTCCTGGAT	0.627													13	46					0	0	0.004007	0	0	
PTH2R	5746	broad.mit.edu	37	2	209308074	209308074	+	Nonsense_Mutation	SNP	C	T	T	rs149710383		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:209308074C>T	uc002vdb.2	+	6	724	c.511C>T	c.(511-513)CGA>TGA	p.R171*	PTH2R_uc010zjb.1_Nonsense_Mutation_p.R182*	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	171	Cytoplasmic (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		TCTCCGTAGACGATTGCATTG	0.433													11	55					0	0	0.010729	0	0	
MAP2	4133	broad.mit.edu	37	2	210559705	210559705	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:210559705G>A	uc002vde.1	+	7	3059	c.2811G>A	c.(2809-2811)GCG>GCA	p.A937A	MAP2_uc002vdc.1_Silent_p.A937A|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Silent_p.A933A	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	937					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	AAGCATCCGCGCATATCTCTG	0.433													12	68					0	0	0.013537	0	0	
UNC80	285175	broad.mit.edu	37	2	210699692	210699692	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:210699692G>A	uc010zjc.1	+	18	3079	c.2999G>A	c.(2998-3000)TGT>TAT	p.C1000Y	UNC80_uc002vdk.2_Missense_Mutation_p.C161Y	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	1000						integral to membrane					0						CCTGAGGAATGTCGCAGCTTC	0.512													3	8					0	0	0.004672	0	0	
CPS1	1373	broad.mit.edu	37	2	211457621	211457621	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:211457621A>G	uc002vee.3	+	11	1237	c.1105A>G	c.(1105-1107)AAA>GAA	p.K369E	CPS1_uc010fur.2_Missense_Mutation_p.K375E|CPS1_uc010fus.2_5'Flank	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	369	Glutamine amidotransferase type-1.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		GCATGAGAGCAAACCCTTCTT	0.418													10	61					0	0	0.013537	0	0	
CPS1	1373	broad.mit.edu	37	2	211540487	211540487	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:211540487C>T	uc002vee.3	+	36	4329	c.4197C>T	c.(4195-4197)AAC>AAT	p.N1399N	CPS1_uc010fur.2_Silent_p.N1405N|CPS1_uc010fus.2_Silent_p.N948N	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1399					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		ACTGGCTCAACGCCAACAATG	0.438													8	36					0	0	0.008291	0	0	
IKZF2	22807	broad.mit.edu	37	2	213921663	213921663	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:213921663T>G	uc002vem.2	-	4	469	c.300A>C	c.(298-300)CAA>CAC	p.Q100H	IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Missense_Mutation_p.Q47H|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Missense_Mutation_p.Q100H|IKZF2_uc002vel.2_Missense_Mutation_p.Q47H|IKZF2_uc010fuw.2_5'UTR|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Missense_Mutation_p.Q100H|IKZF2_uc002ven.2_Missense_Mutation_p.Q100H	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		CTCCCTCGCCTTGAAGCTCCT	0.512													12	73					0	0	0.003163	0	0	
SPAG16	79582	broad.mit.edu	37	2	215274888	215274888	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:215274888G>A	uc002veq.2	+	16	1837	c.1745G>A	c.(1744-1746)GGC>GAC	p.G582D	SPAG16_uc002ver.2_Missense_Mutation_p.G528D|SPAG16_uc010zjk.1_Missense_Mutation_p.G488D|VWC2L_uc002vet.2_5'Flank|VWC2L_uc010zjl.1_5'Flank	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	582	WD 6.				cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		CAGGCAAGTGGCAATGGTGTT	0.438													11	72					0	0	0.010729	0	0	
ABCA12	26154	broad.mit.edu	37	2	215876354	215876354	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:215876354C>T	uc002vew.2	-	17	2361	c.2141G>A	c.(2140-2142)CGA>CAA	p.R714Q	ABCA12_uc002vev.2_Missense_Mutation_p.R396Q|ABCA12_uc010zjn.1_5'UTR	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	714					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TGTGTTCATTCGGTTGCTTCT	0.403													20	96					0	0	0.012319	0	0	
FN1	2335	broad.mit.edu	37	2	216273121	216273121	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:216273121G>A	uc002vfa.2	-	16	2594	c.2328C>T	c.(2326-2328)AAC>AAT	p.N776N	FN1_uc002vfb.2_Silent_p.N776N|FN1_uc002vfc.2_Silent_p.N776N|FN1_uc002vfd.2_Silent_p.N776N|FN1_uc002vfe.2_Silent_p.N776N|FN1_uc002vff.2_Silent_p.N776N|FN1_uc002vfg.2_Silent_p.N776N|FN1_uc002vfh.2_Silent_p.N776N|FN1_uc002vfi.2_Silent_p.N776N|FN1_uc002vfj.2_Silent_p.N776N	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	776	Fibronectin type-III 2.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GGTCAGGGATGTTCACAGAAG	0.408													7	33					0	0	0.004482	0	0	
TNS1	7145	broad.mit.edu	37	2	218683462	218683462	+	Missense_Mutation	SNP	G	A	A	rs149785174	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:218683462G>A	uc002vgt.2	-	24	3679	c.3281C>T	c.(3280-3282)CCG>CTG	p.P1094L	TNS1_uc002vgr.2_Missense_Mutation_p.P1081L|TNS1_uc002vgs.2_Missense_Mutation_p.P1073L|TNS1_uc010zjv.1_Missense_Mutation_p.P1073L	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	1094	Ser-rich.					cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CTCTCCCGACGGGAAACTCCC	0.627													3	21					0	0	0.000602	0	0	
CYP27A1	1593	broad.mit.edu	37	2	219676971	219676971	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:219676971G>A	uc002viz.3	+	3	907	c.473G>A	c.(472-474)CGC>CAC	p.R158H		NM_000784	NP_000775	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A,	158					bile acid biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	cholestanetriol 26-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Cholecalciferol(DB00169)	TACCAGCTGCGCCAGGCTCTG	0.537													7	45					0	0	0.001984	0	0	
CCDC108	255101	broad.mit.edu	37	2	219893035	219893035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:219893035C>T	uc002vjl.1	-	12	1823	c.1739G>A	c.(1738-1740)CGC>CAC	p.R580H	CCDC108_uc010fwa.1_Missense_Mutation_p.R23H|CCDC108_uc010zkp.1_Missense_Mutation_p.R569H|CCDC108_uc010zkq.1_Missense_Mutation_p.R515H	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	580						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGGTGTGTGCGGTACCAGGT	0.617													20	38					0	0	0.012319	0	0	
ABCB6	10058	broad.mit.edu	37	2	220074986	220074986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:220074986C>T	uc002vkc.1	-	18	2663	c.2386G>A	c.(2386-2388)GTC>ATC	p.V796I	ABCB6_uc010fwe.1_Missense_Mutation_p.V750I	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6	796	ABC transporter.				cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCTTGATGACGAGGATCTGG	0.552													10	49					0	0	0.008291	0	0	
INHA	3623	broad.mit.edu	37	2	220440169	220440169	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:220440169G>A	uc002vmk.1	+	2	1166	c.1022G>A	c.(1021-1023)CGC>CAC	p.R341H		NM_002191	NP_002182	P05111	INHA_HUMAN	inhibin alpha subunit precursor	341					cell cycle arrest|cell surface receptor linked signaling pathway|cell-cell signaling|erythrocyte differentiation|hemoglobin biosynthetic process|induction of apoptosis|negative regulation of B cell differentiation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|regulation of cell proliferation|response to external stimulus|skeletal system development	inhibin A complex|inhibin-betaglycan-ActRII complex	cytokine activity|growth factor activity|hormone activity|signal transducer activity			ovary(1)	1		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CTACATGTCCGCACCACCTCG	0.612													24	118					0	0	0.006320	0	0	
WDFY1	57590	broad.mit.edu	37	2	224758993	224758993	+	Silent	SNP	G	A	A	rs145535635		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:224758993G>A	uc002vnq.2	-	8	840	c.789C>T	c.(787-789)GAC>GAT	p.D263D		NM_020830	NP_065881	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	263	WD 6.					cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		CAATTCCGCCGTCCGAGGAAC	0.557													10	42					0	0	0.003163	0	0	
DOCK10	55619	broad.mit.edu	37	2	225637874	225637874	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:225637874C>A	uc010fwz.1	-	53	6443	c.6204G>T	c.(6202-6204)AAG>AAT	p.K2068N	DOCK10_uc002vob.2_Missense_Mutation_p.K2062N|DOCK10_uc002voa.2_Missense_Mutation_p.K724N	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2068	DHR-2.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GCTTACTCACCTTCACGCTGA	0.433													8	31					3.09899e-07	3.37248e-07	0.004482	1	0	
SPHKAP	80309	broad.mit.edu	37	2	228883406	228883406	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:228883406T>C	uc002vpq.2	-	7	2211	c.2164A>G	c.(2164-2166)AAG>GAG	p.K722E	SPHKAP_uc002vpp.2_Missense_Mutation_p.K722E|SPHKAP_uc010zlx.1_Missense_Mutation_p.K722E	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	722						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CTCATCTTCTTGAACGTGAAG	0.438													27	145					0	0	0.007291	0	0	
SLC16A14	151473	broad.mit.edu	37	2	230923861	230923861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:230923861C>T	uc002vqd.1	-	2	571	c.208G>A	c.(208-210)GGC>AGC	p.G70S	FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Missense_Mutation_p.G70S|SLC16A14_uc002vqf.2_Missense_Mutation_p.G70S	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid	70	Cytoplasmic (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		GCGGTCAGGCCGCGGCTCTGG	0.537													5	25					0	0	0.000602	0	0	
ALPI	248	broad.mit.edu	37	2	233322294	233322294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:233322294G>A	uc002vst.3	+	6	745	c.668G>A	c.(667-669)CGC>CAC	p.R223H	ALPI_uc002vsu.3_Missense_Mutation_p.R134H	NM_001631	NP_001622	P09923	PPBI_HUMAN	intestinal alkaline phosphatase precursor	223					phosphorylation	anchored to membrane|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding|protein binding			central_nervous_system(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		GGCGGAGGCCGCAAGTACATG	0.632													7	45					0	0	0.004482	0	0	
HJURP	55355	broad.mit.edu	37	2	234750556	234750556	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:234750556C>T	uc002vvg.2	-	8	936	c.870G>A	c.(868-870)ATG>ATA	p.M290I	HJURP_uc010znd.1_Missense_Mutation_p.M229I|HJURP_uc010zne.1_Missense_Mutation_p.M198I	NM_018410	NP_060880	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	290					cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		TCCAGTTTTGCATGATGAACG	0.493													10	76					0	0	0.006214	0	0	
COL6A3	1293	broad.mit.edu	37	2	238245163	238245163	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:238245163A>G	uc002vwl.2	-	40	8865	c.8580T>C	c.(8578-8580)AAT>AAC	p.N2860N	COL6A3_uc002vwo.2_Silent_p.N2654N|COL6A3_uc010znj.1_Silent_p.N2253N|COL6A3_uc002vwj.2_Silent_p.N241N	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2860	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AAGTAACGTTATTCGGAACAT	0.398													5	120					0	0	0.001168	0	0	
ILKAP	80895	broad.mit.edu	37	2	239090722	239090722	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:239090722C>T	uc002vxv.2	-	9	950	c.820G>A	c.(820-822)GCT>ACT	p.A274T	ILKAP_uc010zns.1_Missense_Mutation_p.A206T|ILKAP_uc002vxw.2_Missense_Mutation_p.A154T|ILKAP_uc010znt.1_Missense_Mutation_p.A154T	NM_030768	NP_110395	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated protein	274	PP2C-like.					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)		TTTCCTCCAGCCTTCTGTATC	0.488													37	157					0	0	0.007835	0	0	
PER2	8864	broad.mit.edu	37	2	239161605	239161605	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:239161605G>A	uc002vyc.2	-	19	3296	c.3059C>T	c.(3058-3060)GCG>GTG	p.A1020V	PER2_uc010znv.1_Missense_Mutation_p.A1020V	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	1020					circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TTTGCAGTCCGCCCCTACAGC	0.622													16	54					0	0	0.006122	0	0	
PRR21	643905	broad.mit.edu	37	2	240981288	240981288	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:240981288G>C	uc010zod.1	-	1	1112	c.1112C>G	c.(1111-1113)GCC>GGC	p.A371G		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	371										ovary(1)|skin(1)	2						GTTGAAGGTGGCCCTGGCAGA	0.478													18	59					0	0	0.014323	0	0	
ANKMY1	51281	broad.mit.edu	37	2	241463615	241463615	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:241463615C>T	uc002vyz.1	-	7	1481	c.1252G>A	c.(1252-1254)GGG>AGG	p.G418R	ANKMY1_uc002vza.1_Missense_Mutation_p.G277R|ANKMY1_uc010fzd.1_Missense_Mutation_p.G507R|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Missense_Mutation_p.G277R|ANKMY1_uc002vzd.1_Missense_Mutation_p.G277R|ANKMY1_uc010fze.1_Missense_Mutation_p.G87R|ANKMY1_uc002vze.2_Missense_Mutation_p.G179R	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	418							zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CCACACTGCCCGGTGTCCTGG	0.657													4	19					0	0	0.001984	0	0	
KIF1A	547	broad.mit.edu	37	2	241712648	241712648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:241712648G>A	uc002vzy.2	-	13	1209	c.1063C>T	c.(1063-1065)CGC>TGC	p.R355C	KIF1A_uc010fzk.2_Missense_Mutation_p.R355C|KIF1A_uc002vzz.1_Missense_Mutation_p.R355C	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	355	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GCATTGCAGCGGATCTGCTTG	0.627													6	35					0	0	0.003080	0	0	
KIF1A	547	broad.mit.edu	37	2	241726674	241726674	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:241726674G>A	uc002vzy.2	-	5	569	c.423C>T	c.(421-423)TCC>TCT	p.S141S	KIF1A_uc010fzk.2_Silent_p.S141S|KIF1A_uc002vzz.1_Silent_p.S141S	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	141	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CTACCTCCACGGAGTAGGACA	0.632													4	22					0	0	0.001984	0	0	
MTERFD2	130916	broad.mit.edu	37	2	242039193	242039193	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:242039193G>T	uc002wan.1	-	1	718	c.225C>A	c.(223-225)GCC>GCA	p.A75A	MTERFD2_uc010zoj.1_Intron|MTERFD2_uc010zok.1_Silent_p.A46A	NM_182501	NP_872307	Q7Z6M4	MTER2_HUMAN	MTERF domain containing 2	46										ovary(1)	1		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		CTCCATTGGAGGCTGTAGTCA	0.507													8	60					0.000442599	0.000469772	0.006214	1	0	
PASK	23178	broad.mit.edu	37	2	242066171	242066171	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:242066171G>A	uc002wao.1	-	10	2251	c.2159C>T	c.(2158-2160)ACG>ATG	p.T720M	PASK_uc010zol.1_Missense_Mutation_p.T534M|PASK_uc010zom.1_Missense_Mutation_p.T685M|PASK_uc010fzl.1_Missense_Mutation_p.T720M|PASK_uc010zon.1_Missense_Mutation_p.T501M|PASK_uc002wap.2_Missense_Mutation_p.T263M|PASK_uc002waq.2_Missense_Mutation_p.T720M	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	720					regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		AGGGAGGTCCGTGGCCAAGGC	0.607													7	40					0	0	0.001984	0	0	
PASK	23178	broad.mit.edu	37	2	242066359	242066359	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:242066359C>T	uc002wao.1	-	10	2063	c.1971G>A	c.(1969-1971)CTG>CTA	p.L657L	PASK_uc010zol.1_Silent_p.L471L|PASK_uc010zom.1_Silent_p.L622L|PASK_uc010fzl.1_Silent_p.L657L|PASK_uc010zon.1_Silent_p.L438L|PASK_uc002wap.2_Silent_p.L200L|PASK_uc002waq.2_Silent_p.L657L	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	657					regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		AGCAGGTCTGCAGCTCTTCTC	0.607													16	104					0	0	0.004990	0	0	
ANO7	50636	broad.mit.edu	37	2	242163537	242163537	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:242163537C>T	uc002wax.2	+	25	2874	c.2771C>T	c.(2770-2772)ACG>ATG	p.T924M		NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	924	Cytoplasmic (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3						ACACCCTTCACGGTTCCCAAG	0.652													4	24					0	0	0.009096	0	0	
HDLBP	3069	broad.mit.edu	37	2	242174626	242174626	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:242174626G>A	uc002waz.2	-	23	3282	c.3054C>T	c.(3052-3054)ATC>ATT	p.I1018I	HDLBP_uc002wba.2_Silent_p.I1018I|HDLBP_uc002wbb.2_Silent_p.I970I	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1018	KH 12.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CCGTGATGGCGATGATGTCAG	0.597													14	74					0	0	0.003163	0	0	
TGM3	7053	broad.mit.edu	37	20	2308989	2308989	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:2308989G>A	uc002wfx.3	+	9	1408	c.1311G>A	c.(1309-1311)ACG>ACA	p.T437T		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	437					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)	TGGACGTCACGGACAAGTACA	0.567													8	42					0	0	0.004482	0	0	
FAM113A	64773	broad.mit.edu	37	20	2820491	2820491	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:2820491G>A	uc002wgz.1	-	2	565	c.68C>T	c.(67-69)GCC>GTC	p.A23V	FAM113A_uc002whb.1_5'UTR|FAM113A_uc002wha.1_5'UTR|FAM113A_uc010zqa.1_5'UTR|FAM113A_uc002whc.1_Missense_Mutation_p.A23V|VPS16_uc002whe.2_5'Flank|VPS16_uc002whf.2_5'Flank|VPS16_uc002whd.2_5'Flank	NM_022760	NP_073597	Q9H1Q7	F113A_HUMAN	hypothetical protein LOC64773	23							hydrolase activity|protein binding			ovary(2)	2						GACTTCCGAGGCCTGGAAGTG	0.622													7	76					0	0	0.003080	0	0	
SMOX	54498	broad.mit.edu	37	20	4167954	4167954	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:4167954G>A	uc002wkm.1	+	7	1769	c.1568G>A	c.(1567-1569)CGC>CAC	p.R523H	SMOX_uc002wkk.1_Missense_Mutation_p.R500H|SMOX_uc002wkl.1_Missense_Mutation_p.R470H|SMOX_uc002wkn.1_Missense_Mutation_p.R158H|SMOX_uc002wkp.2_Missense_Mutation_p.R553H|SMOX_uc010zqo.1_Missense_Mutation_p.R447H|SMOX_uc002wko.1_Missense_Mutation_p.R523H	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	523					polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)	GCCACCCACCGCAAGTACTAT	0.647													7	38					0	0	0.001984	0	0	
PROKR2	128674	broad.mit.edu	37	20	5282888	5282888	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:5282888A>G	uc010zqw.1	-	2	953	c.953T>C	c.(952-954)GTC>GCC	p.V318A	PROKR2_uc010zqx.1_Missense_Mutation_p.V318A|PROKR2_uc010zqy.1_Missense_Mutation_p.V318A	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	318	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GATGCACTCGACCACGTAGAA	0.517										HNSCC(71;0.22)			13	108					0	0	0.002450	0	0	
PLCB4	5332	broad.mit.edu	37	20	9404516	9404516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:9404516G>A	uc002wnf.2	+	26	2541	c.2405G>A	c.(2404-2406)CGA>CAA	p.R802Q	PLCB4_uc010gbw.1_Missense_Mutation_p.R802Q|PLCB4_uc010gbx.2_Missense_Mutation_p.R814Q|PLCB4_uc002wne.2_Missense_Mutation_p.R802Q|PLCB4_uc002wnh.2_Missense_Mutation_p.R649Q	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	802					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						ATTTCCCTTCGAAATGAGGGA	0.408													8	50					0	0	0.006214	0	0	
ZNF133	7692	broad.mit.edu	37	20	18295755	18295755	+	Missense_Mutation	SNP	C	T	T	rs151186857	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:18295755C>T	uc010gcq.2	+	5	565	c.260C>T	c.(259-261)CCG>CTG	p.P87L	ZNF133_uc010zrv.1_Missense_Mutation_p.P90L|ZNF133_uc010zrw.1_Missense_Mutation_p.P24L|ZNF133_uc010gcr.2_Missense_Mutation_p.P87L|ZNF133_uc010zrx.1_5'UTR|ZNF133_uc002wql.3_Missense_Mutation_p.P86L|ZNF133_uc010gcs.2_Missense_Mutation_p.P86L|ZNF133_uc010zry.1_5'UTR|ZNF133_uc002wqm.2_Missense_Mutation_p.P87L	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	87						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2						TTCTGCCCTCCGGGTTTCTCC	0.532													13	93					0	0	0.003163	0	0	
PAX1	5075	broad.mit.edu	37	20	21687619	21687619	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:21687619C>T	uc002wsj.2	+	2	884	c.830C>T	c.(829-831)GCG>GTG	p.A277V	PAX1_uc010zsl.1_Missense_Mutation_p.A277V|PAX1_uc010zsm.1_Missense_Mutation_p.A253V	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	277					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2						CCGGGCACGGCGGGCCACGTC	0.667													4	11					0	0	0.000602	0	0	
GGTLC1	92086	broad.mit.edu	37	20	23967095	23967095	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:23967095C>T	uc002wts.2	-	2	287	c.154G>A	c.(154-156)GCC>ACC	p.A52T	GGTLC1_uc002wtu.2_Missense_Mutation_p.A52T	NM_178312	NP_842564	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	52							gamma-glutamyltransferase activity			ovary(1)	1						GTGCTGGTGGCGGACACAGCA	0.627													6	17					0	0	0.001168	0	0	
PYGB	5834	broad.mit.edu	37	20	25239910	25239910	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:25239910G>A	uc002wup.2	+	2	390	c.281G>A	c.(280-282)CGC>CAC	p.R94H		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	94					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)	TACATGGGTCGCACGCTGCAG	0.493													14	48					0	0	0.004007	0	0	
SUN5	140732	broad.mit.edu	37	20	31590444	31590444	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:31590444G>A	uc002wyi.2	-	3	253	c.160C>T	c.(160-162)CGC>TGC	p.R54C		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	54					spermatogenesis					skin(1)	1						TCATTGTTGCGGACAGGCAAC	0.438													16	33					0	0	0.004990	0	0	
NCOA6	23054	broad.mit.edu	37	20	33356268	33356268	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:33356268T>C	uc002xav.2	-	6	3084	c.513A>G	c.(511-513)CCA>CCG	p.P171P	NCOA6_uc002xaw.2_Silent_p.P171P|NCOA6_uc010gew.1_Silent_p.P171P	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	171	TBP/GTF2A-binding region.|NCOA1-binding region.|CREBBP-binding region.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7						AGGTCTTACCTGGACCACTTG	0.458													17	103					0	0	0.004990	0	0	
RBM39	9584	broad.mit.edu	37	20	34295045	34295045	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:34295045T>C	uc002xeb.2	-	14	1648	c.1304A>G	c.(1303-1305)CAA>CGA	p.Q435R	RBM39_uc002xdz.2_Missense_Mutation_p.Q411R|RBM39_uc002xea.2_Missense_Mutation_p.Q278R|RBM39_uc010gfn.2_Missense_Mutation_p.Q278R|RBM39_uc010zvm.1_Missense_Mutation_p.Q407R|RBM39_uc002xeg.2_Missense_Mutation_p.Q413R|RBM39_uc002xec.2_Missense_Mutation_p.Q429R|RBM39_uc002xed.2_Missense_Mutation_p.Q153R|RBM39_uc002xee.2_Missense_Mutation_p.Q278R|RBM39_uc002xef.2_Missense_Mutation_p.Q272R|RBM39_uc010zvn.1_Missense_Mutation_p.Q278R	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	435	Interaction with NCOA6 (By similarity).				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TACTTACGTTTGAGGGTTAAA	0.294													8	58					0	0	0.006214	0	0	
SLC32A1	140679	broad.mit.edu	37	20	37357184	37357184	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:37357184G>A	uc002xjc.2	+	2	1743	c.1480G>A	c.(1480-1482)GTC>ATC	p.V494I		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	494	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|integral to membrane|plasma membrane|synaptic vesicle membrane	vesicular hydrogen:amino acid antiporter activity				0		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CTTCTTCGACGTCGCCATCTT	0.647													7	16					0	0	0.008291	0	0	
CHD6	84181	broad.mit.edu	37	20	40081539	40081539	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:40081539T>G	uc002xka.1	-	21	3342	c.3164A>C	c.(3163-3165)AAA>ACA	p.K1055T		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1055					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				GTTGTAGTGTTTGGTCTGCTT	0.483													4	68					0	0	0.009096	0	0	
SFRS6	6431	broad.mit.edu	37	20	42089154	42089154	+	Splice_Site	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:42089154G>T	uc010zwg.1	+	5	761	c.591_splice	c.e5-1	p.R197_splice	SFRS6_uc002xki.2_Splice_Site_p.R68_splice|SFRS6_uc002xkk.2_Splice_Site_p.R197_splice	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)			TCTCCTAATAGGTCTCGATCT	0.408													11	76					0.00010058	0.000107298	0.013537	1	0	
MATN4	8785	broad.mit.edu	37	20	43933295	43933295	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:43933295G>A	uc002xnn.2	-	3	403	c.216C>T	c.(214-216)CGC>CGT	p.R72R	MATN4_uc002xno.2_Silent_p.R72R|MATN4_uc002xnp.2_Silent_p.R72R|MATN4_uc010zwr.1_Silent_p.R20R|MATN4_uc002xnr.1_Silent_p.R72R|RBPJL_uc002xns.2_5'Flank|RBPJL_uc002xnt.2_5'Flank	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	72	VWFA 1.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)				TCACGCCAACGCGCGTGGCGT	0.652													11	23					0	0	0.010729	0	0	
SYS1-DBNDD2	767557	broad.mit.edu	37	20	44037177	44037177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:44037177G>A	uc002xnx.2	+	4	566	c.70G>A	c.(70-72)GAG>AAG	p.E24K	DBNDD2_uc002xnz.2_Missense_Mutation_p.E24K|DBNDD2_uc002xoa.2_Missense_Mutation_p.E24K|DBNDD2_uc002xob.2_Missense_Mutation_p.E24K|DBNDD2_uc002xoc.2_Missense_Mutation_p.E24K|DBNDD2_uc002xod.2_Missense_Mutation_p.E24K|DBNDD2_uc002xoe.2_Missense_Mutation_p.E24K|DBNDD2_uc002xof.2_Missense_Mutation_p.E24K|DBNDD2_uc002xog.2_Missense_Mutation_p.E24K	NM_001048225	NP_001041690			SCF apoptosis response protein 1 isoform a												0						AAAATTCTTCGAGGACATTTT	0.562													23	49					0	0	0.004656	0	0	
SPINLW1	57119	broad.mit.edu	37	20	44166631	44166631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:44166631C>T	uc010zxc.1	-	4	526	c.494G>A	c.(493-495)CGT>CAT	p.R165H	WFDC6_uc002xos.1_Missense_Mutation_p.R65H	NM_020398	NP_065131	O95925	EPPI_HUMAN	serine peptidase inhibitor-like, with Kunitz and	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						extracellular region	serine-type endopeptidase inhibitor activity			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				TTTCTTTCCACGGCTGAACGG	0.473													39	73					0	0	0.008740	0	0	
CTSA	5476	broad.mit.edu	37	20	44521441	44521441	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:44521441G>A	uc002xqj.3	+	6	996	c.522G>A	c.(520-522)CTG>CTA	p.L174L	NEURL2_uc002xqg.1_5'Flank|CTSA_uc002xqh.2_Silent_p.L192L|CTSA_uc002xqi.2_RNA|CTSA_uc010zxi.1_Silent_p.L175L|CTSA_uc002xqk.3_Silent_p.L174L	NM_001127695	NP_001121167	P10619	PPGB_HUMAN	cathepsin A isoform b precursor	174					intracellular protein transport|proteolysis	endoplasmic reticulum|lysosome|nucleus	enzyme activator activity|protein binding|serine-type carboxypeptidase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				AACTTTTCCTGACCGGGGAGA	0.562													6	45					0	0	0.001984	0	0	
CTCFL	140690	broad.mit.edu	37	20	56098737	56098737	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:56098737T>A	uc010gix.1	-	1	1187	c.525A>T	c.(523-525)GAA>GAT	p.E175D	CTCFL_uc010giw.1_Missense_Mutation_p.E175D|CTCFL_uc002xym.2_Missense_Mutation_p.E175D|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Missense_Mutation_p.E175D|CTCFL_uc010gjb.1_Missense_Mutation_p.E175D|CTCFL_uc010gjc.1_Missense_Mutation_p.E175D|CTCFL_uc010gjd.1_Missense_Mutation_p.E175D|CTCFL_uc010gje.2_Missense_Mutation_p.E175D|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Missense_Mutation_p.E175D|CTCFL_uc010gji.1_Intron|CTCFL_uc010gjj.1_Missense_Mutation_p.E175D|CTCFL_uc010gjk.1_Missense_Mutation_p.E175D|CTCFL_uc010gjl.1_Missense_Mutation_p.E175D	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	175					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GTCCAGTAGTTTCAGCCAGGC	0.443													7	91					0	0	0.001984	0	0	
GNAS	2778	broad.mit.edu	37	20	57415375	57415375	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:57415375G>A	uc002xzt.2	+	1	581	c.214G>A	c.(214-216)GGC>AGC	p.G72S	GNASAS_uc002xzs.1_Intron|GNAS_uc002xzu.3_5'Flank|GNAS_uc010gjq.2_5'Flank	NM_016592	NP_057676	P63092	GNAS2_HUMAN	GNAS complex locus NESP55	72				Missing (in Ref. 8; AAH66923).	activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CCACCGCTCCGGCGCCCAGGT	0.677			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			6	35					0	0	0.003080	0	0	
TH1L	51497	broad.mit.edu	37	20	57564992	57564992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:57564992G>A	uc002yag.2	+	7	791	c.764G>A	c.(763-765)GGC>GAC	p.G255D	TH1L_uc002yaf.1_RNA|TH1L_uc002yah.2_Missense_Mutation_p.G255D	NM_198976	NP_945327	Q8IXH7	NELFD_HUMAN	TH1-like protein	255					negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	all_lung(29;0.00711)		Colorectal(105;0.109)			GAGCAGGGGGGCTCCGCTGTG	0.622													6	40					0	0	0.006214	0	0	
C20orf197	284756	broad.mit.edu	37	20	58645855	58645855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:58645855G>A	uc002ybj.1	+	4	579	c.273G>A	c.(271-273)ATG>ATA	p.M91I		NM_173644	NP_775915	Q8N268	CT197_HUMAN	hypothetical protein LOC284756	91										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(7;2.33e-09)			cagtcacaatgtgcatttggg	0.219													4	39					0	0	0.009096	0	0	
PSMA7	5688	broad.mit.edu	37	20	60714901	60714901	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:60714901C>T	uc002ybx.1	-	3	399	c.284G>A	c.(283-285)CGG>CAG	p.R95Q	PSMA7_uc002yby.1_RNA	NM_002792	NP_002783	O14818	PSA7_HUMAN	proteasome alpha 7 subunit	95					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|interspecies interaction between organisms|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|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity				0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CACAGTCAGCCGGTGGCTCTG	0.612													7	27					0	0	0.001984	0	0	
OSBPL2	9885	broad.mit.edu	37	20	60854271	60854271	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:60854271G>A	uc002yck.1	+	7	752	c.550G>A	c.(550-552)GCG>ACG	p.A184T	OSBPL2_uc002ycl.1_Missense_Mutation_p.A172T|OSBPL2_uc011aah.1_Missense_Mutation_p.A92T|OSBPL2_uc002ycm.1_5'UTR	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform	184					lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			CCCCATCAGTGCGTTCCACTC	0.507													24	59					0	0	0.004656	0	0	
DIDO1	11083	broad.mit.edu	37	20	61525803	61525803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:61525803C>T	uc002ydr.1	-	11	2798	c.2534G>A	c.(2533-2535)CGC>CAC	p.R845H	DIDO1_uc002yds.1_Missense_Mutation_p.R845H|DIDO1_uc002ydt.1_Missense_Mutation_p.R845H|DIDO1_uc002ydu.1_Missense_Mutation_p.R845H	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	845					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)					GAGGTGTGCGCGGTGCTGACT	0.507													19	57					0	0	0.008871	0	0	
YTHDF1	54915	broad.mit.edu	37	20	61835152	61835152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:61835152C>T	uc002yeh.2	-	4	434	c.140G>A	c.(139-141)AGT>AAT	p.S47N	YTHDF1_uc011aaq.1_5'UTR	NM_017798	NP_060268	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	47										ovary(2)	2						TGAGGGGTAACTGTTACTCTG	0.512													8	22					0	0	0.003080	0	0	
PRIC285	85441	broad.mit.edu	37	20	62196162	62196162	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:62196162C>T	uc002yfm.2	-	9	4905	c.4013G>A	c.(4012-4014)CGC>CAC	p.R1338H	PRIC285_uc002yfl.1_Missense_Mutation_p.R769H	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	1338					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			CAAGAAGGCGCGGCAGTCCTC	0.662													5	20					0	0	0.001984	0	0	
TNFRSF6B	8771	broad.mit.edu	37	20	62329757	62329757	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:62329757G>A	uc002yfy.2	+	7	1178	c.744G>A	c.(742-744)GCG>GCA	p.A248A	RTEL1_uc002yfw.2_RNA|TNFRSF6B_uc002yfz.2_Silent_p.A248A	NM_032945	NP_116563	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily,	248					anti-apoptosis|apoptosis	extracellular region|soluble fraction	protein binding|receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			CACCAAGGGCGGGCCGCGCGG	0.716													4	4					0	0	0.009096	0	0	
TCEA2	6919	broad.mit.edu	37	20	62697836	62697836	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:62697836C>T	uc011abs.1	+	2	736	c.80C>T	c.(79-81)GCC>GTC	p.A27V	TCEA2_uc011abr.1_5'UTR|TCEA2_uc010gkq.2_5'UTR|TCEA2_uc010gks.2_Missense_Mutation_p.A27V|TCEA2_uc010gkt.2_5'UTR|TCEA2_uc010gku.1_5'UTR	NM_003195	NP_003186	Q15560	TCEA2_HUMAN	transcription elongation factor A protein 2	27	TFIIS N-terminal.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	transcription elongation factor complex	DNA binding|protein binding|translation elongation factor activity|zinc ion binding				0	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					CAGGAGGGAGCCATGGATTTG	0.567													8	81					0	0	0.003080	0	0	
NPBWR2	2832	broad.mit.edu	37	20	62737901	62737901	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:62737901G>A	uc011abt.1	-	1	284	c.284C>T	c.(283-285)ACG>ATG	p.T95M		NM_005286	NP_005277	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	95	Helical; Name=2; (Potential).					plasma membrane	opioid receptor activity|protein binding			large_intestine(1)	1	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					CAGTACCAGCGTGAAGAGCCC	0.612													4	27					0	0	0.000602	0	0	
C21orf99	149992	broad.mit.edu	37	21	14424254	14424254	+	RNA	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:14424254C>T	uc002yiy.3	+	5		c.3069C>T			C21orf99_uc002yja.3_RNA					Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						AGCCTGTAAACATCCTTTAAA	0.279													4	37					0	0	0.001168	0	0	
NRIP1	8204	broad.mit.edu	37	21	16340294	16340294	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:16340294G>T	uc002yjx.2	-	4	818	c.220C>A	c.(220-222)CAG>AAG	p.Q74K		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	74					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		CCAGACCCCTGATATGTATGT	0.458													6	33					3.59834e-05	3.85339e-05	0.001168	1	0	
USP25	29761	broad.mit.edu	37	21	17250724	17250724	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:17250724C>T	uc002yjy.1	+	24	3315	c.3098C>T	c.(3097-3099)ACG>ATG	p.T1033M	USP25_uc011aby.1_Missense_Mutation_p.T1103M|USP25_uc002yjz.1_Missense_Mutation_p.T1065M|USP25_uc010gla.1_Missense_Mutation_p.T428M	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	1033					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		TCATATTCCACGCATGAACTC	0.433													9	61					0	0	0.006214	0	0	
ADAMTS1	9510	broad.mit.edu	37	21	28212641	28212641	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:28212641C>T	uc002ymf.2	-	5	2074	c.1619G>A	c.(1618-1620)TGT>TAT	p.C540Y		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	540	Disintegrin.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)		GCCGTTGATACACCATTTCCC	0.473													7	77					0	0	0.004482	0	0	
KRTAP27-1	643812	broad.mit.edu	37	21	31709741	31709741	+	Silent	SNP	G	T	T	rs139729864		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:31709741G>T	uc002ynx.1	-	1	272	c.246C>A	c.(244-246)CCC>CCA	p.P82P		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	82						intermediate filament				ovary(2)	2						GGACAACTCCGGGGAAGCAGT	0.478													23	111					3.5997e-14	4.03253e-14	0.014323	1	0	
C21orf59	56683	broad.mit.edu	37	21	33954519	33954519	+	Silent	SNP	C	T	T	rs145187250		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:33954519C>T	uc002ypy.1	-	7	1082	c.969G>A	c.(967-969)TCG>TCA	p.S323S	TCP10L_uc002ypw.3_Silent_p.S117S|C21orf59_uc002ypx.1_Silent_p.S140S|C21orf59_uc002ypz.1_Silent_p.S291S	NM_021254	NP_067077	P57076	CU059_HUMAN	hypothetical protein LOC56683	Error:Variant_position_missing_in_P57076_after_alignment						cytosol|nucleus					0						CCAGAGTGTGCGATTCTTGCC	0.502													19	102					0	0	0.007413	0	0	
SON	6651	broad.mit.edu	37	21	34923905	34923905	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:34923905A>T	uc002yse.1	+	3	2417	c.2368A>T	c.(2368-2370)ACT>TCT	p.T790S	SON_uc002ysb.1_Missense_Mutation_p.T790S|SON_uc002ysc.2_Missense_Mutation_p.T790S|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	790	17 X 10 AA tandem repeats of L-A-[ST]- [NSG]-[TS]-MDSQM.				anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						AGCAACTAGCACTATGGACTC	0.512													13	215					0	0	0.007413	0	0	
SON	6651	broad.mit.edu	37	21	34923907	34923907	+	Silent	SNP	T	C	C	rs146626998		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:34923907T>C	uc002yse.1	+	3	2419	c.2370T>C	c.(2368-2370)ACT>ACC	p.T790T	SON_uc002ysb.1_Silent_p.T790T|SON_uc002ysc.2_Silent_p.T790T|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	790	17 X 10 AA tandem repeats of L-A-[ST]- [NSG]-[TS]-MDSQM.				anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						CAACTAGCACTATGGACTCCC	0.517													13	211					0	0	0.008871	0	0	
KCNJ15	3772	broad.mit.edu	37	21	39672159	39672159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:39672159G>A	uc002ywv.2	+	4	1278	c.976G>A	c.(976-978)GAT>AAT	p.D326N	KCNJ15_uc002yww.2_Missense_Mutation_p.D326N|KCNJ15_uc002ywx.2_Missense_Mutation_p.D326N	NM_002243	NP_002234	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	326	Cytoplasmic (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6						ATATGTGGCTGATTTCAGTCA	0.443													10	34					0	0	0.010729	0	0	
TRAPPC10	7109	broad.mit.edu	37	21	45511891	45511891	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:45511891C>T	uc002zea.2	+	19	3127	c.2958C>T	c.(2956-2958)ACC>ACT	p.T986T	TRAPPC10_uc010gpo.2_Silent_p.T697T|TRAPPC10_uc011afa.1_Silent_p.T364T|TRAPPC10_uc011afb.1_Silent_p.T91T	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	986					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2						GTGATAGTACCGACCTGCAAC	0.418													23	137					0	0	0.014323	0	0	
ADARB1	104	broad.mit.edu	37	21	46640907	46640907	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:46640907G>A	uc002zgy.2	+	11	2459	c.2024G>A	c.(2023-2025)CGC>CAC	p.R675H	ADARB1_uc002zgr.2_Missense_Mutation_p.R675H|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Missense_Mutation_p.R635H|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Missense_Mutation_p.R635H|ADARB1_uc010gpx.2_RNA|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	675	A to I editase.				adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		TTGTACTGTCGCTGGATGCGT	0.612													4	22					0	0	0.009096	0	0	
PCNT	5116	broad.mit.edu	37	21	47808672	47808672	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:47808672C>T	uc002zji.3	+	18	3587	c.3480C>T	c.(3478-3480)GAC>GAT	p.D1160D	PCNT_uc002zjj.2_Silent_p.D1042D	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	1160					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					CCCTCCAGGACGCCCTGCGCA	0.667													6	29					0	0	0.001168	0	0	
C22orf29	79680	broad.mit.edu	37	22	19839076	19839076	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:19839076C>T	uc002zqg.2	-	2	1308	c.709G>A	c.(709-711)GCC>ACC	p.A237T	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Missense_Mutation_p.A237T|C22orf29_uc002zqi.2_Missense_Mutation_p.A237T|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	237											0	Colorectal(54;0.0993)					GTGGCCATGGCGGCTGGTAAA	0.607													4	43					0	0	0.001168	0	0	
C22orf29	79680	broad.mit.edu	37	22	19839620	19839620	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:19839620G>A	uc002zqg.2	-	2	764	c.165C>T	c.(163-165)ACC>ACT	p.T55T	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Silent_p.T55T|C22orf29_uc002zqi.2_Silent_p.T55T|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	55											0	Colorectal(54;0.0993)					GCACACACACGGTGTCCCCAC	0.612													9	40					0	0	0.008291	0	0	
ZDHHC8	29801	broad.mit.edu	37	22	20128528	20128528	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:20128528G>A	uc002zrq.2	+	7	993	c.887G>A	c.(886-888)CGT>CAT	p.R296H	ZDHHC8_uc002zrr.1_Missense_Mutation_p.R296H|ZDHHC8_uc010gsa.2_Missense_Mutation_p.R102H	NM_013373	NP_037505	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC domain containing 8	296	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Colorectal(54;0.0993)					GGCCTGGGCCGTAGCAAGGTG	0.622													7	31					0	0	0.001984	0	0	
RTN4R	65078	broad.mit.edu	37	22	20229616	20229616	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:20229616A>G	uc002zrv.2	-	2	1241	c.1040T>C	c.(1039-1041)CTG>CCG	p.L347P	RTN4R_uc002zru.2_Missense_Mutation_p.L119P	NM_023004	NP_075380	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor precursor	347					axonogenesis|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	anchored to membrane|cell surface|endoplasmic reticulum|plasma membrane	protein binding|receptor activity				0	Colorectal(54;0.0993)					TCCAGGCTCCAGTACTGAGGC	0.672													6	23					0	0	0.003080	0	0	
ZNF74	7625	broad.mit.edu	37	22	20760748	20760748	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:20760748C>T	uc010gsm.2	+	6	1637	c.1425C>T	c.(1423-1425)AAC>AAT	p.N475N	ZNF74_uc002zsg.2_Silent_p.N404N|ZNF74_uc002zsh.2_Silent_p.N475N|ZNF74_uc002zsi.2_Silent_p.N404N|ZNF74_uc010gsn.2_Silent_p.N404N	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	475	C2H2-type 9.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|nucleus	DNA binding|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			TCAAGTGCAACGAGTGCGGCA	0.642													7	46					0	0	0.004482	0	0	
KLHL22	84861	broad.mit.edu	37	22	20796481	20796481	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:20796481C>T	uc002zsl.1	-	7	1893	c.1784G>A	c.(1783-1785)CGC>CAC	p.R595H	KLHL22_uc011ahr.1_Missense_Mutation_p.R452H	NM_032775	NP_116164	Q53GT1	KLH22_HUMAN	kelch-like	595					cell division	Cul3-RING ubiquitin ligase complex				lung(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GAGCAGGGAGCGGGGCAGGGT	0.642													4	13					0	0	0.000602	0	0	
MED15	51586	broad.mit.edu	37	22	20929406	20929406	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:20929406A>G	uc002zsp.2	+	9	1239	c.1159A>G	c.(1159-1161)ACG>GCG	p.T387A	MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc002zss.2_Intron|MED15_uc011ahu.1_Missense_Mutation_p.T113A|MED15_uc002zst.2_Missense_Mutation_p.T3A	NM_001003891	NP_001003891	Q96RN5	MED15_HUMAN	mediator complex subunit 15 isoform a	387	Pro-rich.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			AAAGATGATCACGGAAGCCTT	0.577													24	152					0	0	0.004656	0	0	
SLC7A4	6545	broad.mit.edu	37	22	21385960	21385960	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:21385960C>A	uc002zud.2	-	2	210	c.142G>T	c.(142-144)GGT>TGT	p.G48C	SLC7A4_uc002zue.2_Missense_Mutation_p.G48C	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	48	Helical; (Potential).				cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	ACCATGCCACCCACGCCCAGA	0.657													7	17					0.000157383	0.000167469	0.003080	1	0	
TOP3B	8940	broad.mit.edu	37	22	22316806	22316806	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:22316806C>A	uc002zvs.2	-	13	1955	c.1520G>T	c.(1519-1521)GGC>GTC	p.G507V	TOP3B_uc010gtm.1_Missense_Mutation_p.G52V|TOP3B_uc002zvr.2_Missense_Mutation_p.G232V|TOP3B_uc010gtl.2_Missense_Mutation_p.G507V|TOP3B_uc002zvt.3_Missense_Mutation_p.G507V	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	507					DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CCCACCGATGCCATGCTTCTC	0.642													7	37					0.000673444	0.00071074	0.008291	1	0	
ZNF280A	129025	broad.mit.edu	37	22	22869868	22869868	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:22869868A>T	uc002zwe.2	-	2	340	c.87T>A	c.(85-87)GAT>GAA	p.D29E	LOC96610_uc011aim.1_Intron	NM_080740	NP_542778	P59817	Z280A_HUMAN	zinc finger protein 280A	29					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TCAGATCTGGATCTTCATCAT	0.368													25	103					0	0	0.005443	0	0	
CABIN1	23523	broad.mit.edu	37	22	24573539	24573539	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:24573539C>A	uc002zzi.1	+	36	6400	c.6273C>A	c.(6271-6273)CCC>CCA	p.P2091P	CABIN1_uc002zzj.1_Silent_p.P2012P|CABIN1_uc002zzl.1_Silent_p.P2091P|CABIN1_uc010gul.1_Silent_p.P29P	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	2091					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						AGACTCAGCCCCTGAGCTCTC	0.647													5	21					0.000602214	0.000636366	0.000602	1	0	
C22orf13	83606	broad.mit.edu	37	22	24939903	24939903	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:24939903G>A	uc003aah.2	-	5	851	c.535C>T	c.(535-537)CGC>TGC	p.R179C	C22orf13_uc003aal.2_Missense_Mutation_p.R235C|C22orf13_uc003aai.3_Missense_Mutation_p.R136C|C22orf13_uc003aaj.3_Missense_Mutation_p.R179C|C22orf13_uc003aak.3_Missense_Mutation_p.R235C	NM_031444	NP_113632	Q96NT3	CV013_HUMAN	chromosome 22 open reading frame 13	179											0						TCAGGAGTGCGGCAGAAGCAG	0.617													4	18					0	0	0.000602	0	0	
SGSM1	129049	broad.mit.edu	37	22	25246318	25246318	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:25246318C>T	uc003abg.2	+	5	531	c.374C>T	c.(373-375)GCC>GTC	p.A125V	SGSM1_uc003abh.2_Missense_Mutation_p.A125V|SGSM1_uc010guu.1_Missense_Mutation_p.A125V|SGSM1_uc003abj.2_Missense_Mutation_p.A125V|SGSM1_uc003abi.1_Missense_Mutation_p.A100V|SGSM1_uc003abf.2_Missense_Mutation_p.A125V	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	125	RUN.					Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						TCCCCACTTGCCATCAAGCAT	0.448											OREG0026418	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	40					0	0	0.010729	0	0	
SGSM1	129049	broad.mit.edu	37	22	25264717	25264717	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:25264717C>T	uc003abg.2	+	12	1343	c.1186C>T	c.(1186-1188)CGA>TGA	p.R396*	SGSM1_uc003abh.2_Nonsense_Mutation_p.R396*|SGSM1_uc010guu.1_Nonsense_Mutation_p.R396*|SGSM1_uc003abj.2_Nonsense_Mutation_p.R396*|SGSM1_uc003abi.1_Nonsense_Mutation_p.R371*	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	396						Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						ACTGCGCAAGCGAAGCCCTCA	0.502													25	98					0	0	0.006320	0	0	
ADRBK2	157	broad.mit.edu	37	22	26091137	26091137	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:26091137C>T	uc003abx.3	+	13	1263	c.1116C>T	c.(1114-1116)GCC>GCT	p.A372A	ADRBK2_uc010gux.2_Silent_p.A372A|ADRBK2_uc003abw.2_Silent_p.A259A|ADRBK2_uc003aby.3_RNA	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2	372	Protein kinase.						ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	ACAGCAGTGCCGACTGGTTCT	0.532													7	40					0	0	0.001984	0	0	
EIF4ENIF1	56478	broad.mit.edu	37	22	31850237	31850237	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:31850237C>T	uc003akz.1	-	10	1569	c.1405G>A	c.(1405-1407)GTA>ATA	p.V469I	EIF4ENIF1_uc003akx.1_Missense_Mutation_p.V148I|EIF4ENIF1_uc003aky.1_Missense_Mutation_p.V148I|EIF4ENIF1_uc003ala.1_Missense_Mutation_p.V469I|EIF4ENIF1_uc003alb.1_Missense_Mutation_p.V306I|EIF4ENIF1_uc003akw.1_5'Flank	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E	469						nucleus	protein binding|protein transporter activity			ovary(1)	1						TTGTTGGTTACGGCACTCAAG	0.493													10	61					0	0	0.010729	0	0	
MYH9	4627	broad.mit.edu	37	22	36696961	36696961	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:36696961T>A	uc003apg.2	-	22	3005	c.2774A>T	c.(2773-2775)GAG>GTG	p.E925V	MYH9_uc003aph.1_Missense_Mutation_p.E789V	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	925	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						CTCCTCCTCCTCCACCCTGGC	0.647			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				6	35					0	0	0.001984	0	0	
GGA1	26088	broad.mit.edu	37	22	38026101	38026101	+	Missense_Mutation	SNP	G	A	A	rs150957887		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:38026101G>A	uc003atc.2	+	13	1620	c.1255G>A	c.(1255-1257)GGT>AGT	p.G419S	GGA1_uc003atd.2_Missense_Mutation_p.G332S|GGA1_uc003ate.2_Missense_Mutation_p.G419S|GGA1_uc003atf.2_Missense_Mutation_p.G346S	NM_013365	NP_037497	Q9UJY5	GGA1_HUMAN	golgi associated, gamma adaptin ear containing,	419	Unstructured hinge.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|Golgi apparatus part	protein binding			breast(2)|ovary(1)	3	Melanoma(58;0.0574)					AGCAAGCAGCGGTCTGGACGA	0.672													5	26					0	0	0.001168	0	0	
SH3BP1	23616	broad.mit.edu	37	22	38039705	38039705	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:38039705G>A	uc003ati.2	+	7	639	c.528G>A	c.(526-528)CCG>CCA	p.P176P	SH3BP1_uc003atg.1_RNA|SH3BP1_uc011anl.1_Silent_p.P176P|SH3BP1_uc003ath.1_Silent_p.P176P|SH3BP1_uc003atj.1_Silent_p.P112P|SH3BP1_uc003atk.1_Silent_p.P90P|uc003atl.1_RNA	NM_018957	NP_061830	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	176	BAR.				signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GAGGCAGCCCGGGTAGTCACA	0.582											OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	39					0	0	0.008291	0	0	
SMCR7L	54471	broad.mit.edu	37	22	39910152	39910152	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:39910152G>A	uc003axx.2	+	6	1714	c.1216G>A	c.(1216-1218)GAC>AAC	p.D406N	SMCR7L_uc003axw.2_Missense_Mutation_p.D406N|SMCR7L_uc010gxz.1_Missense_Mutation_p.D228N|SMCR7L_uc003axy.2_Missense_Mutation_p.D228N	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	406						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)					TATGCTGGCCGACCGTTTCCT	0.592											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	69					0	0	0.004990	0	0	
MKL1	57591	broad.mit.edu	37	22	40807697	40807697	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:40807697A>G	uc003ayv.1	-	12	2700	c.2493T>C	c.(2491-2493)CAT>CAC	p.H831H	MKL1_uc003ayw.1_Silent_p.H831H|MKL1_uc010gye.1_3'UTR|MKL1_uc010gyf.1_Silent_p.H781H	NM_020831	NP_065882	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia 1 protein	831					positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						CTGGCCCGTCATGCCCACTGG	0.672			T	RBM15	acute megakaryocytic leukemia								7	32					0	0	0.003080	0	0	
EP300	2033	broad.mit.edu	37	22	41513716	41513716	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:41513716A>G	uc003azl.3	+	2	1015	c.620A>G	c.(619-621)TAC>TGC	p.Y207C		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	207					apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						AATATGCAGTACCCAAACCCA	0.537			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				4	36					0	0	0.009096	0	0	
EP300	2033	broad.mit.edu	37	22	41523693	41523693	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:41523693G>A	uc003azl.3	+	4	1504	c.1109G>A	c.(1108-1110)CGC>CAC	p.R370H		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	370	TAZ-type 1.				apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						CCCCACTGTCGCACAATGAAG	0.517			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				19	71					0	0	0.007413	0	0	
PARVB	29780	broad.mit.edu	37	22	44536011	44536011	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:44536011A>G	uc003ben.2	+	8	752	c.700A>G	c.(700-702)ATG>GTG	p.M234V	PARVB_uc003bem.2_Missense_Mutation_p.M267V|PARVB_uc010gzn.2_Missense_Mutation_p.M182V|PARVB_uc003beo.2_Missense_Mutation_p.M197V	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b	234					cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				CAGGATGATGATGGGCCGGTT	0.542													21	84					0	0	0.012319	0	0	
KIAA1644	85352	broad.mit.edu	37	22	44681393	44681393	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:44681393G>A	uc003bet.2	-	4	647	c.514C>T	c.(514-516)CTG>TTG	p.L172L		NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor	172	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				GCTTGTGGCAGCGGGCCTGGG	0.687													5	13					0	0	0.000602	0	0	
BRD1	23774	broad.mit.edu	37	22	50217191	50217191	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:50217191G>A	uc003biv.2	-	1	1262	c.775C>T	c.(775-777)CGC>TGC	p.R259C	BRD1_uc011arf.1_5'UTR|BRD1_uc011arg.1_Missense_Mutation_p.R259C|BRD1_uc011arh.1_Missense_Mutation_p.R259C|BRD1_uc003biu.3_Missense_Mutation_p.R259C	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	259	PHD-type.				histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		AGGCAGTGGCGGCAGAGCCAC	0.642													4	10					0	0	0.006214	0	0	
ZBED4	9889	broad.mit.edu	37	22	50278153	50278153	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:50278153C>T	uc003bix.2	+	2	1313	c.843C>T	c.(841-843)ACC>ACT	p.T281T		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	281						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CAAAGAGCACCTCTGGGTCCA	0.557													4	124					0	0	0.000602	0	0	
TTLL8	164714	broad.mit.edu	37	22	50487735	50487735	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:50487735T>G	uc011ark.1	-	3	207	c.207A>C	c.(205-207)AAA>AAC	p.K69N		NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)		TTTCTTTGACTTTGGCACATG	0.532													22	96					0	0	0.012319	0	0	
TUBGCP6	85378	broad.mit.edu	37	22	50671772	50671772	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr22:50671772G>A	uc003bkb.1	-	3	1601	c.1089C>T	c.(1087-1089)GTC>GTT	p.V363V	TUBGCP6_uc010har.1_Silent_p.V363V|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	363					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TGGCAGACACGACCCCAATCA	0.642													5	24					0	0	0.001168	0	0	
ITPR1	3708	broad.mit.edu	37	3	4856237	4856237	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:4856237G>A	uc003bqa.2	+	55	7896	c.7548G>A	c.(7546-7548)CCG>CCA	p.P2516P	ITPR1_uc010hca.1_Silent_p.P2501P|ITPR1_uc011asu.1_Silent_p.P527P|ITPR1_uc003bqc.2_Silent_p.P1486P|ITPR1_uc010hcc.1_Silent_p.P284P|ITPR1_uc011asv.1_Silent_p.P240P	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	2564	Lumenal (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		TCAGGAAGCCGTCCAAAGAGG	0.562													14	38					0	0	0.002450	0	0	
GRM7	2917	broad.mit.edu	37	3	7620434	7620434	+	Missense_Mutation	SNP	G	A	A	rs150165030	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:7620434G>A	uc003bqm.2	+	8	2115	c.1841G>A	c.(1840-1842)CGC>CAC	p.R614H	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.R614H|GRM7_uc003bql.2_Missense_Mutation_p.R614H|GRM7_uc003bqn.1_Missense_Mutation_p.R197H|GRM7_uc010hch.1_Missense_Mutation_p.R125H	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	614	Helical; Name=1; (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)	ACTTTCATCCGCTACAATGAC	0.502													21	95					0	0	0.012319	0	0	
C3orf32	51066	broad.mit.edu	37	3	8669394	8669394	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:8669394C>T	uc003bqu.2	-	8	844	c.598G>A	c.(598-600)GGC>AGC	p.G200S	C3orf32_uc003bqz.2_Missense_Mutation_p.G200S|C3orf32_uc003bqt.2_Missense_Mutation_p.G149S|C3orf32_uc011atg.1_Missense_Mutation_p.G222S|C3orf32_uc003bqv.2_Missense_Mutation_p.G149S|C3orf32_uc003bqw.2_RNA|C3orf32_uc003bqx.2_RNA|C3orf32_uc003bqy.2_Missense_Mutation_p.G200S	NM_015931	NP_057015	Q9Y2M2	CC032_HUMAN	hypothetical protein LOC51066	200	Cys-rich.									skin(1)	1						CTTCGCCTGCCGGACCCCGCG	0.592													8	19					0	0	0.006214	0	0	
BRPF1	7862	broad.mit.edu	37	3	9784848	9784848	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:9784848A>G	uc003bse.2	+	7	2603	c.2204A>G	c.(2203-2205)CAG>CGG	p.Q735R	BRPF1_uc003bsf.2_Missense_Mutation_p.Q741R|BRPF1_uc003bsg.2_Missense_Mutation_p.Q735R|BRPF1_uc011ati.1_Missense_Mutation_p.Q735R	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	735	Required for RUNX1 and RUNX2 transcriptional activation.|Interaction with MEAF6 and ING5.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)					GCCCGGCGCCAGGCAGAAAAA	0.582													6	33					0	0	0.001168	0	0	
CRELD1	78987	broad.mit.edu	37	3	9986201	9986201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:9986201A>G	uc003bug.2	+	11	1319	c.1201A>G	c.(1201-1203)ACT>GCT	p.T401A	CIDEC_uc003bto.2_Intron|CRELD1_uc003buf.2_3'UTR|CRELD1_uc003buh.2_Missense_Mutation_p.T401A|CRELD1_uc003bui.2_Missense_Mutation_p.T401A|CRELD1_uc003buj.2_RNA	NM_001077415	NP_001070883	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1 isoform 3	401	Helical; (Potential).				cardiac septum development|endocardial cushion development	integral to membrane	calcium ion binding			ovary(1)	1						GGCGGCCATGACTGGCTACTG	0.597													7	38					0	0	0.001984	0	0	
NUP210	23225	broad.mit.edu	37	3	13372050	13372050	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:13372050T>C	uc003bxv.1	-	30	4103	c.4020A>G	c.(4018-4020)CTA>CTG	p.L1340L		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	1340	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)					ACCCTGATGCTAGAAAGCCTT	0.502													31	120					0	0	0.009535	0	0	
XPC	7508	broad.mit.edu	37	3	14199997	14199997	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:14199997A>G	uc011ave.1	-	9	1490	c.1386T>C	c.(1384-1386)CCT>CCC	p.P462P	XPC_uc011avf.1_Silent_p.P269P|XPC_uc011avg.1_Silent_p.P425P	NM_004628	NP_004619	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	462					nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal	cytoplasm|nucleoplasm|XPC complex	bubble DNA binding|damaged DNA binding|loop DNA binding|protein binding|single-stranded DNA binding			ovary(2)|breast(1)	3						TTGGAGGGCCAGGTTCGGAAT	0.572			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				4	35					0	0	0.009096	0	0	
GALNTL2	117248	broad.mit.edu	37	3	16254150	16254150	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:16254150C>A	uc003car.3	+	6	1747	c.1272C>A	c.(1270-1272)TCC>TCA	p.S424S	GALNTL2_uc003caq.3_Silent_p.S157S	NM_054110	NP_473451	Q8N3T1	GLTL2_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	424	Lumenal (Potential).					Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1						ATCAGGATTCCCATTCCCCCC	0.542													8	41					1.26484e-09	1.39274e-09	0.003080	1	0	
RFTN1	23180	broad.mit.edu	37	3	16358435	16358435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:16358435G>A	uc003cay.2	-	10	1919	c.1637C>T	c.(1636-1638)GCC>GTC	p.A546V	RFTN1_uc010hes.2_Missense_Mutation_p.A510V|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein	546						plasma membrane				ovary(3)|central_nervous_system(1)	4						CCCCACCAGGGCCCTGCTGTG	0.602													5	68					0	0	0.000602	0	0	
PLCL2	23228	broad.mit.edu	37	3	17052707	17052707	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:17052707C>T	uc011awc.1	+	5	1950	c.1845C>T	c.(1843-1845)AGC>AGT	p.S615S	PLCL2_uc011awd.1_Silent_p.S497S	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	623	PI-PLC Y-box.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4						AACTGGTCAGCATCTGCAAAT	0.433													14	61					0	0	0.002450	0	0	
TBC1D5	9779	broad.mit.edu	37	3	17415970	17415970	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:17415970C>T	uc003cbf.2	-	12	2480	c.815G>A	c.(814-816)GGT>GAT	p.G272D	TBC1D5_uc010hev.2_Missense_Mutation_p.G272D|TBC1D5_uc003cbe.2_Missense_Mutation_p.G272D|TBC1D5_uc010hew.1_Missense_Mutation_p.G224D	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b	272	Rab-GAP TBC.					intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						TACCTTCTGACCATCATGCTC	0.318													4	27					0	0	0.009096	0	0	
RARB	5915	broad.mit.edu	37	3	25622154	25622154	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:25622154A>G	uc011awl.1	+	5	814	c.748A>G	c.(748-750)ACT>GCT	p.T250A	RARB_uc003cdi.1_Missense_Mutation_p.T131A|RARB_uc003cdh.2_Missense_Mutation_p.T243A	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2	250	Ligand-binding.				embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GCCTGGTTTCACTGGCTTGAC	0.537													10	40					0	0	0.010729	0	0	
EOMES	8320	broad.mit.edu	37	3	27759084	27759084	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:27759084T>C	uc003cdx.2	-	6	1538	c.1538A>G	c.(1537-1539)AAC>AGC	p.N513S	EOMES_uc003cdy.3_Missense_Mutation_p.N532S|EOMES_uc010hfn.2_3'UTR|EOMES_uc011axc.1_Missense_Mutation_p.N237S	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	513					CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4						CTGGGGAGGGTTGGCCACCTC	0.517													3	70					0	0	0.009096	0	0	
CMTM7	112616	broad.mit.edu	37	3	32493946	32493946	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:32493946G>A	uc003cey.1	+	4	731	c.495G>A	c.(493-495)TCG>TCA	p.S165S	CMTM7_uc003cez.1_Silent_p.S132S	NM_138410	NP_612419	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing	165	MARVEL.				chemotaxis	extracellular space|integral to membrane	cytokine activity				0						ATAAGATCTCGTGTGTAACCC	0.507													16	99					0	0	0.004007	0	0	
CCR4	1233	broad.mit.edu	37	3	32995805	32995805	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:32995805C>T	uc003cfg.1	+	2	1059	c.891C>T	c.(889-891)TGC>TGT	p.C297C		NM_005508	NP_005499	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	297	Helical; Name=7; (Potential).				chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response	integral to plasma membrane				lung(1)	1						TTGTTCACTGCTGCCTTAATC	0.473													12	59					0	0	0.013537	0	0	
MLH1	4292	broad.mit.edu	37	3	37092047	37092047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:37092047G>A	uc003cgl.2	+	19	2234	c.2174G>A	c.(2173-2175)CGC>CAC	p.R725H	MLH1_uc011aye.1_Intron|MLH1_uc011ayb.1_Missense_Mutation_p.R484H|MLH1_uc010hge.2_Missense_Mutation_p.R656H|MLH1_uc003cgn.3_Missense_Mutation_p.R484H|MLH1_uc011ayc.1_Missense_Mutation_p.R627H|MLH1_uc011ayd.1_Missense_Mutation_p.R484H|MLH1_uc003cgo.2_Missense_Mutation_p.R484H|MLH1_uc010hgk.2_Missense_Mutation_p.R312H|MLH1_uc010hgn.2_Missense_Mutation_p.A222T|MLH1_uc010hgm.2_RNA|MLH1_uc010hgo.2_3'UTR|MLH1_uc010hgp.2_Missense_Mutation_p.R108H|MLH1_uc010hgq.2_RNA	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1	725					mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						AAAGCCTTGCGCTCACACATT	0.433		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				13	56					0	0	0.001855	0	0	
MYD88	4615	broad.mit.edu	37	3	38182330	38182330	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:38182330C>T	uc003chx.2	+	4	974	c.790C>T	c.(790-792)CTC>TTC	p.L264F	MYD88_uc011ayi.1_Missense_Mutation_p.L256F|MYD88_uc011ayj.1_Silent_p.A195A|MYD88_uc011ayk.1_Silent_p.A150A|MYD88_uc011ayl.1_Missense_Mutation_p.L211F	NM_002468	NP_002459	Q99836	MYD88_HUMAN	myeloid differentiation primary response gene	243	TIR.				3'-UTR-mediated mRNA stabilization|anti-apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-17 production|positive regulation of interleukin-23 production|positive regulation of interleukin-6 production|regulation of inflammatory response|response to interleukin-1|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|intrinsic to membrane|plasma membrane	death receptor binding|TIR domain binding|transmembrane receptor activity			haematopoietic_and_lymphoid_tissue(93)|breast(1)	94				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TGCACTCAGCCTCTCTCCAGG	0.557			Mis 		ABC-DLBCL								16	50					0	0	0.003163	0	0	
EXOG	9941	broad.mit.edu	37	3	38565416	38565416	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:38565416G>A	uc003cih.2	+	6	766	c.670G>A	c.(670-672)GTC>ATC	p.V224I	EXOG_uc010hhg.2_RNA|EXOG_uc011ayq.1_Missense_Mutation_p.V174I|EXOG_uc003cij.2_Missense_Mutation_p.V84I|EXOG_uc010hhd.2_Missense_Mutation_p.V84I|EXOG_uc010hhe.2_Missense_Mutation_p.V84I|EXOG_uc003cik.2_Missense_Mutation_p.V84I|EXOG_uc010hhf.2_Missense_Mutation_p.V84I|EXOG_uc003cii.2_Missense_Mutation_p.V84I	NM_005107	NP_005098	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	224						mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0						CAACGTGGCAGTCCCCTCACA	0.463													14	47					0	0	0.001855	0	0	
SCN11A	11280	broad.mit.edu	37	3	38936340	38936340	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:38936340C>T	uc011ays.1	-	15	2718	c.2519G>A	c.(2518-2520)CGC>CAC	p.R840H	SCN11A_uc010hhn.1_5'UTR	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	840					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	AAAAGCCCGGCGGAATCGATC	0.453													11	56					0	0	0.008291	0	0	
WDR48	57599	broad.mit.edu	37	3	39119656	39119656	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:39119656C>T	uc003cit.2	+	10	1011	c.1001C>T	c.(1000-1002)GCC>GTC	p.A334V	WDR48_uc011ayt.1_Missense_Mutation_p.A325V|WDR48_uc011ayu.1_Missense_Mutation_p.A252V|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_RNA	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	334	WD 7.				interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AATTTTAGAGCCTCTGGAGAT	0.353													11	50					0	0	0.013537	0	0	
CX3CR1	1524	broad.mit.edu	37	3	39307048	39307048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:39307048C>T	uc003cjl.2	-	2	1045	c.953G>A	c.(952-954)CGC>CAC	p.R318H		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	318	Cytoplasmic (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		GTGGACTGAGCGCCCACACAG	0.478													37	134					0	0	0.004289	0	0	
ZNF445	353274	broad.mit.edu	37	3	44489280	44489280	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:44489280G>A	uc003cnf.2	-	8	2231	c.1883C>T	c.(1882-1884)ACC>ATC	p.T628I	ZNF445_uc011azv.1_Missense_Mutation_p.T616I|ZNF445_uc011azw.1_Missense_Mutation_p.T628I	NM_181489	NP_852466	P59923	ZN445_HUMAN	zinc finger protein 445	628	C2H2-type 5.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		CCTACATTTGGTACATTTATA	0.403													14	76					0	0	0.002450	0	0	
LARS2	23395	broad.mit.edu	37	3	45527238	45527238	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:45527238T>A	uc003cop.1	+	11	1258	c.1073T>A	c.(1072-1074)GTC>GAC	p.V358D	LARS2_uc010hit.1_Missense_Mutation_p.V315D	NM_015340	NP_056155	Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	358					leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	GAGGTCCCTGTCGTTATTTTG	0.433													23	127					0	0	0.002780	0	0	
ALS2CL	259173	broad.mit.edu	37	3	46718370	46718370	+	Missense_Mutation	SNP	G	A	A	rs140829916	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:46718370G>A	uc003cqa.1	-	17	2090	c.1900C>T	c.(1900-1902)CGT>TGT	p.R634C	ALS2CL_uc003cpx.1_5'UTR|ALS2CL_uc003cpy.1_RNA|ALS2CL_uc003cpz.1_Missense_Mutation_p.R149C|ALS2CL_uc003cqb.1_Missense_Mutation_p.R634C|ALS2CL_uc003cqc.1_RNA	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1	634					endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		TGAGACCTACGCAGCTCCCTG	0.662													16	56					0	0	0.004007	0	0	
PRSS45	377047	broad.mit.edu	37	3	46783906	46783906	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:46783906T>C	uc010hjl.2	-	4	621	c.621A>G	c.(619-621)TCA>TCG	p.S207S	PRSS45_uc011bam.1_RNA	NM_199183	NP_954652	Q7RTY3	PRS45_HUMAN	testis serine protease 5	239					proteolysis		serine-type endopeptidase activity				0						CACAGGGACCTGAGAAGGCTC	0.567													17	75					0	0	0.006122	0	0	
SMARCC1	6599	broad.mit.edu	37	3	47719763	47719763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:47719763C>T	uc003crq.2	-	16	1614	c.1496G>A	c.(1495-1497)CGT>CAT	p.R499H	SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Missense_Mutation_p.R390H	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	499	SWIRM.				chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity	p.R499C(1)		skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		GGGGTTTAGACGATACGTGTC	0.383													24	132					0	0	0.004656	0	0	
ZNF589	51385	broad.mit.edu	37	3	48302376	48302376	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:48302376G>T	uc003csl.3	+	3	236	c.170G>T	c.(169-171)AGG>ATG	p.R57M	ZNF589_uc010hjt.1_Missense_Mutation_p.R55M|ZNF589_uc003csn.2_RNA|ZNF589_uc011bbg.1_Missense_Mutation_p.R57M|ZNF589_uc003csm.2_RNA	NM_016089	NP_057173	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	57	KRAB.				regulation of transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTTGAGCAGAGGAACCTATAC	0.388													13	67					1.49906e-05	1.61046e-05	0.002450	1	0	
NDUFAF3	25915	broad.mit.edu	37	3	49059972	49059972	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:49059972G>A	uc003cvq.2	+	2	774	c.270_splice	c.e2+1	p.N90_splice	DALRD3_uc003cvm.1_5'Flank|DALRD3_uc010hko.1_5'Flank|uc011bcb.1_5'Flank|MIR425_hsa-mir-425|MI0001448_5'Flank|NDUFAF3_uc003cvn.2_Splice_Site_p.N33_splice|uc003cvo.1_5'Flank|MIR191_hsa-mir-191|MI0000465_5'Flank|NDUFAF3_uc003cvp.2_Splice_Site_p.N33_splice|NDUFAF3_uc003cvr.2_Splice_Site_p.N33_splice|NDUFAF3_uc003cvs.2_Splice_Site_p.N33_splice	NM_199069	NP_951032	Q9BU61	NDUF3_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial respiratory chain complex I assembly	mitochondrial inner membrane|nucleus	protein binding				0						GCAGTGGAACGTGAGTCCTGG	0.602													4	21					0	0	0.009096	0	0	
USP19	10869	broad.mit.edu	37	3	49149019	49149019	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:49149019G>T	uc003cwd.1	-	20	2983	c.2822C>A	c.(2821-2823)ACC>AAC	p.T941N	USP19_uc003cwa.2_Missense_Mutation_p.T749N|USP19_uc003cvz.3_Missense_Mutation_p.T1044N|USP19_uc011bcg.1_Missense_Mutation_p.T1032N|USP19_uc003cwb.2_Intron|USP19_uc003cwc.1_Missense_Mutation_p.T699N|USP19_uc011bch.1_Missense_Mutation_p.T1042N	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	941	Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AATTCCACTGGTGCTGGGCAC	0.632													3	16					0.00909568	0.00949188	0.009096	1	0	
MST1R	4486	broad.mit.edu	37	3	49933705	49933705	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:49933705G>A	uc003cxy.3	-	10	2836	c.2572C>T	c.(2572-2574)CGC>TGC	p.R858C	MST1R_uc011bdd.1_Missense_Mutation_p.R859C|MST1R_uc011bdc.1_5'UTR	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	858	IPT/TIG 3.|Extracellular (Potential).				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GGTAGGAAGCGAAAGCCAGGC	0.582													11	56					0	0	0.010729	0	0	
NAT6	24142	broad.mit.edu	37	3	50334066	50334066	+	Missense_Mutation	SNP	G	A	A	rs74426485	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:50334066G>A	uc003czi.2	-	2	932	c.829C>T	c.(829-831)CGC>TGC	p.R277C	HYAL3_uc003czc.1_Intron|HYAL3_uc003czd.1_Intron|HYAL3_uc003cze.1_Intron|HYAL3_uc003czf.1_Intron|HYAL3_uc003czg.1_Intron|NAT6_uc003czj.2_Missense_Mutation_p.R299C|NAT6_uc003czk.3_Missense_Mutation_p.R277C|NAT6_uc003czl.1_Missense_Mutation_p.R277C	NM_012191	NP_036323	Q93015	NAT6_HUMAN	N-acetyltransferase 6	277						cytoplasm	N-acetyltransferase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		AATATGGGGCGCCCCCTCACA	0.547													4	33					0	0	0.000602	0	0	
RASSF1	11186	broad.mit.edu	37	3	50369149	50369149	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:50369149G>A	uc003dad.1	-	4	744	c.613C>T	c.(613-615)CGC>TGC	p.R205C	RASSF1_uc003daa.1_Missense_Mutation_p.R50C|RASSF1_uc003dab.1_Missense_Mutation_p.R131C|RASSF1_uc003dac.2_Missense_Mutation_p.R50C|RASSF1_uc003dae.1_Missense_Mutation_p.R201C|RASSF1_uc010hlk.1_RNA|RASSF1_uc003daf.1_Missense_Mutation_p.R50C	NM_170714	NP_733832	Q9NS23	RASF1_HUMAN	Ras association domain family 1 isoform D	205	Ras-associating.				cell cycle arrest|negative regulation of cell cycle arrest|positive regulation of protein ubiquitination|protein stabilization|Ras protein signal transduction|response to DNA damage stimulus	microtubule|microtubule cytoskeleton|microtubule organizing center|nucleus|spindle pole	identical protein binding|protein binding|protein N-terminus binding|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AAGGAAGTGCGGCGCCTGACA	0.617													12	40					0	0	0.004007	0	0	
GRM2	2912	broad.mit.edu	37	3	51746888	51746888	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:51746888C>T	uc010hlv.2	+	3	1089	c.850C>T	c.(850-852)CGC>TGC	p.R284C	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	284	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)	TGCCAGCCAGCGCCTCAATGC	0.657													4	20					0	0	0.000602	0	0	
ABHD14A	25864	broad.mit.edu	37	3	52014951	52014951	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:52014951C>T	uc003dco.2	+	5	843	c.733C>T	c.(733-735)CGC>TGC	p.R245C	ABHD14B_uc003dcn.2_Intron|ACY1_uc011bea.1_Intron|ACY1_uc011beb.1_5'Flank|ACY1_uc003dcp.2_5'Flank|ACY1_uc003dcq.2_5'Flank	NM_015407	NP_056222	Q9BUJ0	ABHEA_HUMAN	abhydrolase domain containing 14A	245						cytoplasm|integral to membrane	hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGTGAAGCTACGCAATGCAGG	0.572													6	49					0	0	0.006214	0	0	
DNAH1	25981	broad.mit.edu	37	3	52400871	52400871	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:52400871G>A	uc011bef.1	+	36	5994	c.5733G>A	c.(5731-5733)CTG>CTA	p.L1911L		NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1911	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGGCCAGCTGTACGGGGAGT	0.612													16	70					0	0	0.003163	0	0	
BAP1	8314	broad.mit.edu	37	3	52437234	52437234	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:52437234C>T	uc003ddx.2	-	14	1925	c.1810G>A	c.(1810-1812)GTG>ATG	p.V604M	BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_Intron	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	604	Interaction with BRCA1.				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTGGCTTCCACGACCTCCTTC	0.607			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								4	27					0	0	0.001168	0	0	
GLT8D1	55830	broad.mit.edu	37	3	52729486	52729486	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:52729486G>A	uc003dfi.3	-	8	902	c.763C>T	c.(763-765)CGA>TGA	p.R255*	GLT8D1_uc003dfj.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfk.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfl.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfm.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfn.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfo.1_Nonsense_Mutation_p.R255*	NM_152932	NP_690909	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	255	Lumenal (Potential).					integral to membrane|mitochondrion	transferase activity, transferring glycosyl groups				0				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ATATTCTGTCGTTTCCATTCC	0.363													20	105					0	0	0.008871	0	0	
ITIH4	3700	broad.mit.edu	37	3	52858944	52858944	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:52858944C>T	uc003dfz.2	-	7	826	c.790G>A	c.(790-792)GCC>ACC	p.A264T	ITIH4_uc011bel.1_5'UTR|ITIH4_uc003dfy.2_Missense_Mutation_p.A128T|ITIH4_uc011bem.1_Missense_Mutation_p.A264T|ITIH4_uc011ben.1_Missense_Mutation_p.A264T	NM_002218	NP_002209	Q14624	ITIH4_HUMAN	inter-alpha (globulin) inhibitor H4	264					acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CCCTCGGGGGCAAAGTAGTGT	0.542													4	22					0	0	0.001168	0	0	
IL17RD	54756	broad.mit.edu	37	3	57132279	57132279	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:57132279G>T	uc003dil.2	-	12	1541	c.1452C>A	c.(1450-1452)TGC>TGA	p.C484*	IL17RD_uc003dik.2_Nonsense_Mutation_p.C460*|IL17RD_uc010hna.2_Nonsense_Mutation_p.C340*|IL17RD_uc011bex.1_Nonsense_Mutation_p.C340*	NM_017563	NP_060033	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D precursor	484	SEFIR.|Cytoplasmic (Potential).					Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		CGTCTCCCTCGCAGGAATAAT	0.572													5	23					0.000602214	0.000636366	0.000602	1	0	
PTPRG	5793	broad.mit.edu	37	3	62253473	62253473	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:62253473G>A	uc003dlb.2	+	19	3572	c.2853G>A	c.(2851-2853)ACG>ACA	p.T951T	PTPRG_uc003dlc.2_Silent_p.T922T|PTPRG_uc011bfi.1_Silent_p.T197T|uc010hno.2_Intron|uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	951	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TGATGATTACGAACCTTGTGG	0.398													10	99					0	0	0.013537	0	0	
FEZF2	55079	broad.mit.edu	37	3	62355818	62355818	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:62355818G>A	uc003dlh.2	-	4	1527	c.1320C>T	c.(1318-1320)CAC>CAT	p.H440H	FEZF2_uc003dli.2_Silent_p.H440H	NM_018008	NP_060478	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	440	C2H2-type 6.				transcription, DNA-dependent	nucleus	zinc ion binding			lung(1)	1		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)		CCACGCTGTCGTGGAGTTTGC	0.552													8	43					0	0	0.004482	0	0	
SYNPR	132204	broad.mit.edu	37	3	63466538	63466538	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:63466538G>A	uc003dlq.2	+	2	424	c.55G>A	c.(55-57)GGT>AGT	p.G19S	SYNPR_uc003dlp.2_Missense_Mutation_p.G39S|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_RNA|SYNPR_uc010hnt.2_Missense_Mutation_p.G28S|SYNPR_uc011bfm.1_RNA	NM_144642	NP_653243	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 2	19	MARVEL.|Helical; (Potential).					cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		TGCAACATGCGGTGGCTATTC	0.438													25	120					0	0	0.005443	0	0	
ADAMTS9	56999	broad.mit.edu	37	3	64547403	64547403	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:64547403C>T	uc003dmg.2	-	30	4581	c.4549G>A	c.(4549-4551)GTA>ATA	p.V1517I	ADAMTS9_uc011bfo.1_Missense_Mutation_p.V1489I|ADAMTS9_uc003dmh.1_Missense_Mutation_p.V1346I|ADAMTS9_uc011bfp.1_Missense_Mutation_p.V428I|uc003dmi.1_RNA	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1517	TSP type-1 12.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CTCTGCTGTACGCCTCGGCCA	0.567													20	66					0	0	0.008871	0	0	
LMOD3	56203	broad.mit.edu	37	3	69167997	69167997	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:69167997T>C	uc003dns.2	-	2	1718	c.1509A>G	c.(1507-1509)AGA>AGG	p.R503R	LMOD3_uc003dnt.2_Silent_p.R503R	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	503						cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		CGGGTGGTTCTCTGGCTTCCG	0.547													5	27					0	0	0.001984	0	0	
OR5H2	79310	broad.mit.edu	37	3	98001806	98001806	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:98001806G>A	uc003dsj.1	+	1	75	c.75G>A	c.(73-75)CAG>CAA	p.Q25Q		NM_001005482	NP_001005482	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3						TTACATATCAGCCAGAGTGGA	0.423													37	192					0	0	0.005524	0	0	
CEP97	79598	broad.mit.edu	37	3	101451389	101451389	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:101451389T>C	uc003dvk.1	+	6	646	c.619T>C	c.(619-621)TGT>CGT	p.C207R	CEP97_uc010hpm.1_Missense_Mutation_p.C173R|CEP97_uc011bhf.1_Missense_Mutation_p.C207R|CEP97_uc003dvl.1_5'UTR|CEP97_uc003dvm.1_Missense_Mutation_p.C45R	NM_024548	NP_078824	Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	207						centrosome|nucleus	protein binding			ovary(2)	2						GAACAATCCTTGTGTGATGGC	0.413													5	36					0	0	0.001168	0	0	
CD96	10225	broad.mit.edu	37	3	111319601	111319601	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:111319601A>G	uc003dxw.2	+	8	1145	c.975A>G	c.(973-975)AAA>AAG	p.K325K	CD96_uc003dxv.2_Silent_p.K309K|CD96_uc003dxx.2_Silent_p.K309K|CD96_uc010hpy.1_Silent_p.K309K	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	325	Extracellular (Potential).|Ig-like C2-type.				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3						AAGAGAGAAAAGGCAAAGATG	0.373									Opitz_Trigonocephaly_syndrome				16	69					0	0	0.004990	0	0	
BOC	91653	broad.mit.edu	37	3	112999994	112999994	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:112999994A>G	uc003dzx.2	+	15	3046	c.2425A>G	c.(2425-2427)ACC>GCC	p.T809A	BOC_uc003dzy.2_Missense_Mutation_p.T809A|BOC_uc003dzz.2_Missense_Mutation_p.T810A|BOC_uc003eab.2_Missense_Mutation_p.T510A|BOC_uc003eac.2_Missense_Mutation_p.T124A	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	809	Fibronectin type-III 3.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			GATCTGTGAGACCAAAGGTGA	0.547													7	38					0	0	0.001984	0	0	
GRAMD1C	54762	broad.mit.edu	37	3	113627946	113627946	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:113627946A>G	uc003eaq.3	+	9	1007	c.931A>G	c.(931-933)ACT>GCT	p.T311A	GRAMD1C_uc011bil.1_RNA|GRAMD1C_uc011bim.1_RNA|GRAMD1C_uc003ear.2_Missense_Mutation_p.T144A|GRAMD1C_uc003eas.2_Missense_Mutation_p.T106A	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	311						integral to membrane				ovary(2)|skin(1)	3						CAAAAGCAGCACTTCAGATTC	0.299													15	50					0	0	0.004007	0	0	
ZBTB20	26137	broad.mit.edu	37	3	114069597	114069597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:114069597C>T	uc003ebi.2	-	4	1508	c.1328G>A	c.(1327-1329)AGC>AAC	p.S443N	ZBTB20_uc003ebj.2_Missense_Mutation_p.S370N|ZBTB20_uc010hqp.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebk.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebl.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebm.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebn.2_Missense_Mutation_p.S370N|uc003ebo.1_5'Flank	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	443					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GATAACAGTGCTGTCCATCTC	0.567													5	52					0	0	0.000602	0	0	
ZBTB20	26137	broad.mit.edu	37	3	114070442	114070442	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:114070442G>A	uc003ebi.2	-	4	663	c.483C>T	c.(481-483)GGC>GGT	p.G161G	ZBTB20_uc003ebj.2_Silent_p.G88G|ZBTB20_uc010hqp.2_Silent_p.G88G|ZBTB20_uc003ebk.2_Silent_p.G88G|ZBTB20_uc003ebl.2_Silent_p.G88G|ZBTB20_uc003ebm.2_Silent_p.G88G|ZBTB20_uc003ebn.2_Silent_p.G88G|uc003ebo.1_5'Flank	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	161	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		CCCGTAGCACGCCGCTGTACA	0.567													11	35					0	0	0.002450	0	0	
GAP43	2596	broad.mit.edu	37	3	115395025	115395025	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:115395025G>A	uc003ebq.2	+	2	582	c.196G>A	c.(196-198)GCT>ACT	p.A66T	GAP43_uc003ebr.2_Missense_Mutation_p.A102T	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	66					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)		TGAGGCTGAAGCTAATAAGAA	0.527													6	98					0	0	0.004482	0	0	
IGSF11	152404	broad.mit.edu	37	3	118621438	118621438	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:118621438C>T	uc003ebw.2	-	7	1472	c.1225G>A	c.(1225-1227)GCA>ACA	p.A409T	IGSF11_uc011biv.1_Missense_Mutation_p.A381T|IGSF11_uc003ebx.2_Missense_Mutation_p.A385T|IGSF11_uc003eby.2_Missense_Mutation_p.A408T|IGSF11_uc003ebz.2_Missense_Mutation_p.A384T|IGSF11_uc010hqs.2_Missense_Mutation_p.A408T	NM_001015887	NP_001015887	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11 isoform b	409	Cytoplasmic (Potential).				cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0						TCCAGTGTTGCGTGGCTGATG	0.537													13	75					0	0	0.004007	0	0	
B4GALT4	8702	broad.mit.edu	37	3	118931514	118931514	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:118931514T>C	uc003ecg.2	-	8	1558	c.917A>G	c.(916-918)CAC>CGC	p.H306R	B4GALT4_uc003ece.1_3'UTR|B4GALT4_uc003ecf.2_RNA|B4GALT4_uc003ech.2_Missense_Mutation_p.H306R|B4GALT4_uc003eci.2_Missense_Mutation_p.H306R	NM_212543	NP_997708	O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	306	Lumenal (Potential).				membrane lipid metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding|N-acetyllactosamine synthase activity				0				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	TGACACTTGGTGTAAGAGCTT	0.363													13	45					0	0	0.002450	0	0	
CASR	846	broad.mit.edu	37	3	122003470	122003470	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:122003470G>A	uc003eev.3	+	7	3041	c.2669G>A	c.(2668-2670)CGC>CAC	p.R890H	CASR_uc003eew.3_Missense_Mutation_p.R900H	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	890	Cytoplasmic (Potential).|Interaction with RNF19A.				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GCCACGCTGCGCCGCAGCAAC	0.627													6	17					0	0	0.001168	0	0	
SEMA5B	54437	broad.mit.edu	37	3	122629836	122629836	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:122629836G>A	uc003efz.1	-	22	3452	c.3148C>T	c.(3148-3150)CTC>TTC	p.L1050F	SEMA5B_uc011bju.1_Missense_Mutation_p.L956F|SEMA5B_uc003ega.1_RNA|SEMA5B_uc003egb.1_Missense_Mutation_p.L1050F|SEMA5B_uc003efy.1_Missense_Mutation_p.L28F	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1	1050	Helical; Signal-anchor for type III membrane protein; (Potential).				cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		AGGGTCAGGAGCCCAGAGCCC	0.577													7	23					0	0	0.001984	0	0	
KALRN	8997	broad.mit.edu	37	3	124149556	124149556	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:124149556T>C	uc003ehg.2	+	16	2884	c.2757T>C	c.(2755-2757)AAT>AAC	p.N919N	KALRN_uc010hrv.1_Silent_p.N919N|KALRN_uc003ehf.1_Silent_p.N919N|KALRN_uc011bjy.1_Silent_p.N919N|KALRN_uc003ehh.1_Silent_p.N265N	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	919	Spectrin 4.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GCCTGGTCAATGCCAGCTCTT	0.567													9	34					0	0	0.004482	0	0	
KLF15	28999	broad.mit.edu	37	3	126070789	126070789	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:126070789G>T	uc011bkk.1	-	2	1159	c.977C>A	c.(976-978)CCT>CAT	p.P326H		NM_014079	NP_054798	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	326	C2H2-type 1.					nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)		GCTGCAGCCAGGGAAAGTACA	0.627													6	16					0.00116845	0.00122775	0.001168	1	0	
SEC61A1	29927	broad.mit.edu	37	3	127786377	127786377	+	Silent	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:127786377A>T	uc003ekb.2	+	10	1273	c.1089A>T	c.(1087-1089)GTA>GTT	p.V363V	RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Intron|SEC61A1_uc003ekc.2_Silent_p.V310V|SEC61A1_uc003ekd.2_Silent_p.V243V|SEC61A1_uc003ekg.2_Silent_p.V57V	NM_013336	NP_037468	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit	363	Helical; (Potential).				protein targeting to ER	integral to endoplasmic reticulum membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding|ribosome binding			ovary(1)	1						ATGCAGTTGTATACATAGTGT	0.493													21	82					0	0	0.003954	0	0	
MBD4	8930	broad.mit.edu	37	3	129152936	129152936	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:129152936G>A	uc003emh.1	-	4	1421	c.1245C>T	c.(1243-1245)AGC>AGT	p.S415S	MBD4_uc003emi.1_Silent_p.S415S|MBD4_uc003emj.1_Silent_p.S409S|MBD4_uc003emk.1_Silent_p.S97S|MBD4_uc011bkw.1_Silent_p.S415S	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	415					depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						AAAAATACAGGCTTGTTTTCC	0.348								BER_DNA_glycosylases					6	49					0	0	0.001168	0	0	
COL6A6	131873	broad.mit.edu	37	3	130380888	130380888	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:130380888A>G	uc010htl.2	+	34	6269	c.6238A>G	c.(6238-6240)AGA>GGA	p.R2080G	COL6A6_uc003eni.3_Missense_Mutation_p.R179G	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	2080	VWFA 9.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						ACCCAATCTGAGAAGAAACAA	0.408													9	51					0	0	0.008291	0	0	
PIK3R4	30849	broad.mit.edu	37	3	130422673	130422673	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:130422673G>A	uc003enj.2	-	13	3573	c.2992C>T	c.(2992-2994)CGA>TGA	p.R998*		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	998	WD 1.				fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						ACTCTAATTCGATTCACAGCA	0.418													24	110					0	0	0.003954	0	0	
CPNE4	131034	broad.mit.edu	37	3	131283121	131283121	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:131283121G>A	uc003eok.2	-	11	1435	c.1000C>T	c.(1000-1002)CAA>TAA	p.Q334*	CPNE4_uc011blq.1_Nonsense_Mutation_p.Q352*|CPNE4_uc003eol.2_Nonsense_Mutation_p.Q352*|CPNE4_uc003eom.2_Nonsense_Mutation_p.Q334*	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV	334	VWFA.									upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TCATTGGGTTGGTAAGGGTGG	0.453													9	85					0	0	0.010729	0	0	
PPP2R3A	5523	broad.mit.edu	37	3	135721928	135721928	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:135721928C>T	uc003eqv.1	+	2	2153	c.1588C>T	c.(1588-1590)CCA>TCA	p.P530S	PPP2R3A_uc011blz.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',	530					protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7						TCTAAGAGAGCCACTTGCGAA	0.388													9	82					0	0	0.006214	0	0	
STAG1	10274	broad.mit.edu	37	3	136059352	136059352	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:136059352T>C	uc003era.1	-	32	3945	c.3653A>G	c.(3652-3654)GAC>GGC	p.D1218G	STAG1_uc003erb.1_Missense_Mutation_p.D1181G	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1218					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						AACCATGGTGTCCTCAAATTC	0.373													18	62					0	0	0.006122	0	0	
SOX14	8403	broad.mit.edu	37	3	137484306	137484306	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:137484306C>T	uc003erm.1	+	1	728	c.680C>T	c.(679-681)ACT>ATT	p.T227I		NM_004189	NP_004180	O95416	SOX14_HUMAN	SRY-box 14	227					negative regulation of transcription from RNA polymerase II promoter|nervous system development|transcription, DNA-dependent	nucleus	sequence-specific DNA binding				0						ATGACCAAGACTGGCATAGAC	0.642													6	34					0	0	0.004482	0	0	
COPB2	9276	broad.mit.edu	37	3	139080026	139080026	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:139080026C>T	uc003etf.3	-	17	2237	c.2107G>A	c.(2107-2109)GCC>ACC	p.A703T	COPB2_uc011bmv.1_Missense_Mutation_p.A674T|COPB2_uc010hui.2_Missense_Mutation_p.A674T	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta	703					COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2						GAGGCAGTGGCCAAAAGCAGC	0.483													22	101					0	0	0.014323	0	0	
ATR	545	broad.mit.edu	37	3	142176461	142176461	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:142176461C>T	uc003eux.3	-	45	7762	c.7640G>A	c.(7639-7641)CGA>CAA	p.R2547Q	ATR_uc003euy.1_Missense_Mutation_p.R433Q	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2547	PI3K/PI4K.				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						TAAAGGCTCTCGCTGATCACG	0.378								Other_conserved_DNA_damage_response_genes					16	62					0	0	0.004007	0	0	
TRPC1	7220	broad.mit.edu	37	3	142521156	142521156	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:142521156G>A	uc003evc.2	+	10	1863	c.1727G>A	c.(1726-1728)TGT>TAT	p.C576Y	TRPC1_uc003evb.2_Missense_Mutation_p.C542Y|TRPC1_uc011bni.1_Missense_Mutation_p.C95Y	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,	576	Cytoplasmic (Potential).				axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						GGCATCTTCTGTGAACAGCAA	0.308													6	50					0	0	0.003080	0	0	
PAQR9	344838	broad.mit.edu	37	3	142681261	142681261	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:142681261A>G	uc003evg.2	-	1	918	c.918T>C	c.(916-918)ATT>ATC	p.I306I	PAQR9_uc003evf.1_RNA	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	306	Helical; (Potential).					integral to membrane	receptor activity				0						TGTGGCCGATAATGTCGAAAA	0.587													4	31					0	0	0.000602	0	0	
IGSF10	285313	broad.mit.edu	37	3	151164676	151164676	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:151164676C>T	uc011bod.1	-	4	3093	c.3093G>A	c.(3091-3093)CTG>CTA	p.L1031L		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1031					cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TATGCCGTCGCAGAACTGGAG	0.473													9	91					0	0	0.008291	0	0	
SUCNR1	56670	broad.mit.edu	37	3	151598580	151598580	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:151598580T>A	uc003ezf.1	+	3	348	c.249T>A	c.(247-249)TAT>TAA	p.Y83*		NM_033050	NP_149039	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	83	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	TAAGGAGTTATGCCAATGGAA	0.423													7	62					0	0	0.001984	0	0	
P2RY1	5028	broad.mit.edu	37	3	152553661	152553661	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:152553661C>T	uc003ezq.2	+	1	926	c.90C>T	c.(88-90)GTC>GTT	p.V30V		NM_002563	NP_002554	P47900	P2RY1_HUMAN	purinergic receptor P2Y1	30	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|platelet activation	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			ACAGCACGGTCGCCTCCACTG	0.617													9	22					0	0	0.006214	0	0	
MYNN	55892	broad.mit.edu	37	3	169497257	169497257	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:169497257T>A	uc003fft.2	+	3	1397	c.968T>A	c.(967-969)ATA>AAA	p.I323K	MYNN_uc011bpm.1_Missense_Mutation_p.I209K|MYNN_uc003ffu.2_Missense_Mutation_p.I323K|MYNN_uc003ffv.2_Missense_Mutation_p.I50K|MYNN_uc010hwo.2_Missense_Mutation_p.I323K|MYNN_uc003ffw.1_RNA	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	323	C2H2-type 1.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			CACATGAGAATACATAAAGGA	0.453													6	49					0	0	0.001984	0	0	
LOC100128164	100128164	broad.mit.edu	37	3	169664031	169664031	+	RNA	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:169664031C>T	uc011bpp.1	-	2		c.3772G>A				NR_027622				Homo sapiens cDNA FLJ41016 fis, clone UTERU2018784.												0						CCCCAAGATGCGATGGCCTTG	0.502													24	64					0	0	0.002780	0	0	
ABCC5	10057	broad.mit.edu	37	3	183682976	183682976	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:183682976C>T	uc003fmg.2	-	14	2193	c.2028G>A	c.(2026-2028)ACG>ACA	p.T676T	ABCC5_uc011bqt.1_Silent_p.T204T|ABCC5_uc010hxl.2_Silent_p.T676T	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	676	ABC transporter 1.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CCTGTACCTCCGTCAGGTCGC	0.592													8	29					0	0	0.004482	0	0	
EIF4G1	1981	broad.mit.edu	37	3	184040373	184040373	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:184040373A>G	uc003fnp.2	+	12	1848	c.1650A>G	c.(1648-1650)GCA>GCG	p.A550A	EIF4G1_uc003fno.1_Silent_p.A491A|EIF4G1_uc010hxw.1_Silent_p.A386A|EIF4G1_uc003fnt.2_Silent_p.A261A|EIF4G1_uc003fnq.2_Silent_p.A463A|EIF4G1_uc003fnr.2_Silent_p.A386A|EIF4G1_uc010hxx.2_Silent_p.A557A|EIF4G1_uc003fns.2_Silent_p.A510A|EIF4G1_uc010hxy.2_Silent_p.A557A|EIF4G1_uc003fnv.3_Silent_p.A550A|EIF4G1_uc003fnu.3_Silent_p.A550A|EIF4G1_uc003fnw.2_Silent_p.A557A|EIF4G1_uc003fnx.2_Silent_p.A354A|EIF4G1_uc003fny.3_Silent_p.A354A	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	550					insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGCCTCCTGCAGGCAGCAATC	0.532													8	32					0	0	0.004482	0	0	
EPHB3	2049	broad.mit.edu	37	3	184299146	184299146	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:184299146C>T	uc003foz.2	+	15	3275	c.2838C>T	c.(2836-2838)TTC>TTT	p.F946F		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	946	Cytoplasmic (Potential).|SAM.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			AGGAGAGCTTCGTCAGTGCGG	0.592													11	43					0	0	0.010729	0	0	
IGF2BP2	10644	broad.mit.edu	37	3	185363401	185363401	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:185363401C>T	uc003fpo.2	-	16	1797	c.1718G>A	c.(1717-1719)CGC>CAC	p.R573H	IGF2BP2_uc010hyi.2_Missense_Mutation_p.R516H|IGF2BP2_uc010hyj.2_Missense_Mutation_p.R510H|IGF2BP2_uc010hyk.2_Missense_Mutation_p.R437H|IGF2BP2_uc010hyl.2_Missense_Mutation_p.R467H|IGF2BP2_uc003fpp.2_Missense_Mutation_p.R530H|IGF2BP2_uc003fpq.2_Missense_Mutation_p.R578H	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	573	KH 4.				anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			CCTGATCTTGCGCTGTGCAGT	0.577													6	41					0	0	0.001168	0	0	
ETV5	2119	broad.mit.edu	37	3	185797681	185797681	+	Missense_Mutation	SNP	G	A	A	rs141531791		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:185797681G>A	uc003fpz.2	-	7	822	c.575C>T	c.(574-576)GCG>GTG	p.A192V	ETV5_uc003fpy.2_Missense_Mutation_p.A234V	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	192					cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			TCGGGGGACCGCAAATGTTTG	0.607			T	TMPRSS2|SCL45A3	Prostate 								7	30					0	0	0.003080	0	0	
EIF4A2	1974	broad.mit.edu	37	3	186504931	186504931	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:186504931A>G	uc003fqs.2	+	8	826	c.787A>G	c.(787-789)ACA>GCA	p.T263A	EIF4A2_uc003fqt.2_RNA|EIF4A2_uc003fqu.2_Missense_Mutation_p.T264A|EIF4A2_uc003fqv.2_Missense_Mutation_p.T168A|EIF4A2_uc003fqw.2_Missense_Mutation_p.T168A|EIF4A2_uc011bsb.1_Missense_Mutation_p.T136A|SNORA63_uc010hyw.1_5'Flank|SNORA4_uc010hyx.1_5'Flank	NM_001967	NP_001958	Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	263	Helicase C-terminal.				interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|protein binding|translation initiation factor activity			ovary(2)|breast(2)	4	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GAAGTTGGATACACTTTGTGA	0.363			T	BCL6	NHL								17	101					0	0	0.014323	0	0	
MUC4	4585	broad.mit.edu	37	3	195505811	195505811	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:195505811T>C	uc011bto.1	-	3	12716	c.12256A>G	c.(12256-12258)ACT>GCT	p.T4086A	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)		GCTGAGGAAGTGTCGGTGACA	0.592													5	23					0	0	0.001168	0	0	
MUC4	4585	broad.mit.edu	37	3	195506181	195506181	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:195506181G>T	uc011bto.1	-	3	12346	c.11886C>A	c.(11884-11886)TCC>TCA	p.S3962S	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_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	856	Ser-rich.				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)		CGTGACCGGTGGATGCTGAGG	0.582													6	3					5.9392e-07	6.45498e-07	0.001168	1	0	
MUC4	4585	broad.mit.edu	37	3	195507798	195507798	+	Silent	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:195507798G>C	uc011bto.1	-	3	10729	c.10269C>G	c.(10267-10269)ACC>ACG	p.T3423T	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_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	350					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)		CAGGAAGAGGGGTGGTGTCAC	0.602													3	31					0	0	0.001168	0	0	
PIGX	54965	broad.mit.edu	37	3	196454970	196454970	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:196454970G>A	uc010iaj.2	+	4	653	c.372G>A	c.(370-372)GTG>GTA	p.V124V	PIGX_uc003fwx.3_Silent_p.V124V|PIGX_uc011btx.1_RNA	NM_017861	NP_060331	Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	165	Lumenal (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane					0	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00322)		CCTCGATTGTGGTCAATAACC	0.468													3	53					0	0	0.009096	0	0	
PAK2	5062	broad.mit.edu	37	3	196509566	196509566	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr3:196509566C>T	uc003fwy.3	+	2	371	c.49C>T	c.(49-51)CGA>TGA	p.R17*		NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2	17					axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		ACCTCCTGTGCGAATGAGCAG	0.438													31	188					0	0	0.013726	0	0	
ZNF876P	642280	broad.mit.edu	37	4	248550	248550	+	RNA	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:248550A>G	uc010iba.2	+	2		c.1384A>G				NR_027481				Homo sapiens cDNA clone IMAGE:4828836.												0						TTGGAGAGAAACCCTACACAT	0.388													4	30					0	0	0.009096	0	0	
GAK	2580	broad.mit.edu	37	4	860918	860918	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:860918C>G	uc003gbm.3	-	21	2897	c.2698G>C	c.(2698-2700)GCC>CCC	p.A900P	GAK_uc003gbn.3_Missense_Mutation_p.A821P|GAK_uc010ibk.1_Missense_Mutation_p.A794P|GAK_uc010ibi.2_Missense_Mutation_p.A81P|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Missense_Mutation_p.A764P	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	900					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		GCCTTGCAGGCCTGCGGGGGT	0.716													4	10					0	0	0.009096	0	0	
GAK	2580	broad.mit.edu	37	4	861151	861151	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:861151T>C	uc003gbm.3	-	21	2664	c.2465A>G	c.(2464-2466)GAC>GGC	p.D822G	GAK_uc003gbn.3_Missense_Mutation_p.D743G|GAK_uc010ibk.1_Missense_Mutation_p.D716G|GAK_uc010ibi.2_Missense_Mutation_p.D3G|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Missense_Mutation_p.D686G	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	822					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		CTCGTCTCTGTCCTCCATCAG	0.602													15	61					0	0	0.007413	0	0	
FAM193A	8603	broad.mit.edu	37	4	2673877	2673877	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:2673877T>A	uc010icl.2	+	11	1587	c.1236T>A	c.(1234-1236)TGT>TGA	p.C412*	FAM193A_uc010ick.2_Nonsense_Mutation_p.C612*|FAM193A_uc003gfd.2_Nonsense_Mutation_p.C412*|FAM193A_uc011bvm.1_Nonsense_Mutation_p.C434*|FAM193A_uc011bvn.1_Nonsense_Mutation_p.C412*|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Nonsense_Mutation_p.C266*	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	412										ovary(3)	3						CTTGTGAATGTCATGTTTGTA	0.433													16	45					0	0	0.004007	0	0	
ADD1	118	broad.mit.edu	37	4	2906508	2906508	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:2906508C>T	uc003gfr.2	+	10	1367	c.1179C>T	c.(1177-1179)TAC>TAT	p.Y393Y	ADD1_uc003gfn.2_Intron|ADD1_uc003gfo.2_Silent_p.Y393Y|ADD1_uc003gfp.2_Silent_p.Y393Y|ADD1_uc003gfq.2_Silent_p.Y393Y|ADD1_uc003gfs.2_Silent_p.Y393Y|ADD1_uc003gft.3_Silent_p.Y393Y	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	393					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GAACTGGCTACCCTTATCGAT	0.398													8	88					0	0	0.008291	0	0	
ADD1	118	broad.mit.edu	37	4	2916624	2916624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:2916624C>T	uc003gfr.2	+	13	1807	c.1619C>T	c.(1618-1620)ACG>ATG	p.T540M	ADD1_uc003gfn.2_Intron|ADD1_uc003gfo.2_Missense_Mutation_p.T571M|ADD1_uc003gfp.2_Missense_Mutation_p.T540M|ADD1_uc003gfq.2_Missense_Mutation_p.T571M|ADD1_uc003gfs.2_Missense_Mutation_p.T571M	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	540					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GAGCTGGTGACGGCCTCCAAG	0.642													8	47					0	0	0.006214	0	0	
LYAR	55646	broad.mit.edu	37	4	4283520	4283520	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:4283520G>T	uc011bvy.1	-	4	370	c.227C>A	c.(226-228)GCG>GAG	p.A76E	LYAR_uc011bvx.1_5'Flank|LYAR_uc003ght.2_Missense_Mutation_p.A76E	NM_001145725	NP_001139197	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive homolog	76						nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTGAATCCACGCCTGCTGTTT	0.443													19	115					2.54575e-18	2.86717e-18	0.010504	1	0	
STK32B	55351	broad.mit.edu	37	4	5468447	5468447	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:5468447C>T	uc003gih.1	+	10	991	c.927C>T	c.(925-927)TGC>TGT	p.C309C	STK32B_uc010ida.1_Silent_p.C262C	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B	309							ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						GGTTGAACTGCGATCCCACAT	0.418													11	39					0	0	0.013537	0	0	
EVC2	132884	broad.mit.edu	37	4	5624508	5624508	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:5624508G>A	uc003gij.2	-	14	2311	c.2257C>T	c.(2257-2259)CGC>TGC	p.R753C	EVC2_uc011bwb.1_Missense_Mutation_p.R193C|EVC2_uc003gik.2_Missense_Mutation_p.R673C	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	753	Potential.					integral to membrane				large_intestine(3)|ovary(2)	5						TTCTGCAGGCGCCGCAGCTCG	0.647													4	33					0	0	0.000602	0	0	
EVC	2121	broad.mit.edu	37	4	5754686	5754686	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:5754686G>A	uc003gil.1	+	9	1406	c.1222G>A	c.(1222-1224)GCT>ACT	p.A408T	EVC_uc003gim.1_RNA|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	408					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)				GGAGCTGCTGGCTGGTGAGGG	0.652													3	9					0	0	0.004672	0	0	
PPP2R2C	5522	broad.mit.edu	37	4	6377649	6377649	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:6377649A>G	uc003gjc.2	-	4	714	c.344T>C	c.(343-345)ATC>ACC	p.I115T	PPP2R2C_uc003gjb.2_Missense_Mutation_p.I98T|PPP2R2C_uc011bwd.1_Missense_Mutation_p.I108T|PPP2R2C_uc011bwe.1_Missense_Mutation_p.I108T|PPP2R2C_uc003gja.2_Missense_Mutation_p.I115T|PPP2R2C_uc003gjd.1_Missense_Mutation_p.I203T	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein	115	WD 2.				signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						CCATAATTTGATAGTTTTATC	0.413													18	57					0	0	0.008871	0	0	
KIAA0232	9778	broad.mit.edu	37	4	6865064	6865064	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:6865064G>A	uc003gjr.3	+	7	3418	c.2955G>A	c.(2953-2955)GGG>GGA	p.G985G	KIAA0232_uc003gjq.3_Silent_p.G985G	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	985							ATP binding			ovary(2)	2						TTGCTCCTGGGCACAGGCAGT	0.438													5	65					0	0	0.000602	0	0	
BOD1L	259282	broad.mit.edu	37	4	13597501	13597501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:13597501C>T	uc003gmz.1	-	12	8204	c.8087G>A	c.(8086-8088)GGA>GAA	p.G2696E		NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	2696							DNA binding			ovary(5)|breast(1)	6						ACTTGGCTTTCCCCCACACAG	0.378													24	168					0	0	0.004656	0	0	
PROM1	8842	broad.mit.edu	37	4	15982050	15982050	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:15982050G>A	uc003goo.2	-	23	2696	c.2484C>T	c.(2482-2484)TAC>TAT	p.Y828Y	PROM1_uc003gor.2_Silent_p.Y828Y|PROM1_uc003gos.2_Silent_p.Y819Y|PROM1_uc003got.2_Silent_p.Y828Y|PROM1_uc003gou.2_Silent_p.Y819Y|PROM1_uc003gop.2_Silent_p.Y819Y|PROM1_uc003goq.3_Silent_p.Y819Y	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1	828	Cytoplasmic (Potential).				camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						CTTACTCATCGTACACGTCCT	0.433													5	29					0	0	0.000602	0	0	
STIM2	57620	broad.mit.edu	37	4	27024459	27024459	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:27024459C>T	uc003gsh.3	+	13	2583	c.2367C>T	c.(2365-2367)CGC>CGT	p.R789R	STIM2_uc003gsg.3_Silent_p.R781R|STIM2_uc010iex.2_3'UTR|STIM2_uc010iey.2_3'UTR	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	694	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				CTAAACCTCGCCACACATCAT	0.483													15	81					0	0	0.003163	0	0	
PCDH7	5099	broad.mit.edu	37	4	30723234	30723234	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:30723234G>A	uc003gsk.1	+	1	1198	c.190G>A	c.(190-192)GTG>ATG	p.V64M	PCDH7_uc011bxw.1_Missense_Mutation_p.V64M|PCDH7_uc011bxx.1_Missense_Mutation_p.V64M	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	64	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						ATCGGGTGAGGTGACTTTCAG	0.662													3	19					0	0	0.009096	0	0	
PCDH7	5099	broad.mit.edu	37	4	30724012	30724012	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:30724012C>T	uc003gsk.1	+	1	1976	c.968C>T	c.(967-969)CCG>CTG	p.P323L	PCDH7_uc011bxw.1_Missense_Mutation_p.P276L|PCDH7_uc011bxx.1_Missense_Mutation_p.P323L	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	323	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						AACAGCGCCCCGGGGACCCCC	0.662													4	11					0	0	0.009096	0	0	
APBB2	323	broad.mit.edu	37	4	41016202	41016202	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:41016202G>A	uc003gvl.2	-	6	863	c.233C>T	c.(232-234)GCC>GTC	p.A78V	APBB2_uc003gvm.2_Missense_Mutation_p.A78V|APBB2_uc003gvn.2_Missense_Mutation_p.A78V|APBB2_uc011byt.1_Missense_Mutation_p.A61V	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,	78					cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						GAGGCCCATGGCCGCCTGGAT	0.502													16	55					0	0	0.003163	0	0	
GABRA4	2557	broad.mit.edu	37	4	46976326	46976326	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:46976326G>A	uc003gxg.2	-	6	783	c.644C>T	c.(643-645)CCG>CTG	p.P215L		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	215	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)	4					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	AGACTCCTTCGGAACTTCAAC	0.393													15	68					0	0	0.004007	0	0	
SCFD2	152579	broad.mit.edu	37	4	54231634	54231634	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:54231634A>C	uc003gzu.2	-	1	609	c.475T>G	c.(475-477)TTG>GTG	p.L159V	SCFD2_uc010igm.2_Missense_Mutation_p.L159V	NM_152540	NP_689753	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	159					protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			GGGGCAAGCAATAACGGGACA	0.572													4	34					0	0	0.009096	0	0	
CENPC1	1060	broad.mit.edu	37	4	68380266	68380266	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:68380266C>T	uc003hdd.1	-	8	1153	c.970G>A	c.(970-972)GCA>ACA	p.A324T	CENPC1_uc010ihj.1_RNA|CENPC1_uc010ihk.1_RNA|CENPC1_uc010ihm.1_Missense_Mutation_p.A324T	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1	324					mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						AGAGACCCTGCCTTTCTTGGT	0.413													4	16					0	0	0.009096	0	0	
CSN3	1448	broad.mit.edu	37	4	71114881	71114881	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:71114881C>T	uc003hfe.3	+	4	312	c.254C>T	c.(253-255)GCT>GTT	p.A85V		NM_005212	NP_005203	P07498	CASK_HUMAN	casein kappa precursor	85						extracellular region	protein binding			ovary(2)|kidney(1)|central_nervous_system(1)	4						GCAAACCCAGCTGTAGTTAGG	0.448													11	50					0	0	0.008291	0	0	
PPEF2	5470	broad.mit.edu	37	4	76787346	76787346	+	Missense_Mutation	SNP	C	T	T	rs138384094	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:76787346C>T	uc003hix.2	-	15	2273	c.1916G>A	c.(1915-1917)CGC>CAC	p.R639H	PPEF2_uc003hiy.2_RNA|PPEF2_uc003hiz.1_3'UTR	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	639					detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CGTTACCTCGCGACTCAGTTG	0.478													26	107					0	0	0.010818	0	0	
FRAS1	80144	broad.mit.edu	37	4	79437097	79437097	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:79437097C>A	uc003hlb.2	+	66	10759	c.10319C>A	c.(10318-10320)ACC>AAC	p.T3440N		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3435	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						TGCGTGTGGACCTTTGATGCT	0.572													10	42					6.40141e-05	6.83769e-05	0.010729	1	0	
ARHGAP24	83478	broad.mit.edu	37	4	86898809	86898809	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:86898809G>A	uc003hpk.2	+	8	1342	c.893G>A	c.(892-894)CGC>CAC	p.R298H	ARHGAP24_uc003hpl.2_Missense_Mutation_p.R203H|ARHGAP24_uc010ikf.2_Missense_Mutation_p.R213H|ARHGAP24_uc003hpm.2_Missense_Mutation_p.R205H	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1	298	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AATATCCTGCGCCCCAAAGTG	0.403													10	57					0	0	0.006214	0	0	
SPP1	6696	broad.mit.edu	37	4	88903760	88903760	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:88903760C>T	uc003hra.2	+	7	822	c.657C>T	c.(655-657)AGC>AGT	p.S219S	SPP1_uc003hrb.2_Silent_p.S192S|SPP1_uc003hrc.2_Silent_p.S205S|SPP1_uc011cde.1_Silent_p.S232S|SPP1_uc003hrd.2_Silent_p.S178S	NM_001040058	NP_001035147	P10451	OSTP_HUMAN	secreted phosphoprotein 1 isoform a	219					biomineral tissue development|cell adhesion|decidualization|embryo implantation|ossification|response to vitamin D	extracellular space	cytokine activity			ovary(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		ATTGGGACAGCCGTGGGAAGG	0.527													16	101					0	0	0.006122	0	0	
RAP1GDS1	5910	broad.mit.edu	37	4	99313170	99313170	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:99313170C>T	uc003htx.3	+	6	766	c.576C>T	c.(574-576)CAC>CAT	p.H192H	RAP1GDS1_uc003htu.2_Silent_p.H192H|RAP1GDS1_uc003htw.3_Silent_p.H193H|RAP1GDS1_uc003htv.3_Silent_p.H193H|RAP1GDS1_uc003htz.3_Silent_p.H143H|RAP1GDS1_uc003hty.3_Silent_p.H144H|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1 isoform	192	ARM 2.						binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		TGGGCATCCACTGCCAAAATG	0.343			T	NUP98	T-ALL								7	46					0	0	0.001984	0	0	
TET2	54790	broad.mit.edu	37	4	106157341	106157341	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:106157341T>A	uc003hxk.2	+	3	2628	c.2242T>A	c.(2242-2244)TTA>ATA	p.L748I	TET2_uc011cez.1_Missense_Mutation_p.L769I|TET2_uc003hxj.2_RNA|TET2_uc010ilp.1_Missense_Mutation_p.L748I|TET2_uc003hxi.1_Missense_Mutation_p.L748I	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a	748	Gln-rich.				cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GCAGCAAAAATTACAAATAAA	0.408			Mis N|F		MDS								18	66					0	0	0.007413	0	0	
SYNPO2	171024	broad.mit.edu	37	4	119952870	119952870	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:119952870A>G	uc003icm.3	+	4	3136	c.2940A>G	c.(2938-2940)CAA>CAG	p.Q980Q	SYNPO2_uc010ina.2_Silent_p.Q980Q|SYNPO2_uc010inb.2_Silent_p.Q980Q|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Silent_p.Q908Q	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b	980						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2						TTACTTTCCAACCTCCAGATG	0.498													19	62					0	0	0.008871	0	0	
MAD2L1	4085	broad.mit.edu	37	4	120983144	120983144	+	Silent	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:120983144A>C	uc003idl.2	-	3	451	c.327T>G	c.(325-327)ACT>ACG	p.T109T	MAD2L1_uc003idm.2_Intron	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1	109	HORMA.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0						CATCTTTTGCAGTCTTGTCAC	0.299													6	37					0	0	0.001984	0	0	
BBS7	55212	broad.mit.edu	37	4	122770069	122770069	+	Silent	SNP	G	A	A	rs142376157		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:122770069G>A	uc003ied.2	-	9	1038	c.864C>T	c.(862-864)AGC>AGT	p.S288S	BBS7_uc003iee.1_Silent_p.S288S	NM_176824	NP_789794	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein isoform a	288					cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|centrosome|cilium membrane	protein binding			ovary(1)	1						TAGATGTGACGCTTTCAGACA	0.358									Bardet-Biedl_syndrome				12	78					0	0	0.002450	0	0	
SPRY1	10252	broad.mit.edu	37	4	124323363	124323363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:124323363G>A	uc003ifa.2	+	2	805	c.617G>A	c.(616-618)CGG>CAG	p.R206Q	SPRY1_uc003ifb.2_Missense_Mutation_p.R206Q	NM_199327	NP_955359	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling	206	Cys-rich.|SPR.				epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|lamellipodium|plasma membrane				skin(2)|ovary(1)	3						GCCTGTAACCGGCAGTGCCTT	0.522													17	74					0	0	0.004007	0	0	
FAT4	79633	broad.mit.edu	37	4	126370353	126370353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:126370353G>A	uc003ifj.3	+	9	8182	c.8182G>A	c.(8182-8184)GTT>ATT	p.V2728I	FAT4_uc011cgp.1_Missense_Mutation_p.V1026I|FAT4_uc003ifi.1_Missense_Mutation_p.V206I	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	2728	Cadherin 26.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						AATTAGAAGCGTTAGACCTTT	0.383													18	89					0	0	0.006122	0	0	
FAT4	79633	broad.mit.edu	37	4	126398366	126398366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:126398366C>T	uc003ifj.3	+	13	12350	c.12350C>T	c.(12349-12351)CCA>CTA	p.P4117L	FAT4_uc011cgp.1_Missense_Mutation_p.P2380L|FAT4_uc003ifi.1_Missense_Mutation_p.P1595L	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4117	Laminin G-like 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						TCTCTAGAACCAATCCTTCAG	0.393													25	196					0	0	0.007291	0	0	
FAT4	79633	broad.mit.edu	37	4	126411789	126411789	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:126411789C>T	uc003ifj.3	+	17	13812	c.13812C>T	c.(13810-13812)ACC>ACT	p.T4604T	FAT4_uc011cgp.1_Silent_p.T2845T|FAT4_uc003ifi.1_Silent_p.T2081T	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4604	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						ACTCAGAAACCATCCCCAGCG	0.488													9	71					0	0	0.010729	0	0	
PCDH10	57575	broad.mit.edu	37	4	134071537	134071537	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:134071537G>A	uc003iha.2	+	1	1068	c.242G>A	c.(241-243)CGC>CAC	p.R81H	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.R81H	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	81	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		AAAATAGACCGCGAACAAATC	0.567													14	113					0	0	0.003163	0	0	
PCDH10	57575	broad.mit.edu	37	4	134072675	134072675	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:134072675G>A	uc003iha.2	+	1	2206	c.1380G>A	c.(1378-1380)GCG>GCA	p.A460A	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Silent_p.A460A	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	460	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		ACGACAACGCGCCGCGTTTCA	0.617													7	42					0	0	0.004482	0	0	
LRBA	987	broad.mit.edu	37	4	151773292	151773292	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:151773292C>T	uc010ipj.2	-	23	4044	c.3570G>A	c.(3568-3570)ATG>ATA	p.M1190I	LRBA_uc003ilt.3_5'Flank|LRBA_uc003ilu.3_Missense_Mutation_p.M1190I	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1190						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TTTCTGGTGACATAGCTGAAG	0.403													17	74					0	0	0.004990	0	0	
FBXW7	55294	broad.mit.edu	37	4	153271192	153271192	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:153271192A>G	uc003ims.2	-	3	733	c.584_splice	c.e3+1	p.S195_splice	FBXW7_uc011cii.1_Splice_Site_p.S195_splice|FBXW7_uc003imt.2_Splice_Site_p.S195_splice|FBXW7_uc011cih.1_5'Flank|FBXW7_uc003imq.2_Splice_Site_p.S115_splice|FBXW7_uc003imr.2_Splice_Site_p.S77_splice	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATTTAATATTACCTTGTATAT	0.303			Mis|N|D|F		colorectal|endometrial|T-ALL								4	8					0	0	0.009096	0	0	
FHDC1	85462	broad.mit.edu	37	4	153897150	153897150	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:153897150C>T	uc003inf.2	+	11	2782	c.2707C>T	c.(2707-2709)CGC>TGC	p.R903C		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	903					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)					CGAGAGCATGCGCAAGGTCAT	0.701													7	23					0	0	0.001984	0	0	
TRIM2	23321	broad.mit.edu	37	4	154243896	154243896	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:154243896T>C	uc003ing.2	+	9	1999	c.1798T>C	c.(1798-1800)TTT>CTT	p.F600L	TRIM2_uc003inh.2_Missense_Mutation_p.F627L	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2	600	NHL 3.					cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		GTGCTGCGTGTTTATCTTCCA	0.483													12	50					0	0	0.013537	0	0	
DCHS2	54798	broad.mit.edu	37	4	155253791	155253791	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:155253791G>A	uc003inw.2	-	9	2072	c.2072C>T	c.(2071-2073)ACC>ATC	p.T691I	DCHS2_uc003inx.2_Missense_Mutation_p.T1190I	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	691	Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ATGCAAGAAGGTGGGGGAATT	0.438													6	129					0	0	0.001168	0	0	
MAP9	79884	broad.mit.edu	37	4	156289916	156289916	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:156289916C>T	uc003ios.2	-	5	794	c.530G>A	c.(529-531)CGG>CAG	p.R177Q	MAP9_uc011cin.1_Missense_Mutation_p.R176Q|MAP9_uc010iqa.1_RNA|MAP9_uc003iot.1_Missense_Mutation_p.R176Q|MAP9_uc010iqb.1_Missense_Mutation_p.R104Q	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein	177					cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		ACTCCTTGGCCGAGGTGATGG	0.378													9	58					0	0	0.010729	0	0	
GLRB	2743	broad.mit.edu	37	4	158074033	158074033	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:158074033C>G	uc003ipj.2	+	9	1270	c.1068C>G	c.(1066-1068)AAC>AAG	p.N356K		NM_000824	NP_000815	P48167	GLRB_HUMAN	glycine receptor, beta isoform A precursor	356	Cytoplasmic (Probable).				nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)	TGCTGAACAACCCCAAAAGGG	0.448													10	65					0	0	0.006214	0	0	
FAM198B	51313	broad.mit.edu	37	4	159092395	159092395	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:159092395C>T	uc003ipp.3	-	2	585	c.133G>A	c.(133-135)GCC>ACC	p.A45T	uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Missense_Mutation_p.A45T|FAM198B_uc003ipr.3_Missense_Mutation_p.A45T|FAM198B_uc003ips.2_Missense_Mutation_p.A45T|uc003ipt.1_RNA	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	45	Helical; Signal-anchor for type II membrane protein; (Potential).					Golgi membrane|integral to membrane					0						AAGTAGATGGCACACGCAGTG	0.652													9	21					0	0	0.010729	0	0	
KLHL2	11275	broad.mit.edu	37	4	166215608	166215608	+	Silent	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:166215608T>G	uc003irb.2	+	6	901	c.642T>G	c.(640-642)TCT>TCG	p.S214S	KLHL2_uc011cjm.1_Silent_p.S218S|KLHL2_uc003irc.2_Silent_p.S126S|KLHL2_uc010ira.2_5'UTR	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	214					intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		TTACCATTTCTTCAGAAGAGA	0.338													7	39					0	0	0.001984	0	0	
DDX60	55601	broad.mit.edu	37	4	169194431	169194431	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:169194431T>C	uc003irp.2	-	18	2865	c.2573A>G	c.(2572-2574)CAG>CGG	p.Q858R		NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	858	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		ATACCCTACCTGACAGTTTAA	0.363													8	61					0	0	0.004482	0	0	
KIAA1712	80817	broad.mit.edu	37	4	175231102	175231102	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:175231102T>C	uc003itr.2	+	8	1194	c.780T>C	c.(778-780)TGT>TGC	p.C260C	KIAA1712_uc010iro.2_Silent_p.C260C|KIAA1712_uc003its.2_RNA	NM_001040157	NP_001035247	Q9C0F1	CEP44_HUMAN	HBV PreS1-transactivated protein 3 isoform a	260	Potential.					centrosome|midbody|spindle pole					0		Prostate(90;0.00276)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;4.06e-18)|Epithelial(43;1.18e-15)|OV - Ovarian serous cystadenocarcinoma(60;4.65e-09)|GBM - Glioblastoma multiforme(59;0.00098)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0949)		GGTTAGACTGTTTGGAACAAA	0.348													20	41					0	0	0.012319	0	0	
GLRA3	8001	broad.mit.edu	37	4	175598374	175598374	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:175598374T>C	uc003ity.1	-	7	1285	c.782A>G	c.(781-783)TAC>TGC	p.Y261C	GLRA3_uc003itz.1_Missense_Mutation_p.Y261C	NM_006529	NP_006520	O75311	GLRA3_HUMAN	glycine receptor, alpha 3 isoform a	261	Helical; (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(3)	3		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)	ACTGGGAATGTACATCTGGAT	0.443													9	50					0	0	0.006214	0	0	
ASB5	140458	broad.mit.edu	37	4	177142368	177142368	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:177142368G>A	uc003iuq.1	-	5	624	c.608C>T	c.(607-609)ACT>ATT	p.T203I	ASB5_uc003iup.1_Missense_Mutation_p.T150I	NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	203	ANK 5.				intracellular signal transduction					skin(2)	2		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		ATAGAGAGGAGTTCCCAAATG	0.408													17	67					0	0	0.004990	0	0	
VEGFC	7424	broad.mit.edu	37	4	177648991	177648991	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:177648991A>G	uc003ius.1	-	3	923	c.493T>C	c.(493-495)TGC>CGC	p.C165R		NM_005429	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	165					angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(5)	5		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		CTATTGCAGCAACCCCCACAT	0.547													12	78					0	0	0.010729	0	0	
CDKN2AIP	55602	broad.mit.edu	37	4	184368553	184368553	+	Silent	SNP	A	G	G	rs143559678		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:184368553A>G	uc003ivp.1	+	3	1878	c.1716A>G	c.(1714-1716)GCA>GCG	p.A572A	CDKN2AIP_uc003ivq.1_Silent_p.A317A	NM_017632	NP_060102	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein	572					negative regulation of cell growth|positive regulation of signal transduction|regulation of protein stability	granular component|nucleoplasm	double-stranded RNA binding|p53 binding				0		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		TACCTCCAGCACTAAAACATC	0.338													35	212					0	0	0.005524	0	0	
C4orf41	60684	broad.mit.edu	37	4	184585026	184585026	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:184585026C>T	uc003ivx.2	+	2	182	c.6C>T	c.(4-6)AGC>AGT	p.S2S	C4orf41_uc003ivw.2_Silent_p.S2S|C4orf41_uc010isc.2_5'UTR	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	2											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)		TAAACATGAGCCCCACACAGT	0.348													11	50					0	0	0.013537	0	0	
CCDC111	201973	broad.mit.edu	37	4	185593391	185593391	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:185593391C>T	uc003iwk.2	+	7	1054	c.621C>T	c.(619-621)AGC>AGT	p.S207S	CCDC111_uc010isd.1_RNA|CCDC111_uc003iwj.2_Silent_p.S207S|CCDC111_uc003iwl.2_Silent_p.S207S|CCDC111_uc003iwm.2_Silent_p.S78S|CCDC111_uc003iwn.2_Silent_p.S32S	NM_152683	NP_689896	Q96LW4	CC111_HUMAN	coiled-coil domain containing 111	207					DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)		ATGATGATAGCGCTCCAGAGA	0.398													6	121					0	0	0.001984	0	0	
CCDC110	256309	broad.mit.edu	37	4	186381064	186381064	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:186381064G>T	uc003ixu.3	-	6	753	c.677C>A	c.(676-678)ACT>AAT	p.T226N	CCDC110_uc003ixv.3_Missense_Mutation_p.T189N|CCDC110_uc011ckt.1_Missense_Mutation_p.T226N	NM_152775	NP_689988	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110 isoform a	226						nucleus				central_nervous_system(1)	1		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		AAAAGGCACAGTAATTTTGGA	0.333													5	63					0.000602214	0.000636366	0.000602	1	0	
F11	2160	broad.mit.edu	37	4	187195296	187195296	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr4:187195296C>A	uc003iza.1	+	5	685	c.352C>A	c.(352-354)CTA>ATA	p.L118I	F11_uc003iyz.2_Missense_Mutation_p.L118I	NM_000128	NP_000119	P03951	FA11_HUMAN	coagulation factor XI precursor	118	Apple 2.				blood coagulation, intrinsic pathway|plasminogen activation|positive regulation of fibrinolysis	extracellular space|plasma membrane	heparin binding|serine-type endopeptidase activity				0		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	TTATGTGGACCTAGACATGAA	0.448													10	84					0.000673444	0.00071074	0.008291	1	0	
FAM173B	134145	broad.mit.edu	37	5	10239183	10239183	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:10239183C>T	uc003jeo.2	-	2	331	c.302G>A	c.(301-303)CGC>CAC	p.R101H	FAM173B_uc003jep.2_RNA|FAM173B_uc010itr.2_Missense_Mutation_p.R101H	NM_199133	NP_954584	Q6P4H8	F173B_HUMAN	hypothetical protein LOC134145	101						integral to membrane				kidney(1)|central_nervous_system(1)	2						ACTCACAATGCGTCCGTCCCC	0.398													22	75					0	0	0.004656	0	0	
DNAH5	1767	broad.mit.edu	37	5	13845019	13845019	+	Missense_Mutation	SNP	G	A	A	rs146087064		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:13845019G>A	uc003jfd.2	-	32	5240	c.5198C>T	c.(5197-5199)TCG>TTG	p.S1733L		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1733	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					GTGGGAGTCCGACGCCTGCCC	0.463									Kartagener_syndrome				11	63					0	0	0.001855	0	0	
MYO10	4651	broad.mit.edu	37	5	16699619	16699619	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:16699619G>A	uc003jft.3	-	26	3964	c.3496C>T	c.(3496-3498)CGT>TGT	p.R1166C	MYO10_uc011cnc.1_Missense_Mutation_p.R45C|MYO10_uc011cnd.1_Missense_Mutation_p.R523C|MYO10_uc011cne.1_Missense_Mutation_p.R523C|MYO10_uc010itx.2_Missense_Mutation_p.R789C	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1166					axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						ACAGAGTCACGCCGGTATGAA	0.493													15	50					0	0	0.004007	0	0	
MYO10	4651	broad.mit.edu	37	5	16764481	16764481	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:16764481C>T	uc003jft.3	-	12	1672	c.1204G>A	c.(1204-1206)GCC>ACC	p.A402T	MYO10_uc010itx.2_Missense_Mutation_p.A25T	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	402	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						AGAGCCATGGCCAGGGAGTCC	0.547													20	67					0	0	0.008871	0	0	
RNASEN	29102	broad.mit.edu	37	5	31515179	31515179	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:31515179C>T	uc003jhg.2	-	7	1565	c.1206G>A	c.(1204-1206)GAG>GAA	p.E402E	RNASEN_uc003jhh.2_Silent_p.E365E|RNASEN_uc003jhi.2_Silent_p.E365E|RNASEN_uc010iui.1_Silent_p.E325E	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	402					gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						CTTCTTCTTCCTCCTCATTCT	0.468													29	92					0	0	0.013726	0	0	
PDZD2	23037	broad.mit.edu	37	5	32069705	32069705	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:32069705G>A	uc003jhl.2	+	15	2870	c.2482G>A	c.(2482-2484)GCA>ACA	p.A828T	PDZD2_uc003jhm.2_Missense_Mutation_p.A828T|PDZD2_uc011cnx.1_Missense_Mutation_p.A654T	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	828					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						TGAAGTCATAGCACGCAGCAC	0.388													14	62					0	0	0.002450	0	0	
PDZD2	23037	broad.mit.edu	37	5	32088835	32088835	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:32088835A>G	uc003jhl.2	+	20	5669	c.5281A>G	c.(5281-5283)AGT>GGT	p.S1761G	PDZD2_uc003jhm.2_Missense_Mutation_p.S1761G	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1761					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						GTCCTCCTTCAGTGTGGATGT	0.448													12	42					0	0	0.003163	0	0	
ADAMTS12	81792	broad.mit.edu	37	5	33576232	33576232	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:33576232A>G	uc003jia.1	-	19	4062	c.3899T>C	c.(3898-3900)CTA>CCA	p.L1300P	ADAMTS12_uc010iuq.1_Missense_Mutation_p.L1215P	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1300	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						GGAGGCATTTAGCAAAAAGCC	0.488										HNSCC(64;0.19)			30	116					0	0	0.009535	0	0	
NIPBL	25836	broad.mit.edu	37	5	36976272	36976272	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:36976272G>A	uc003jkl.3	+	9	1762	c.1263G>A	c.(1261-1263)TCG>TCA	p.S421S	NIPBL_uc003jkk.3_Silent_p.S421S|NIPBL_uc003jkm.1_Silent_p.S300S	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	421	Gln-rich.				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AATGTTTGTCGCAGCAAGAAC	0.423													15	79					0	0	0.002450	0	0	
NIPBL	25836	broad.mit.edu	37	5	37022373	37022373	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:37022373C>T	uc003jkl.3	+	29	5954	c.5455C>T	c.(5455-5457)CGA>TGA	p.R1819*	NIPBL_uc003jkk.3_Nonsense_Mutation_p.R1819*	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1819					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TGTTCATGGACGATTGATGGA	0.358													7	35					0	0	0.006214	0	0	
LIFR	3977	broad.mit.edu	37	5	38506042	38506042	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:38506042G>A	uc010ive.1	-	9	1588	c.1256C>T	c.(1255-1257)TCA>TTA	p.S419L	LIFR_uc003jli.2_Missense_Mutation_p.S419L	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	419	Fibronectin type-III 2.|Extracellular (Potential).				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)					TGTTGATTGTGATCGACCCAG	0.284			T	PLAG1	salivary adenoma								14	98					0	0	0.004007	0	0	
PLCXD3	345557	broad.mit.edu	37	5	41382224	41382224	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:41382224T>C	uc003jmm.1	-	2	618	c.516A>G	c.(514-516)CCA>CCG	p.P172P		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	172	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						CAAAAATCGCTGGGCACATTT	0.428													22	105					0	0	0.014323	0	0	
ARL15	54622	broad.mit.edu	37	5	53409092	53409092	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:53409092A>G	uc003jpg.1	-	4	496	c.402T>C	c.(400-402)ACT>ACC	p.T134T	ARL15_uc010ivs.1_RNA	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	134							GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				AAAAGGGTAAAGTGCATAACT	0.423													11	41					0	0	0.013537	0	0	
MAP3K1	4214	broad.mit.edu	37	5	56177584	56177584	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:56177584C>T	uc003jqw.3	+	14	3058	c.2557C>T	c.(2557-2559)CGT>TGT	p.R853C		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	853					cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CACCAGGATGCGTCGCCGTTT	0.468													15	70					0	0	0.004990	0	0	
ADAMTS6	11174	broad.mit.edu	37	5	64537967	64537967	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:64537967G>A	uc003jtp.2	-	15	2711	c.1897C>T	c.(1897-1899)CGA>TGA	p.R633*	ADAMTS6_uc003jto.2_RNA|ADAMTS6_uc003jtq.2_RNA|ADAMTS6_uc003jtr.1_Nonsense_Mutation_p.R254*	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	633					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		TACTTTCCTCGGAAAGGCATA	0.368													12	51					0	0	0.002450	0	0	
ADAMTS6	11174	broad.mit.edu	37	5	64556430	64556430	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:64556430T>C	uc003jtp.2	-	14	2641	c.1827A>G	c.(1825-1827)ACA>ACG	p.T609T	ADAMTS6_uc003jto.2_RNA|ADAMTS6_uc003jtq.2_RNA|ADAMTS6_uc003jtr.1_Silent_p.T230T	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	609	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		TACTTACATCTGTGTTACAGG	0.264													8	33					0	0	0.004482	0	0	
BDP1	55814	broad.mit.edu	37	5	70840949	70840949	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:70840949C>T	uc003kbp.1	+	32	6910	c.6647C>T	c.(6646-6648)ACA>ATA	p.T2216I	BDP1_uc003kbo.2_Missense_Mutation_p.T2216I|BDP1_uc003kbq.1_RNA|BDP1_uc003kbr.1_RNA	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	2216					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		GGGCCCTGCACACTTGGTTTG	0.473													20	90					0	0	0.010504	0	0	
MAP1B	4131	broad.mit.edu	37	5	71495820	71495820	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:71495820G>A	uc003kbw.3	+	5	6879	c.6638G>A	c.(6637-6639)CGC>CAC	p.R2213H	MAP1B_uc010iyw.1_Missense_Mutation_p.R2230H|MAP1B_uc010iyx.1_Missense_Mutation_p.R2087H|MAP1B_uc010iyy.1_Missense_Mutation_p.R2087H	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2213						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CCTTCGCCACGCCACCCTGAT	0.537													27	133					0	0	0.009535	0	0	
HMGCR	3156	broad.mit.edu	37	5	74655088	74655088	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:74655088G>A	uc003kdp.2	+	17	2407	c.2251G>A	c.(2251-2253)GCC>ACC	p.A751T	HMGCR_uc011cst.1_Missense_Mutation_p.A771T|HMGCR_uc003kdq.2_Missense_Mutation_p.A698T|HMGCR_uc010izo.2_Missense_Mutation_p.A74T|HMGCR_uc010izp.2_Intron	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	751	Catalytic.				cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	AGGCTACAACGCCCATGCAGC	0.468													10	49					0	0	0.013537	0	0	
SV2C	22987	broad.mit.edu	37	5	75596664	75596664	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:75596664T>A	uc003kei.1	+	11	1881	c.1747T>A	c.(1747-1749)TAT>AAT	p.Y583N		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	583	Helical; (Potential).				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CTACTGGATTTATTTTGTCAA	0.393													20	104					0	0	0.014323	0	0	
WDR41	55255	broad.mit.edu	37	5	76788019	76788019	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:76788019G>A	uc003kff.1	-	1	314	c.27C>T	c.(25-27)GGC>GGT	p.G9G	WDR41_uc011csy.1_Silent_p.G9G|WDR41_uc011csz.1_Silent_p.G9G|WDR41_uc011cta.1_RNA|WDR41_uc011ctb.1_RNA	NM_018268	NP_060738	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	9											0		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		GCGGTTCTCGGCCTCCCCCGA	0.697													8	29					0	0	0.004482	0	0	
BHMT2	23743	broad.mit.edu	37	5	78379171	78379171	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:78379171T>C	uc003kft.2	+	6	778	c.755T>C	c.(754-756)TTT>TCT	p.F252S	BHMT2_uc011cth.1_Missense_Mutation_p.F188S	NM_017614	NP_060084	Q9H2M3	BHMT2_HUMAN	betaine-homocysteine methyltransferase 2	252	Hcy-binding.				methionine biosynthetic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	AAAGAGGGGTTTGTGGATCTC	0.512													10	35					0	0	0.013537	0	0	
JMY	133746	broad.mit.edu	37	5	78596523	78596523	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:78596523A>G	uc003kfx.3	+	6	2238	c.1718A>G	c.(1717-1719)TAT>TGT	p.Y573C	JMY_uc003kfw.1_Missense_Mutation_p.Y219C	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein	573					'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		GTGGTATACTATGACACTTAC	0.289													10	44					0	0	0.013537	0	0	
RPS23	6228	broad.mit.edu	37	5	81573573	81573573	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:81573573C>T	uc003khu.2	-	2	196	c.103G>A	c.(103-105)GCC>ACC	p.A35T	ATP6AP1L_uc003khv.2_5'Flank	NM_001025	NP_001016	P62266	RS23_HUMAN	ribosomal protein S23	35					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)		GCCTTTAGGGCTGTGCCCAAA	0.463													23	130					0	0	0.012319	0	0	
VCAN	1462	broad.mit.edu	37	5	82833950	82833950	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:82833950G>A	uc003kii.3	+	8	5484	c.5128G>A	c.(5128-5130)GAC>AAC	p.D1710N	VCAN_uc003kij.3_Missense_Mutation_p.D723N|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.D374N	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1710	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		AAGTGAAACAGACACTTCTGA	0.423													14	88					0	0	0.001855	0	0	
EDIL3	10085	broad.mit.edu	37	5	83402507	83402507	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:83402507G>A	uc003kio.1	-	6	1030	c.611C>T	c.(610-612)GCG>GTG	p.A204V	EDIL3_uc003kip.1_Missense_Mutation_p.A194V	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	204	F5/8 type C 1.				cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		AGCTGTCCACGCATTTATAAG	0.418													18	125					0	0	0.007413	0	0	
NR2F1	7025	broad.mit.edu	37	5	92923897	92923897	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:92923897C>T	uc003kkj.2	+	2	2425	c.738C>T	c.(736-738)ACC>ACT	p.T246T		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	246					negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			urinary_tract(1)|ovary(1)|lung(1)	3		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		TGCAGATCACCGACCAGGTGT	0.662													7	45					0	0	0.003080	0	0	
SPATA9	83890	broad.mit.edu	37	5	95011143	95011143	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:95011143C>T	uc003klj.1	-	3	507	c.351G>A	c.(349-351)GCG>GCA	p.A117A	SPATA9_uc010jbh.1_RNA|SPATA9_uc003klh.1_RNA|SPATA9_uc003kli.1_Intron	NM_031952	NP_114158	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	117					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane					0		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		GTTGCCTCGGCGCATTAACTT	0.408													8	37					0	0	0.008291	0	0	
ST8SIA4	7903	broad.mit.edu	37	5	100222222	100222222	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:100222222A>G	uc003knk.2	-	3	656	c.328T>C	c.(328-330)TAT>CAT	p.Y110H	ST8SIA4_uc003knl.2_Missense_Mutation_p.Y110H	NM_005668	NP_005659	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide	110	Lumenal (Potential).				axon guidance|N-glycan processing	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			large_intestine(1)|central_nervous_system(1)	2		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		TCAAGCACATAGTGTATGACA	0.428													15	79					0	0	0.002450	0	0	
NUDT12	83594	broad.mit.edu	37	5	102890483	102890483	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:102890483G>A	uc003koi.2	-	5	1129	c.1036C>T	c.(1036-1038)CCC>TCC	p.P346S	NUDT12_uc011cvb.1_Missense_Mutation_p.P328S	NM_031438	NP_113626	Q9BQG2	NUD12_HUMAN	nudix-type motif 12	346	Nudix hydrolase.					nucleus|peroxisome	metal ion binding|NAD+ diphosphatase activity				0		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		ATGCCTGGGGGAAATCTTTTC	0.328													12	62					0	0	0.001855	0	0	
FAM170A	340069	broad.mit.edu	37	5	118965518	118965518	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:118965518G>A	uc003ksm.2	+	1	265	c.55G>A	c.(55-57)GCT>ACT	p.A19T	FAM170A_uc003ksl.2_Missense_Mutation_p.A19T|FAM170A_uc003ksn.2_Missense_Mutation_p.A19T|FAM170A_uc003kso.2_Missense_Mutation_p.A19T	NM_182761	NP_877438	A1A519	F170A_HUMAN	family with sequence similarity 170, member A	19						intracellular	zinc ion binding			skin(1)	1						CCAGGAAACCGCTGAGAAGGG	0.433													25	144					0	0	0.006320	0	0	
ZNF608	57507	broad.mit.edu	37	5	124036739	124036739	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:124036739A>G	uc003ktq.1	-	2	1253	c.1130T>C	c.(1129-1131)TTG>TCG	p.L377S	ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Missense_Mutation_p.L377S|ZNF608_uc003ktt.1_Missense_Mutation_p.L377S	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	377						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		GATCCCTTCCAAATTCACACT	0.448													11	87					0	0	0.010729	0	0	
GRAMD3	65983	broad.mit.edu	37	5	125824495	125824495	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:125824495G>A	uc003ktu.2	+	13	1598	c.1168G>A	c.(1168-1170)GCA>ACA	p.A390T	GRAMD3_uc011cwt.1_Missense_Mutation_p.A405T|GRAMD3_uc011cwv.1_Missense_Mutation_p.A398T|GRAMD3_uc011cww.1_Missense_Mutation_p.A286T|GRAMD3_uc011cwx.1_RNA|GRAMD3_uc011cwy.1_Missense_Mutation_p.A281T|GRAMD3_uc011cwz.1_Missense_Mutation_p.A374T	NM_023927	NP_076416	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3 isoform 2	390										central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TTACAGACAGGCAGCACCATC	0.363													11	25					0	0	0.008291	0	0	
MEGF10	84466	broad.mit.edu	37	5	126781226	126781226	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:126781226G>A	uc003kuh.3	+	21	2931	c.2569G>A	c.(2569-2571)GGG>AGG	p.G857R	MEGF10_uc003kui.3_Missense_Mutation_p.G857R	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	857	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		CTACCAGATCGGGGCCATTGC	0.433													17	66					0	0	0.004007	0	0	
ADAMTS19	171019	broad.mit.edu	37	5	128983558	128983558	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:128983558G>A	uc003kvb.1	+	12	1955	c.1955G>A	c.(1954-1956)GGG>GAG	p.G652E	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	652	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TGCAGTGCTGGGATCAGCAGT	0.517													9	116					0	0	0.004482	0	0	
RAPGEF6	51735	broad.mit.edu	37	5	130846113	130846113	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:130846113G>A	uc003kvn.1	-	8	905	c.699C>T	c.(697-699)GAC>GAT	p.D233D	RAPGEF6_uc003kvp.1_Silent_p.D283D|RAPGEF6_uc003kvo.1_Silent_p.D233D|RAPGEF6_uc010jdi.1_Silent_p.D233D|RAPGEF6_uc010jdj.1_Silent_p.D233D|RAPGEF6_uc003kvq.2_5'Flank|RAPGEF6_uc003kvr.2_Silent_p.D233D|RAPGEF6_uc011cxe.1_RNA|RAPGEF6_uc010jdk.2_Silent_p.D233D	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	233					Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CTTCCTCTTCGTCATCCTCAG	0.433													11	60					0	0	0.008291	0	0	
PPP2CA	5515	broad.mit.edu	37	5	133536739	133536739	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:133536739C>T	uc003kze.2	-	4	911	c.513G>A	c.(511-513)TCG>TCA	p.S171S		NM_002715	NP_002706	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha	171					ceramide metabolic process|inactivation of MAPK activity|induction of apoptosis|meiosis|negative regulation of cell growth|negative regulation of epithelial to mesenchymal transition|negative regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of protein serine/threonine kinase activity|protein dephosphorylation|regulation of cell adhesion|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction|spindle pole	metal ion binding|phosphoprotein phosphatase activity			ovary(2)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	CTATAGATGGCGAGAGACCAC	0.323													11	73					0	0	0.003163	0	0	
LECT2	3950	broad.mit.edu	37	5	135283098	135283098	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:135283098C>T	uc003lbe.1	-	4	579	c.378G>A	c.(376-378)TTG>TTA	p.L126L	FBXL21_uc003lbc.2_Intron	NM_002302	NP_002293	O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2 precursor	126					chemotaxis|skeletal system development	cytoplasm|extracellular space				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AAACTTTCTGCAAGGGCAATA	0.383													19	63					0	0	0.008871	0	0	
KLHL3	26249	broad.mit.edu	37	5	136964110	136964110	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:136964110G>A	uc010jek.2	-	13	1911	c.1467C>T	c.(1465-1467)AGC>AGT	p.S489S	KLHL3_uc011cyc.1_Silent_p.S224S|KLHL3_uc003lbr.3_Silent_p.S407S|KLHL3_uc011cyd.1_RNA	NM_017415	NP_059111	Q9UH77	KLHL3_HUMAN	kelch-like 3	489	Kelch 4.					cytoplasm|cytoskeleton	actin binding|structural molecule activity				0		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		ACAGCTGTCCGCTAAGCACTC	0.448													38	105					0	0	0.008740	0	0	
SLC23A1	9963	broad.mit.edu	37	5	138715412	138715412	+	Missense_Mutation	SNP	C	T	T	rs151281788	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:138715412C>T	uc003leh.2	-	8	977	c.880G>A	c.(880-882)GGT>AGT	p.G294S	SLC23A1_uc003leg.2_Missense_Mutation_p.G298S	NM_005847	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (nucleobase	294					brain development|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|response to toxin|transepithelial L-ascorbic acid transport|water-soluble vitamin metabolic process	apical plasma membrane|cytoplasm|integral to plasma membrane|intracellular organelle|membrane fraction	dehydroascorbic acid transporter activity|L-ascorbate:sodium symporter activity|nucleobase transmembrane transporter activity|protein binding|sodium-dependent L-ascorbate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	ATGATGTCACCACGGGCATCG	0.592													8	22					0	0	0.003080	0	0	
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139887448	139887448	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:139887448C>T	uc003lfs.1	+	20	3754	c.3630C>T	c.(3628-3630)CTC>CTT	p.L1210L	ANKHD1_uc003lfq.1_Silent_p.L1229L|ANKHD1_uc003lfr.2_Silent_p.L1210L|ANKHD1_uc003lft.1_Silent_p.L421L|ANKHD1_uc003lfu.1_Silent_p.L690L|ANKHD1_uc003lfv.1_Silent_p.L287L|ANKHD1-EIF4EBP3_uc011czh.1_5'Flank|ANKHD1_uc003lfw.2_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1210						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATTGCTGCTCGATATGGGTT	0.483													15	60					0	0	0.003163	0	0	
PCDHA2	56146	broad.mit.edu	37	5	140176157	140176157	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140176157C>T	uc003lhd.2	+	1	1714	c.1608C>T	c.(1606-1608)AGC>AGT	p.S536S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.S536S|PCDHA2_uc011czy.1_Silent_p.S536S	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	536	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGGTGAGCGCGCGGGATG	0.672													9	29					0	0	0.008291	0	0	
PCDHA3	56145	broad.mit.edu	37	5	140181571	140181571	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140181571C>T	uc003lhf.2	+	1	789	c.789C>T	c.(787-789)ACC>ACT	p.T263T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.T263T	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	263	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAGTGGTGACCGTTAACGCCA	0.413													11	67					0	0	0.008291	0	0	
PCDHA3	56145	broad.mit.edu	37	5	140182272	140182272	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140182272G>A	uc003lhf.2	+	1	1490	c.1490G>A	c.(1489-1491)CGG>CAG	p.R497Q	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.R497Q	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	497	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGGAACGGCGGGTGGGG	0.682													14	30					0	0	0.004990	0	0	
PCDHA4	56144	broad.mit.edu	37	5	140186905	140186905	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140186905G>A	uc003lhi.2	+	1	234	c.133G>A	c.(133-135)GTG>ATG	p.V45M	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.V45M|PCDHA4_uc011daa.1_Missense_Mutation_p.V45M	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	45	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCACCTTCGTGGGCCGCAT	0.672													5	63					0	0	0.000602	0	0	
PCDHA4	56144	broad.mit.edu	37	5	140188263	140188263	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140188263G>A	uc003lhi.2	+	1	1592	c.1491G>A	c.(1489-1491)CGG>CGA	p.R497R	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.R497R|PCDHA4_uc011daa.1_Silent_p.R497R	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	497	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTAGAGCGGCGGGTAGGGG	0.662													12	36					0	0	0.013537	0	0	
PCDHA5	56143	broad.mit.edu	37	5	140203557	140203557	+	Missense_Mutation	SNP	C	T	T	rs140039635		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140203557C>T	uc003lhl.2	+	1	2197	c.2197C>T	c.(2197-2199)CGG>TGG	p.R733W	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Missense_Mutation_p.R733W|PCDHA5_uc003lhj.1_Missense_Mutation_p.R733W	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	733	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTGTGCACACGGGGCAAGCC	0.662													8	30					0	0	0.006214	0	0	
PCDHA6	56142	broad.mit.edu	37	5	140209209	140209209	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140209209C>T	uc003lho.2	+	1	1560	c.1533C>T	c.(1531-1533)CAC>CAT	p.H511H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Silent_p.H511H|PCDHA6_uc011dab.1_Silent_p.H511H	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	511	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCGGTGCACGCGGAGAGCG	0.701													11	55					0	0	0.013537	0	0	
PCDHA6	56142	broad.mit.edu	37	5	140209726	140209726	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140209726G>A	uc003lho.2	+	1	2077	c.2050G>A	c.(2050-2052)GTG>ATG	p.V684M	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc011dab.1_Missense_Mutation_p.V684M	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	684	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGGCGTCGGTGGGCGCCGC	0.667													7	30					0	0	0.004482	0	0	
PCDHA13	56136	broad.mit.edu	37	5	140263605	140263605	+	Silent	SNP	G	A	A	rs61734917	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140263605G>A	uc003lif.2	+	1	1752	c.1752G>A	c.(1750-1752)TCG>TCA	p.S584S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Silent_p.S584S|PCDHA13_uc003lid.2_Silent_p.S584S	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	584	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCCGCGGTCGGTGGGTGCAG	0.687													9	43					0	0	0.002450	0	0	
PCDHA13	56136	broad.mit.edu	37	5	140264042	140264042	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140264042G>A	uc003lif.2	+	1	2189	c.2189G>A	c.(2188-2190)GGC>GAC	p.G730D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Missense_Mutation_p.G730D|PCDHA13_uc003lid.2_Missense_Mutation_p.G730D	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	730	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCACCGAGGGCGCGTGCGCG	0.657													6	31					0	0	0.010729	0	0	
PCDHB11	56125	broad.mit.edu	37	5	140579471	140579471	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140579471G>A	uc003liy.2	+	1	124	c.124G>A	c.(124-126)GGG>AGG	p.G42R	PCDHB11_uc011daj.1_Intron	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	42	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AATGCAGAGCGGGAGTTTTGT	0.517													10	53					0	0	0.008291	0	0	
PCDHB11	56125	broad.mit.edu	37	5	140580614	140580614	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140580614G>A	uc003liy.2	+	1	1267	c.1267G>A	c.(1267-1269)GTC>ATC	p.V423I	PCDHB11_uc011daj.1_Missense_Mutation_p.V58I	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	423	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACCATCACCGTCACCGACTT	0.502													27	133					0	0	0.007291	0	0	
PCDHB11	56125	broad.mit.edu	37	5	140581384	140581384	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140581384C>A	uc003liy.2	+	1	2037	c.2037C>A	c.(2035-2037)GCC>GCA	p.A679A	PCDHB11_uc011daj.1_Silent_p.A314A	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	679	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGCACCGGCCCAGGCCCAGG	0.692													13	54					1.5739e-10	1.74335e-10	0.004007	1	0	
TAF7	6879	broad.mit.edu	37	5	140698866	140698866	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140698866G>A	uc003ljg.2	-	1	1486	c.746C>T	c.(745-747)ACG>ATG	p.T249M		NM_005642	NP_005633	Q15545	TAF7_HUMAN	TATA box-binding protein-associated factor 2F	249	Potential.				negative regulation of histone acetylation|negative regulation of protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|spermine transport|transcription initiation from RNA polymerase II promoter	Golgi apparatus|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	histone acetyltransferase binding|thyroid hormone receptor binding|transcription coactivator activity|transcription regulatory region DNA binding|vitamin D receptor binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCTTCCTCCGTGTCAATGAT	0.443													19	118					0	0	0.002780	0	0	
TAF7	6879	broad.mit.edu	37	5	140699557	140699557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140699557G>A	uc003ljg.2	-	1	795	c.55C>T	c.(55-57)CGT>TGT	p.R19C		NM_005642	NP_005633	Q15545	TAF7_HUMAN	TATA box-binding protein-associated factor 2F	19					negative regulation of histone acetylation|negative regulation of protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|spermine transport|transcription initiation from RNA polymerase II promoter	Golgi apparatus|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	histone acetyltransferase binding|thyroid hormone receptor binding|transcription coactivator activity|transcription regulatory region DNA binding|vitamin D receptor binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGGCAGACGTAAGATAAAC	0.443											OREG0016852	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	94					0	0	0.008361	0	0	
PCDHGA5	56110	broad.mit.edu	37	5	140745350	140745350	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140745350G>A	uc003lju.1	+	1	1453	c.1453G>A	c.(1453-1455)GCT>ACT	p.A485T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.A485T	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	485	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCGACAACGCTCGAGTCAC	0.542													38	124					0	0	0.009718	0	0	
PCDHGA6	56109	broad.mit.edu	37	5	140754322	140754322	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:140754322C>T	uc003ljy.1	+	1	672	c.672C>T	c.(670-672)AGC>AGT	p.S224S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Silent_p.S224S	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	224	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCGCTCAAGCGTCGCCCAAA	0.552													4	20					0	0	0.009096	0	0	
GNPDA1	10007	broad.mit.edu	37	5	141385882	141385882	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:141385882C>T	uc003lmf.3	-	3	995	c.236G>A	c.(235-237)CGA>CAA	p.R79Q	GNPDA1_uc003lmg.3_Missense_Mutation_p.R79Q|GNPDA1_uc010jgh.2_Missense_Mutation_p.R79Q|GNPDA1_uc003lmh.3_Missense_Mutation_p.R45Q	NM_005471	NP_005462	P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	79					generation of precursor metabolites and energy|glucosamine catabolic process|N-acetylglucosamine metabolic process|single fertilization	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity				0		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGTGGTCTCGAGGAAGGCC	0.542													13	55					0	0	0.002450	0	0	
MYOZ3	91977	broad.mit.edu	37	5	150056388	150056388	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:150056388G>A	uc003lss.2	+	7	1294	c.707G>A	c.(706-708)AGA>AAA	p.R236K	MYOZ3_uc003lsr.2_Missense_Mutation_p.R236K	NM_001122853	NP_001116325	Q8TDC0	MYOZ3_HUMAN	myozenin 3	236						sarcomere	protein binding			skin(1)	1		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCTTCAACAGAGTGGCCCAG	0.642													9	61					0	0	0.004482	0	0	
FAT2	2196	broad.mit.edu	37	5	150948214	150948214	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:150948214G>A	uc003lue.3	-	1	292	c.279C>T	c.(277-279)TGC>TGT	p.C93C	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Silent_p.C93C	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	93	Extracellular (Potential).|Cadherin 1.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCTTAGGAAGCAGAAGTTGC	0.512													6	270					0	0	0.001984	0	0	
G3BP1	10146	broad.mit.edu	37	5	151170562	151170562	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:151170562T>A	uc003lun.2	+	4	461	c.290T>A	c.(289-291)CTT>CAT	p.L97H	G3BP1_uc010jhy.1_Missense_Mutation_p.L97H|G3BP1_uc003lum.2_Missense_Mutation_p.L97H|G3BP1_uc011dcu.1_5'UTR|G3BP1_uc010jhz.2_5'UTR	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	97	NTF2.				Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			GTGATGGGGCTTCTCTCTAAC	0.443													5	107					0	0	0.001984	0	0	
GRIA1	2890	broad.mit.edu	37	5	153190682	153190682	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:153190682G>T	uc003lva.3	+	16	2983	c.2618G>T	c.(2617-2619)GGA>GTA	p.G873V	GRIA1_uc003luy.3_Missense_Mutation_p.G873V|GRIA1_uc003luz.3_Missense_Mutation_p.G778V|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Missense_Mutation_p.G793V|GRIA1_uc011dcx.1_Missense_Mutation_p.G804V|GRIA1_uc011dcy.1_Missense_Mutation_p.G883V|GRIA1_uc011dcz.1_Missense_Mutation_p.G883V	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	873	Cytoplasmic (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GGCGGCAGTGGAGAGAATGGT	0.582													4	20					3.59834e-05	3.85339e-05	0.001168	1	0	
ADAM19	8728	broad.mit.edu	37	5	156920119	156920119	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:156920119C>T	uc003lwz.2	-	16	1834	c.1770G>A	c.(1768-1770)GTG>GTA	p.V590V	ADAM19_uc003lww.1_Silent_p.V323V|ADAM19_uc003lwy.2_Silent_p.V189V|ADAM19_uc011ddr.1_Silent_p.V521V	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein	590	Extracellular (Potential).|Cys-rich.				proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGTCAATGGGCACCGCGTTGG	0.607													10	55					0	0	0.010729	0	0	
ATP10B	23120	broad.mit.edu	37	5	160113246	160113246	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:160113246A>G	uc003lym.1	-	6	1157	c.310T>C	c.(310-312)TTG>CTG	p.L104L	ATP10B_uc003lyp.2_Silent_p.L104L|ATP10B_uc011deg.1_Silent_p.L148L|ATP10B_uc003lyo.2_5'Flank	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	104	Helical; (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATCCAGTTCAAAATCACCAGG	0.458													5	23					0	0	0.000602	0	0	
GABRB2	2561	broad.mit.edu	37	5	160721153	160721153	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:160721153G>A	uc003lys.1	-	11	1692	c.1474C>T	c.(1474-1476)CGC>TGC	p.R492C	GABRB2_uc011deh.1_Missense_Mutation_p.R293C|GABRB2_uc003lyr.1_Missense_Mutation_p.R454C|GABRB2_uc003lyt.1_Missense_Mutation_p.R454C|GABRB2_uc010jiu.1_Missense_Mutation_p.R391C	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	492	Helical; (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	AAGAATATGCGGGACCACCGA	0.468													14	60					0	0	0.006122	0	0	
GABRG2	2566	broad.mit.edu	37	5	161520894	161520894	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:161520894C>A	uc003lyz.3	+	2	526	c.168C>A	c.(166-168)GTC>GTA	p.V56V	GABRG2_uc010jjc.2_Silent_p.V56V|GABRG2_uc003lyy.3_Silent_p.V56V|GABRG2_uc011dej.1_5'UTR	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	56	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)		AAACATGGGTCTTGACTCCAA	0.368													10	63					2.80697e-09	3.08473e-09	0.010729	1	0	
LCP2	3937	broad.mit.edu	37	5	169689854	169689854	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:169689854T>C	uc003man.1	-	12	1017	c.810A>G	c.(808-810)CCA>CCG	p.P270P	LCP2_uc011des.1_Silent_p.P65P|LCP2_uc011det.1_Silent_p.P99P|LCP2_uc010jjo.1_Silent_p.P77P	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	270					immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		ACCTTCCCGCTGGAATCGAGG	0.428													8	95					0	0	0.008291	0	0	
NKX2-5	1482	broad.mit.edu	37	5	172659583	172659583	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:172659583G>A	uc003mcm.1	-	2	1140	c.964C>T	c.(964-966)CGA>TGA	p.R322*		NM_004387	NP_004378	P52952	NKX25_HUMAN	NK2 transcription factor related, locus 5	322			R -> Q (in ASD-AVCD; somatic mutation).		adult heart development|atrial cardiac muscle cell development|atrial septum morphogenesis|heart looping|hemopoiesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell apoptosis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|outflow tract septum morphogenesis|pharyngeal system development|positive regulation of calcium ion transport via voltage-gated calcium channel activity|positive regulation of cardioblast differentiation|positive regulation of cell proliferation|positive regulation of heart contraction|positive regulation of neuron differentiation|positive regulation of sodium ion transport|positive regulation of survival gene product expression|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription via serum response element binding|regulation of cardiac muscle contraction|right ventricular cardiac muscle tissue morphogenesis|septum secundum development|spleen development|thyroid gland development|vasculogenesis|ventricular septum morphogenesis		chromatin binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|serum response element binding|transcription factor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TACCAGGCTCGGATACCATGC	0.627													3	14					0	0	0.004672	0	0	
HMP19	51617	broad.mit.edu	37	5	173534316	173534316	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:173534316G>A	uc003mcx.2	+	5	470	c.325_splice	c.e5-1	p.H109_splice	HMP19_uc011dfh.1_Splice_Site_p.S12_splice	NM_015980	NP_057064	Q9Y328	NSG2_HUMAN	HMP19 protein						dopamine receptor signaling pathway	cytoplasmic vesicle membrane|Golgi cisterna membrane|integral to membrane|multivesicular body membrane	dopamine receptor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00925)|all_lung(126;0.0148)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TTCTTCCCCAGCACAAACGCT	0.572													11	55					0	0	0.013537	0	0	
UNC5A	90249	broad.mit.edu	37	5	176297387	176297387	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:176297387C>T	uc003mey.2	+	6	930	c.738C>T	c.(736-738)AGC>AGT	p.S246S	UNC5A_uc003mex.1_Silent_p.S246S|UNC5A_uc010jkg.1_Silent_p.S206S	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor	246	TSP type-1.|Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAGCTGGAGCCCGTGGAGCA	0.687													6	13					0	0	0.001984	0	0	
HK3	3101	broad.mit.edu	37	5	176314232	176314232	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:176314232G>A	uc003mfa.2	-	12	1799	c.1707C>T	c.(1705-1707)CCC>CCT	p.P569P	HK3_uc003mez.2_Silent_p.P125P	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	569	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCACAGTCTCGGGAATGGAGT	0.617													4	25					0	0	0.000602	0	0	
NSD1	64324	broad.mit.edu	37	5	176678848	176678848	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:176678848C>T	uc003mfr.3	+	12	4897	c.4759C>T	c.(4759-4761)CGC>TGC	p.R1587C	NSD1_uc003mft.3_Missense_Mutation_p.R1318C|NSD1_uc003mfs.1_Missense_Mutation_p.R1484C|NSD1_uc011dfx.1_Missense_Mutation_p.R1235C	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1587	PHD-type 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)		CAATGAATGTCGCACAGGTAA	0.423			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			12	74					0	0	0.004007	0	0	
NSD1	64324	broad.mit.edu	37	5	176721549	176721549	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:176721549A>G	uc003mfr.3	+	23	7318	c.7180A>G	c.(7180-7182)ATT>GTT	p.I2394V	NSD1_uc003mft.3_Missense_Mutation_p.I2125V|NSD1_uc011dfx.1_Missense_Mutation_p.I2042V	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2394	Pro-rich.				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)		CAGACTGCTCATTACTAGCAG	0.552			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			20	93					0	0	0.003330	0	0	
GRK6	2870	broad.mit.edu	37	5	176860178	176860178	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:176860178T>C	uc011dfz.1	+	6	631	c.471T>C	c.(469-471)CCT>CCC	p.P157P	GRK6_uc003mgp.2_Silent_p.P157P|GRK6_uc003mgq.2_Silent_p.P157P|GRK6_uc003mgs.1_Silent_p.P127P	NM_002082	NP_002073	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6 isoform B	157	N-terminal.|RGS.				regulation of G-protein coupled receptor protein signaling pathway	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			large_intestine(1)|stomach(1)|breast(1)	3	all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)			GCGTGGCCCCTTTTGCCGACT	0.627													8	46					0	0	0.006214	0	0	
BTNL9	153579	broad.mit.edu	37	5	180475169	180475169	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:180475169C>T	uc003mmt.2	+	3	583	c.352C>T	c.(352-354)CTG>TTG	p.L118L	BTNL9_uc011dhi.1_Silent_p.L49L	NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor	118	Extracellular (Potential).|Ig-like V-type.					integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGCGTGGTCCTGCAGCTTCA	0.602													6	23					0	0	0.001984	0	0	
CDYL	9425	broad.mit.edu	37	6	4935952	4935952	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:4935952A>G	uc003mwi.2	+	5	1188	c.1057A>G	c.(1057-1059)ACC>GCC	p.T353A	CDYL_uc003mwj.2_Missense_Mutation_p.T299A|CDYL_uc003mwk.2_Missense_Mutation_p.T64A|CDYL_uc011dhx.1_Missense_Mutation_p.T167A|CDYL_uc011dhy.1_Missense_Mutation_p.T167A	NM_001143971	NP_001137443	Q9Y232	CDYL1_HUMAN	chromodomain protein, Y chromosome-like isoform	353					regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		GGATGGCTTCACCCACATCTT	0.512													23	83					0	0	0.004656	0	0	
F13A1	2162	broad.mit.edu	37	6	6197549	6197549	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:6197549A>G	uc003mwv.2	-	9	1246	c.1123T>C	c.(1123-1125)TGC>CGC	p.C375R	F13A1_uc011dib.1_Missense_Mutation_p.C312R	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	375					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TCATTCCAGCAGTGGTAGTTC	0.443													7	30					0	0	0.003080	0	0	
MYLIP	29116	broad.mit.edu	37	6	16143371	16143371	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:16143371C>T	uc003nbq.2	+	4	822	c.585C>T	c.(583-585)AGC>AGT	p.S195S	MYLIP_uc003nbr.2_Silent_p.S14S	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	195	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			TGCGGGATAGCGAAGGGCAGA	0.443													14	81					0	0	0.004007	0	0	
KIF13A	63971	broad.mit.edu	37	6	17837152	17837152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:17837152C>T	uc003ncg.3	-	11	1217	c.1112G>A	c.(1111-1113)CGG>CAG	p.R371Q	KIF13A_uc003ncf.2_Missense_Mutation_p.R371Q|KIF13A_uc003nch.3_Missense_Mutation_p.R371Q|KIF13A_uc003nci.3_Missense_Mutation_p.R371Q|KIF13A_uc003ncj.2_Missense_Mutation_p.R47Q	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	371	Potential.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			GACTTCCTCCCGCAGTTCTCG	0.517													56	211					0	0	0.014410	0	0	
E2F3	1871	broad.mit.edu	37	6	20481645	20481645	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:20481645C>T	uc003nda.2	+	3	1041	c.714C>T	c.(712-714)AAC>AAT	p.N238N	E2F3_uc003ncz.2_Silent_p.N232N	NM_001949	NP_001940	O00716	E2F3_HUMAN	E2F transcription factor 3	238	Potential.|DEF box.				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			CTAAAAACAACGTCCAATGGA	0.478													21	124					0	0	0.014323	0	0	
CDKAL1	54901	broad.mit.edu	37	6	20758841	20758841	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:20758841C>T	uc003ndc.1	+	7	658	c.484C>T	c.(484-486)CGT>TGT	p.R162C	CDKAL1_uc003ndd.1_Missense_Mutation_p.R162C|CDKAL1_uc003nde.1_Missense_Mutation_p.R92C	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein	162	MTTase N-terminal.				RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GCAGATAGATCGTGTGGTAGA	0.328													5	28					0	0	0.000602	0	0	
TDP2	51567	broad.mit.edu	37	6	24653309	24653309	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:24653309G>A	uc003nej.2	-	6	734	c.709C>T	c.(709-711)CGA>TGA	p.R237*	TDP2_uc003nei.2_Nonsense_Mutation_p.R125*|TDP2_uc010jpu.1_Nonsense_Mutation_p.R237*	NM_016614	NP_057698	O95551	TYDP2_HUMAN	TRAF and TNF receptor-associated protein	237					cell surface receptor linked signaling pathway|double-strand break repair	PML body	5'-tyrosyl-DNA phosphodiesterase activity|magnesium ion binding|nuclease activity|protein binding|transcription corepressor activity			ovary(1)|lung(1)	2						TGATTCATTCGTTCCGCAGCA	0.433								Direct_reversal_of_damage|Editing_and_processing_nucleases					48	210					0	0	0.014410	0	0	
LRRC16A	55604	broad.mit.edu	37	6	25600624	25600624	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:25600624A>G	uc011djw.1	+	33	3578	c.3202A>G	c.(3202-3204)AGT>GGT	p.S1068G	LRRC16A_uc010jpx.2_Missense_Mutation_p.S1068G|LRRC16A_uc010jpy.2_Missense_Mutation_p.S1068G	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1068	Inhibits capping activity of CAPZA2 (By similarity).				actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						TCGGAAAAGTAGTGGCTTTCT	0.453													16	101					0	0	0.004990	0	0	
HIST1H2BL	8340	broad.mit.edu	37	6	27775557	27775557	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:27775557T>C	uc003njl.2	-	1	153	c.128A>G	c.(127-129)TAC>TGC	p.Y43C	HIST1H3H_uc003njm.2_5'Flank	NM_003519	NP_003510	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	43					nucleosome assembly	nucleosome|nucleus	DNA binding				0						CAGCACCTTGTACACGTACAC	0.582													40	183					0	0	0.014410	0	0	
HIST1H2BN	8341	broad.mit.edu	37	6	27806599	27806599	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:27806599G>T	uc003njv.2	+	1	160	c.160G>T	c.(160-162)GGT>TGT	p.G54C	HIST1H2AK_uc003njs.2_5'Flank|HIST1H2BN_uc003njt.1_RNA|HIST1H2BN_uc003nju.1_Missense_Mutation_p.G54C	NM_003520	NP_003511	Q99877	H2B1N_HUMAN	histone cluster 1, H2bn	54					nucleosome assembly	nucleosome|nucleus	DNA binding				0						CCCCGACACCGGTATCTCGTC	0.592													47	214					2.29192e-23	2.5865e-23	0.014410	1	0	
OR2B6	26212	broad.mit.edu	37	6	27925691	27925691	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:27925691G>C	uc011dkx.1	+	1	673	c.673G>C	c.(673-675)GTA>CTA	p.V225L		NM_012367	NP_036499	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B,	225	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						TGTCCGAGCAGTATTGAGGAT	0.423													19	122					0	0	0.006122	0	0	
TRIM15	89870	broad.mit.edu	37	6	30139991	30139991	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:30139991C>T	uc010jrx.2	+	7	1742	c.1263C>T	c.(1261-1263)TAC>TAT	p.Y421Y		NM_033229	NP_150232	Q9C019	TRI15_HUMAN	tripartite motif protein 15	421	B30.2/SPRY.				mesodermal cell fate determination	intracellular	zinc ion binding				0						CCCTGGACTACGAGGCGGGGC	0.652													3	6					0	0	0.004672	0	0	
C6orf136	221545	broad.mit.edu	37	6	30617500	30617500	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:30617500A>G	uc003nqw.3	+	2	431	c.238A>G	c.(238-240)AGC>GGC	p.S80G	C6orf136_uc003nqx.3_Missense_Mutation_p.S261G|C6orf136_uc011dmn.1_Intron	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1	80											0						CCAGGCCCTCAGCTCAGCATG	0.617													13	116					0	0	0.003163	0	0	
LTA	4049	broad.mit.edu	37	6	31541102	31541102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31541102G>A	uc011dnu.1	+	4	463	c.250G>A	c.(250-252)GAC>AAC	p.D84N	LTA_uc003nue.1_Missense_Mutation_p.D84N|LTA_uc003nuf.2_Intron|LTA_uc003nuh.2_Missense_Mutation_p.D31N|LTA_uc003nug.2_Missense_Mutation_p.D31N|LTA_uc010jsr.2_Intron|TNF_uc003nui.2_5'Flank	NM_001159740	NP_001153212	P01374	TNFB_HUMAN	lymphotoxin alpha precursor	84					cell-cell signaling|induction of apoptosis|signal transduction	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0					Etanercept(DB00005)	AGCAAACACGGACCGTGCCTT	0.567													12	37					0	0	0.002450	0	0	
BAT2	7916	broad.mit.edu	37	6	31593069	31593069	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31593069C>T	uc003nvb.3	+	6	834	c.585C>T	c.(583-585)CCC>CCT	p.P195P	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Silent_p.P195P|BAT2_uc003nve.2_Silent_p.P58P	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	195	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0						CGTCTGGGCCCGGACCAAGCC	0.582													15	36					0	0	0.004007	0	0	
C6orf47	57827	broad.mit.edu	37	6	31627518	31627518	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31627518A>G	uc003nvm.1	-	1	1032	c.207T>C	c.(205-207)GCT>GCC	p.A69A		NM_021184	NP_067007	O95873	CF047_HUMAN	G4 protein	69										ovary(1)	1						GTTCGGAAGCAGCCCCAGAAA	0.542													11	46					0	0	0.010729	0	0	
VARS	7407	broad.mit.edu	37	6	31760564	31760564	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31760564A>T	uc003nxe.2	-	4	1054	c.631T>A	c.(631-633)TCA>ACA	p.S211T	VARS_uc011doi.1_RNA	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase	211	GST C-terminal.				translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)	CTGGCTCCTGAGTATAGAACC	0.567													4	41					0	0	0.001984	0	0	
SLC44A4	80736	broad.mit.edu	37	6	31838664	31838664	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31838664C>T	uc010jti.2	-	10	928	c.862G>A	c.(862-864)GCC>ACC	p.A288T	SLC44A4_uc011dol.1_Missense_Mutation_p.A212T|SLC44A4_uc011dom.1_Missense_Mutation_p.A246T	NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4	288	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)	GAGATGGAGGCGCCCTTGTCC	0.657													5	20					0	0	0.001168	0	0	
EHMT2	10919	broad.mit.edu	37	6	31852688	31852688	+	Splice_Site	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31852688C>T	uc003nxz.1	-	19	2458	c.2448_splice	c.e19+1	p.N816_splice	EHMT2_uc003nxv.1_5'Flank|EHMT2_uc003nxw.1_5'Flank|EHMT2_uc003nxx.1_Intron|EHMT2_uc003nxy.1_Missense_Mutation_p.V608M|EHMT2_uc011don.1_Splice_Site_p.N839_splice|EHMT2_uc003nya.1_Splice_Site_p.N782_splice	NM_006709	NP_006700	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2						DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1						CGCTCACTCACGTTGTCAGTG	0.637													7	18					0	0	0.003080	0	0	
STK19	8859	broad.mit.edu	37	6	31939920	31939920	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:31939920C>T	uc003nyv.2	+	1	275	c.147C>T	c.(145-147)GTC>GTT	p.V49V	DOM3Z_uc003nyo.1_5'UTR|DOM3Z_uc003nyp.1_5'UTR|DOM3Z_uc003nyq.1_5'UTR|DOM3Z_uc003nyr.1_5'UTR|DOM3Z_uc003nys.1_5'Flank|DOM3Z_uc010jtl.1_5'UTR|STK19_uc003nyt.2_5'UTR|DOM3Z_uc003nyu.1_5'UTR|STK19_uc011dow.1_Silent_p.V49V|STK19_uc011dox.1_5'UTR|STK19_uc003nyw.2_Silent_p.V49V|STK19_uc010jtn.1_5'Flank	NM_032454	NP_115830	P49842	STK19_HUMAN	serine/threonine kinase 19 isoform 2	49						nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4						GCCAACGAGTCCCCGGGCGTG	0.731													5	21					0	0	0.004482	0	0	
TNXB	7148	broad.mit.edu	37	6	32039796	32039796	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32039796C>T	uc003nzl.2	-	13	5163	c.4961G>A	c.(4960-4962)CGC>CAC	p.R1654H		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1736	Fibronectin type-III 9.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						GACTGGGCTGCGTCGTTTCCC	0.607													6	25					0	0	0.001984	0	0	
TNXB	7148	broad.mit.edu	37	6	32039876	32039876	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32039876C>A	uc003nzl.2	-	13	5083	c.4881G>T	c.(4879-4881)CAG>CAT	p.Q1627H		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1709	Fibronectin type-III 9.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						TGACCTCCCGCTGATCTGCAG	0.597													5	14					1.23904e-05	1.33197e-05	0.000602	1	0	
TNXB	7148	broad.mit.edu	37	6	32065871	32065871	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32065871T>C	uc003nzl.2	-	2	307	c.105A>G	c.(103-105)CCA>CCG	p.P35P	TNXB_uc010jts.1_Silent_p.P34P|ATF6B_uc003nzm.1_3'UTR	NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	35					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						GCCGGGGGGCTGGCAGTGTCA	0.642													4	14					0	0	0.001168	0	0	
PPT2	9374	broad.mit.edu	37	6	32123717	32123717	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32123717C>A	uc003nzx.2	+	5	1071	c.503C>A	c.(502-504)CCC>CAC	p.P168H	PRRT1_uc003nzu.2_5'Flank|uc003nzv.3_5'Flank|PPT2_uc003nzw.2_Missense_Mutation_p.P174H|PPT2_uc011dpi.1_RNA|PPT2_uc003nzy.1_RNA|PPT2_uc003nzz.2_Missense_Mutation_p.P168H|PPT2_uc003oaa.2_Missense_Mutation_p.P168H|PPT2_uc010jtu.1_Missense_Mutation_p.P168H	NM_005155	NP_005146	Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2 isoform a	168					protein modification process	lysosome	palmitoyl-(protein) hydrolase activity				0						TGCTATAGCCCCTGGGGCCAG	0.547													14	54					1.67942e-08	1.84077e-08	0.006122	1	0	
EGFL8	80864	broad.mit.edu	37	6	32135028	32135028	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32135028G>A	uc003oab.1	+	6	653	c.595G>A	c.(595-597)GTG>ATG	p.V199M	PPT2_uc003nzy.1_RNA|EGFL8_uc003oac.1_Missense_Mutation_p.V199M	NM_030652	NP_085155	Q99944	EGFL8_HUMAN	NG3 protein precursor	199	Potential.					extracellular region|integral to membrane	calcium ion binding				0						CATACTCAGCGTGGCCGGTGA	0.667													5	18					0	0	0.001984	0	0	
GPSM3	63940	broad.mit.edu	37	6	32159535	32159535	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32159535C>T	uc003oay.3	-	3	689	c.296G>A	c.(295-297)CGT>CAT	p.R99H	PBX2_uc003oav.1_5'Flank|PBX2_uc003oaw.2_5'Flank|GPSM3_uc003oax.3_Missense_Mutation_p.R76H|GPSM3_uc003oaz.2_Missense_Mutation_p.R99H	NM_022107	NP_071390	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3 (AGS3-like, C.	99					signal transduction	cytoplasm	GTPase activator activity|protein binding				0						CTCGAGAGGACGGAGTGGGGC	0.632													9	19					0	0	0.008291	0	0	
NOTCH4	4855	broad.mit.edu	37	6	32168997	32168997	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32168997G>A	uc003obb.2	-	22	4175	c.4036C>T	c.(4036-4038)CGG>TGG	p.R1346W	NOTCH4_uc003oba.2_Missense_Mutation_p.R9W|NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA	NM_004557	NP_004548	Q99466	NOTC4_HUMAN	notch4 preproprotein	1346	Extracellular (Potential).				cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1)	22						TCTTCAGCCCGGGCCCCAGGA	0.622													11	20					0	0	0.002450	0	0	
PSMB8	5696	broad.mit.edu	37	6	32809478	32809478	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:32809478G>T	uc003oce.2	-	5	615	c.572C>A	c.(571-573)ACT>AAT	p.T191N	TAP2_uc011dqf.1_5'Flank|TAP2_uc003ocb.1_5'Flank|TAP2_uc003ocd.2_5'Flank|PSMB8_uc003ocf.2_Missense_Mutation_p.T187N	NM_148919	NP_683720	P28062	PSB8_HUMAN	proteasome beta 8 subunit isoform E2 proprotein	191					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|interspecies interaction between organisms|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|type I interferon-mediated signaling pathway|viral reproduction	cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			skin(1)	1						TGAGAGCCGAGTCCCATGTTC	0.488													22	120					1.1804e-14	1.32321e-14	0.003954	1	0	
ITPR3	3710	broad.mit.edu	37	6	33638235	33638235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:33638235G>A	uc011drk.1	+	19	2542	c.2323G>A	c.(2323-2325)GCC>ACC	p.A775T		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	775	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						TGACCTGCGCGCCTCCTTCTG	0.627													19	71					0	0	0.006122	0	0	
UHRF1BP1	54887	broad.mit.edu	37	6	34826613	34826613	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:34826613G>A	uc003oju.3	+	14	2714	c.2480G>A	c.(2479-2481)CGC>CAC	p.R827H	UHRF1BP1_uc010jvm.1_RNA|UHRF1BP1_uc010jvn.2_RNA|UHRF1BP1_uc010jvo.2_RNA	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1	827										ovary(3)	3						GCCCATGTCCGCGTGAGGCTT	0.527													42	167					0	0	0.011902	0	0	
SCUBE3	222663	broad.mit.edu	37	6	35200656	35200656	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:35200656G>A	uc003okf.1	+	5	505	c.499G>A	c.(499-501)GGC>AGC	p.G167S	SCUBE3_uc003okg.1_Missense_Mutation_p.G166S|SCUBE3_uc003okh.1_Missense_Mutation_p.G38S	NM_152753	NP_689966	Q8IX30	SCUB3_HUMAN	signal peptide, CUB domain, EGF-like 3	167	EGF-like 4.				protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1						CAAGAACCACGGCTGTGCCCA	0.493													29	88					0	0	0.010818	0	0	
DNAH8	1769	broad.mit.edu	37	6	38828371	38828371	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:38828371A>G	uc003ooe.1	+	41	6046	c.5446A>G	c.(5446-5448)ACT>GCT	p.T1816A		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						TCTGGGATGTACTGATCGTCT	0.294													5	39					0	0	0.000602	0	0	
TREML1	340205	broad.mit.edu	37	6	41121543	41121543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:41121543C>T	uc011duc.1	-	2	373	c.329G>A	c.(328-330)AGG>AAG	p.R110K	TREML1_uc003opx.2_Missense_Mutation_p.R110K|TREML1_uc011dud.1_Intron	NM_178174	NP_835468	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid	110	Ig-like V-type.|Extracellular (Potential).				calcium-mediated signaling|innate immune response|platelet activation	cell surface|integral to membrane|plasma membrane|platelet alpha granule	protein binding|receptor activity			breast(1)	1	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTGGGGCCCCCTGGCCCCATC	0.602													11	43					0	0	0.001855	0	0	
FOXP4	116113	broad.mit.edu	37	6	41558999	41558999	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:41558999A>G	uc003oql.2	+	13	1933	c.1475A>G	c.(1474-1476)GAG>GGG	p.E492G	FOXP4_uc003oqm.2_Missense_Mutation_p.E490G|FOXP4_uc003oqn.2_Missense_Mutation_p.E479G	NM_001012426	NP_001012426	Q8IVH2	FOXP4_HUMAN	forkhead box P4 isoform 1	492	Fork-head.				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)					ACCCTGAATGAGATCTATAAC	0.592													4	10					0	0	0.003080	0	0	
GUCA1A	2978	broad.mit.edu	37	6	42146094	42146094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:42146094G>A	uc003orx.2	+	4	923	c.278G>A	c.(277-279)CGC>CAC	p.R93H	GUCA1A_uc011duo.1_RNA|GUCA1A_uc010jxt.2_Missense_Mutation_p.R93H	NM_000409	NP_000400	P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	93	EF-hand 3.				signal transduction|visual perception	membrane	calcium ion binding|calcium sensitive guanylate cyclase activator activity				0	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CAGAAGCTCCGCTGGTACTTC	0.617													26	75					0	0	0.007291	0	0	
CUL9	23113	broad.mit.edu	37	6	43167106	43167106	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:43167106C>T	uc003ouk.2	+	13	3228	c.3153C>T	c.(3151-3153)TCC>TCT	p.S1051S	CUL9_uc003oul.2_Silent_p.S1051S|CUL9_uc010jyk.2_Silent_p.S203S	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	1051					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						GCAGTGACTCCGAGGTACCAG	0.592													16	80					0	0	0.010504	0	0	
CUL9	23113	broad.mit.edu	37	6	43167827	43167827	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:43167827C>T	uc003ouk.2	+	14	3392	c.3317C>T	c.(3316-3318)ACA>ATA	p.T1106I	CUL9_uc003oul.2_Missense_Mutation_p.T1106I|CUL9_uc010jyk.2_Missense_Mutation_p.T258I	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	1106					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						GACCTGGTGACAGAGTGTGAG	0.582													9	58					0	0	0.008291	0	0	
ZNF318	24149	broad.mit.edu	37	6	43322422	43322422	+	Missense_Mutation	SNP	G	A	A	rs146670568		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:43322422G>A	uc003oux.2	-	4	2728	c.2650C>T	c.(2650-2652)CGT>TGT	p.R884C	ZNF318_uc003ouw.2_RNA	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	884	Potential.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TGGGAAGCACGGTTCTTCTCA	0.443													23	70					0	0	0.003954	0	0	
CDC5L	988	broad.mit.edu	37	6	44376250	44376250	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:44376250G>A	uc003oxl.2	+	8	1232	c.973G>A	c.(973-975)GAG>AAG	p.E325K		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	325	Interaction with PPP1R8.				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCAAACTGCCGAGGAATCTGG	0.428													17	91					0	0	0.012319	0	0	
DST	667	broad.mit.edu	37	6	56382029	56382029	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:56382029G>A	uc003pdf.2	-	65	11995	c.11967C>T	c.(11965-11967)ACC>ACT	p.T3989T	DST_uc003pcz.3_Silent_p.T3811T|DST_uc011dxj.1_Silent_p.T3840T|DST_uc011dxk.1_Silent_p.T3851T|DST_uc003pcy.3_Silent_p.T3485T	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5897	Spectrin 10.				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)			CACTGCATGCGGTCATGATTT	0.388													25	143					0	0	0.006320	0	0	
KIAA1586	57691	broad.mit.edu	37	6	56917834	56917834	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:56917834T>C	uc003pdj.2	+	4	707	c.537T>C	c.(535-537)CAT>CAC	p.H179H	KIAA1586_uc011dxm.1_Silent_p.H152H	NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	179							nucleic acid binding				0	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGCATGTCCATGTGTCCAAGG	0.368													12	120					0	0	0.013537	0	0	
MCART3P	442229	broad.mit.edu	37	6	66499270	66499270	+	RNA	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:66499270G>T	uc011dxw.1	+	1		c.1499G>T				NR_026540				Homo sapiens mitochondrial carrier triple repeat 3 pseudogene, mRNA (cDNA clone IMAGE:4821649).												0						TTTCTTAGTTGGCCAAATACA	0.368													3	6					0.004672	0.00488768	0.004672	1	0	
BAI3	577	broad.mit.edu	37	6	70042837	70042837	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:70042837T>G	uc003pev.3	+	24	3573	c.3125T>G	c.(3124-3126)TTG>TGG	p.L1042W	BAI3_uc010kak.2_Missense_Mutation_p.L1042W|BAI3_uc011dxx.1_Missense_Mutation_p.L248W|BAI3_uc003pex.1_Missense_Mutation_p.L172W	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1042	Helical; Name=5; (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ATTGGCATTTTGGTATTTAAT	0.373													7	44					0	0	0.006214	0	0	
OGFRL1	79627	broad.mit.edu	37	6	72011673	72011673	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:72011673A>G	uc003pfx.1	+	7	1440	c.1277A>G	c.(1276-1278)AAC>AGC	p.N426S		NM_024576	NP_078852	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	426						membrane	receptor activity				0						CCTGAGAATAACGAAGAAGGT	0.373													32	163					0	0	0.003755	0	0	
KCNQ5	56479	broad.mit.edu	37	6	73787159	73787159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:73787159G>A	uc003pgk.2	+	4	1078	c.731G>A	c.(730-732)CGC>CAC	p.R244H	KCNQ5_uc003pgj.3_Missense_Mutation_p.R244H|KCNQ5_uc011dyh.1_Missense_Mutation_p.R244H|KCNQ5_uc011dyi.1_Missense_Mutation_p.R244H|KCNQ5_uc010kat.2_Missense_Mutation_p.R244H|KCNQ5_uc011dyj.1_Missense_Mutation_p.R244H|KCNQ5_uc011dyk.1_Missense_Mutation_p.R3H	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	244	Helical; Voltage-sensor; Name=Segment S4; (Potential).		R -> C (in a colorectal cancer sample; somatic mutation).		protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity	p.R244C(1)		ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		CGCATGGTGCGCATGGACCGA	0.438													10	45					0	0	0.010729	0	0	
FILIP1	27145	broad.mit.edu	37	6	76022149	76022149	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:76022149C>T	uc003pia.2	-	5	3772	c.3399G>A	c.(3397-3399)CCG>CCA	p.P1133P	FILIP1_uc003phy.1_Silent_p.P1133P|FILIP1_uc003phz.2_Silent_p.P1034P|FILIP1_uc010kbe.2_Silent_p.P1136P|FILIP1_uc003pib.1_Silent_p.P885P	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1133										skin(3)|ovary(1)	4						ACGTTGTGACCGGTGTTATGG	0.562													23	96					0	0	0.003330	0	0	
KIAA1009	22832	broad.mit.edu	37	6	84872863	84872863	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:84872863C>A	uc010kbp.2	-	19	2609	c.2512G>T	c.(2512-2514)GGT>TGT	p.G838C	KIAA1009_uc003pkj.3_Missense_Mutation_p.G762C|KIAA1009_uc003pki.3_Missense_Mutation_p.G224C	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	838	Potential.				cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		AGTGTTTTACCTGTGACATAA	0.338													17	100					6.94344e-10	7.66567e-10	0.006122	1	0	
AKIRIN2	55122	broad.mit.edu	37	6	88391397	88391397	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:88391397G>A	uc003pmk.2	-	2	903	c.320C>T	c.(319-321)CCG>CTG	p.P107L		NM_018064	NP_060534	Q53H80	AKIR2_HUMAN	akirin 2	107					innate immune response|transcription, DNA-dependent	transcriptional repressor complex					0						AGTACAACACGGATCTGTCTG	0.343													10	61					0	0	0.010729	0	0	
CNR1	1268	broad.mit.edu	37	6	88854349	88854349	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:88854349G>A	uc011dzq.1	-	2	4208	c.645C>T	c.(643-645)TAC>TAT	p.Y215Y	CNR1_uc010kbz.2_Silent_p.Y215Y|CNR1_uc011dzr.1_Silent_p.Y215Y|CNR1_uc011dzs.1_Silent_p.Y215Y|CNR1_uc003pmq.3_Silent_p.Y215Y|CNR1_uc011dzt.1_Silent_p.Y215Y|CNR1_uc010kca.2_Silent_p.Y182Y	NM_001160260	NP_001153732	P21554	CNR1_HUMAN	cannabinoid receptor 1 isoform a	215	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	cannabinoid receptor activity|protein binding			skin(2)	2		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Marinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	GAATGGATATGTACCTGTCGA	0.572													10	34					0	0	0.006214	0	0	
BACH2	60468	broad.mit.edu	37	6	90660960	90660960	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:90660960T>C	uc011eab.1	-	7	1674	c.865A>G	c.(865-867)ATC>GTC	p.I289V	BACH2_uc003pnw.2_Missense_Mutation_p.I289V|BACH2_uc010kch.2_Missense_Mutation_p.I289V	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	289						nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CAGAGCGTGATGCTCTCTTCC	0.602													8	56					0	0	0.008291	0	0	
MAP3K7	6885	broad.mit.edu	37	6	91257878	91257878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:91257878G>A	uc003pnz.1	-	10	1130	c.968C>T	c.(967-969)GCT>GTT	p.A323V	MAP3K7_uc003poa.1_Missense_Mutation_p.A323V|MAP3K7_uc003pob.1_Missense_Mutation_p.A323V|MAP3K7_uc003poc.1_Missense_Mutation_p.A323V	NM_145331	NP_663304	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	323					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|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|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		ATTTGTAGAAGCAATGTCCAT	0.333													7	74					0	0	0.004482	0	0	
PRDM13	59336	broad.mit.edu	37	6	100062101	100062101	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:100062101C>T	uc003pqg.1	+	4	1851	c.1590C>T	c.(1588-1590)TCC>TCT	p.S530S		NM_021620	NP_067633	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	530					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		AGCAGCTGTCCGAGATGGCTG	0.527													3	11					0	0	0.009096	0	0	
SIM1	6492	broad.mit.edu	37	6	100897523	100897523	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:100897523T>C	uc003pqj.3	-	4	608	c.401A>G	c.(400-402)GAC>GGC	p.D134G	SIM1_uc010kcu.2_Missense_Mutation_p.D134G	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	134	PAS 1.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CGTCATCTCGTCGTGGTCTGC	0.592													4	30					0	0	0.000602	0	0	
ARMC2	84071	broad.mit.edu	37	6	109274297	109274297	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:109274297G>A	uc003pss.3	+	13	1832	c.1658G>A	c.(1657-1659)CGT>CAT	p.R553H	ARMC2_uc011eao.1_Missense_Mutation_p.R388H	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	553	ARM 7.						binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		AACCAGGCTCGTGAACAATTT	0.458													4	24					0	0	0.000602	0	0	
DDO	8528	broad.mit.edu	37	6	110736691	110736691	+	Missense_Mutation	SNP	T	C	C	rs151067781	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:110736691T>C	uc003puc.2	-	1	63	c.59A>G	c.(58-60)CAA>CGA	p.Q20R	DDO_uc003pud.2_Missense_Mutation_p.Q20R	NM_003649	NP_003640	Q99489	OXDD_HUMAN	D-aspartate oxidase isoform a	Error:Variant_position_missing_in_Q99489_after_alignment					aspartate catabolic process	peroxisome	binding|D-amino-acid oxidase activity|D-aspartate oxidase activity			ovary(2)|breast(1)	3		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		AAAGCAGTCTTGGAAGCCACC	0.502													10	54					0	0	0.013537	0	0	
TUBE1	51175	broad.mit.edu	37	6	112397615	112397615	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:112397615C>A	uc003pvq.2	-	7	660	c.546G>T	c.(544-546)GAG>GAT	p.E182D	TUBE1_uc003pvr.2_Missense_Mutation_p.E107D	NM_016262	NP_057346	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	182					centrosome cycle|microtubule-based movement|protein polymerization	microtubule|pericentriolar material	GTP binding|GTPase activity|structural constituent of cytoskeleton			ovary(1)	1		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		TGACATCATCCTCACCAGAAG	0.398													10	67					0.00621372	0.00649651	0.006214	1	0	
LAMA4	3910	broad.mit.edu	37	6	112430768	112430768	+	Missense_Mutation	SNP	G	A	A	rs145897390	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:112430768G>A	uc003pvu.2	-	39	5653	c.5344C>T	c.(5344-5346)CGC>TGC	p.R1782C	LAMA4_uc003pvv.2_Missense_Mutation_p.R1775C|LAMA4_uc003pvt.2_Missense_Mutation_p.R1775C	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1782	Laminin G-like 5.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GGGGCCAAGCGTGGTGTCAGT	0.463													10	30					0	0	0.010729	0	0	
RSPH4A	345895	broad.mit.edu	37	6	116938220	116938220	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:116938220C>T	uc003pxe.2	+	1	579	c.434C>T	c.(433-435)TCA>TTA	p.S145L	RSPH4A_uc010kee.2_Missense_Mutation_p.S145L	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1	145					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0						ACAAGCCAGTCAGAAGGAAAC	0.463									Kartagener_syndrome				19	77					0	0	0.012319	0	0	
CLVS2	134829	broad.mit.edu	37	6	123369846	123369846	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:123369846G>A	uc003pzi.1	+	4	1513	c.644G>A	c.(643-645)CGG>CAG	p.R215Q		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2	215	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						ACCGTGATCCGGCCTTTCCTG	0.393													34	77					0	0	0.004878	0	0	
PTPRK	5796	broad.mit.edu	37	6	128297831	128297831	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:128297831G>A	uc003qbk.2	-	27	4304	c.3937C>T	c.(3937-3939)CGG>TGG	p.R1313W	PTPRK_uc003qbj.2_Missense_Mutation_p.R1314W|PTPRK_uc010kfc.2_Missense_Mutation_p.R1320W|PTPRK_uc011ebu.1_Missense_Mutation_p.R1336W	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	1313	Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential).				cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CTAAAAATCCGGTTGATCACA	0.428													7	36					0	0	0.003080	0	0	
TMEM200A	114801	broad.mit.edu	37	6	130762848	130762848	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:130762848C>T	uc003qca.2	+	3	2152	c.1281C>T	c.(1279-1281)AGC>AGT	p.S427S	TMEM200A_uc010kfh.2_Silent_p.S427S|TMEM200A_uc010kfi.2_Silent_p.S427S|TMEM200A_uc003qcb.2_Silent_p.S427S	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	427	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		GGAACAACAGCAAGGGATATA	0.468													21	81					0	0	0.012319	0	0	
EYA4	2070	broad.mit.edu	37	6	133783564	133783564	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:133783564G>A	uc003qec.3	+	8	987	c.529G>A	c.(529-531)GTC>ATC	p.V177I	EYA4_uc011ecq.1_Missense_Mutation_p.V123I|EYA4_uc011ecr.1_Missense_Mutation_p.V123I|EYA4_uc003qed.3_Missense_Mutation_p.V177I|EYA4_uc003qee.3_Missense_Mutation_p.V154I|EYA4_uc011ecs.1_Missense_Mutation_p.V177I|uc003qef.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a	177					anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		GCAGCCAGCCGTCTACACAGC	0.488													20	52					0	0	0.003954	0	0	
KIAA1244	57221	broad.mit.edu	37	6	138645253	138645253	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:138645253G>A	uc003qhu.2	+	31	4963	c.4963G>A	c.(4963-4965)GAG>AAG	p.E1655K		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	1655					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CCCAAGTGCCGAGGCCGAGTA	0.647													4	18					0	0	0.009096	0	0	
HECA	51696	broad.mit.edu	37	6	139488112	139488112	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:139488112C>T	uc003qin.2	+	2	1248	c.963C>T	c.(961-963)CAC>CAT	p.H321H		NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase	321					respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		GAAATGCCCACTTTGATTACA	0.597													7	45					0	0	0.001984	0	0	
TXLNB	167838	broad.mit.edu	37	6	139591652	139591652	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:139591652C>T	uc011eds.1	-	4	793	c.628G>A	c.(628-630)GCT>ACT	p.A210T		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	210	Potential.					cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TTGCTTCGAGCGAGGATAGCT	0.438													12	50					0	0	0.004007	0	0	
HIVEP2	3097	broad.mit.edu	37	6	143093401	143093401	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:143093401G>A	uc003qjd.2	-	5	3218	c.2475C>T	c.(2473-2475)TGC>TGT	p.C825C		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	825					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TATCCTGTGTGCAAGCCACAA	0.512													7	40					0	0	0.006214	0	0	
STX11	8676	broad.mit.edu	37	6	144507854	144507854	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:144507854C>T	uc003qks.3	+	2	282	c.90C>T	c.(88-90)CAC>CAT	p.H30H		NM_003764	NP_003755	O75558	STX11_HUMAN	syntaxin 11	30					cellular membrane fusion|intracellular protein transport|vesicle-mediated transport	Golgi apparatus|membrane	SNAP receptor activity			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		ACTCGCCCCACGAGGACATCG	0.552									Familial_Hemophagocytic_Lymphohistiocytosis				6	44					0	0	0.003080	0	0	
FBXO30	84085	broad.mit.edu	37	6	146127423	146127423	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:146127423A>G	uc003qla.2	-	2	318	c.119T>C	c.(118-120)GTT>GCT	p.V40A	uc003qky.1_Intron	NM_032145	NP_115521	Q8TB52	FBX30_HUMAN	F-box only protein 30	40							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		AGAATGGAAAACTGCACCACA	0.448													16	100					0	0	0.003163	0	0	
SHPRH	257218	broad.mit.edu	37	6	146247425	146247425	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:146247425T>C	uc003qlf.2	-	16	3608	c.3209A>G	c.(3208-3210)CAT>CGT	p.H1070R	SHPRH_uc003qld.2_Missense_Mutation_p.H1079R|SHPRH_uc003qle.2_Missense_Mutation_p.H1079R|SHPRH_uc003qlg.1_Missense_Mutation_p.H626R|SHPRH_uc003qlh.2_5'UTR|SHPRH_uc003qli.1_5'UTR	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1070					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ATGGGTAGCATGAAGTCTCTA	0.413													12	68					0	0	0.004990	0	0	
STXBP5	134957	broad.mit.edu	37	6	147704088	147704088	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:147704088C>T	uc003qlz.2	+	27	3529	c.3368C>T	c.(3367-3369)GCG>GTG	p.A1123V	STXBP5_uc010khz.1_Missense_Mutation_p.A1087V|STXBP5_uc003qlx.2_RNA|STXBP5_uc003qly.2_Missense_Mutation_p.A778V	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	1123	v-SNARE coiled-coil homology.				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		GAAAGAACTGCGGCCATGTTA	0.448													18	85					0	0	0.006122	0	0	
PLEKHG1	57480	broad.mit.edu	37	6	151161754	151161754	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:151161754C>T	uc003qny.1	+	17	4192	c.3880C>T	c.(3880-3882)CTA>TTA	p.L1294L	PLEKHG1_uc011eem.1_Silent_p.L1353L	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	1294					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GGAGTTGGAGCTATCTCACAA	0.388													18	84					0	0	0.012319	0	0	
MTHFD1L	25902	broad.mit.edu	37	6	151334921	151334921	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:151334921G>A	uc003qob.2	+	22	2540	c.2272G>A	c.(2272-2274)GCT>ACT	p.A758T	MTHFD1L_uc011een.1_RNA|MTHFD1L_uc011eeo.1_Missense_Mutation_p.A759T|MTHFD1L_uc003qoc.2_Missense_Mutation_p.A706T	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+	758	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TCAGGTAACGGCTGGTGTTCC	0.353													9	14					0	0	0.006214	0	0	
ARID1B	57492	broad.mit.edu	37	6	157405929	157405929	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:157405929C>T	uc003qqn.2	+	5	2110	c.1958C>T	c.(1957-1959)GCG>GTG	p.A653V	ARID1B_uc003qqo.2_Missense_Mutation_p.A666V|ARID1B_uc003qqp.2_Missense_Mutation_p.A653V|ARID1B_uc003qqq.1_Missense_Mutation_p.A95V	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	711	Ser-rich.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TCCCCACATGCGTCCCCTCAT	0.612													10	54					0	0	0.008291	0	0	
SYNJ2	8871	broad.mit.edu	37	6	158490659	158490659	+	Missense_Mutation	SNP	G	A	A	rs144180367	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:158490659G>A	uc003qqx.1	+	14	1969	c.1894G>A	c.(1894-1896)GTC>ATC	p.V632I	SYNJ2_uc003qqw.1_Missense_Mutation_p.V632I|SYNJ2_uc003qqy.1_Missense_Mutation_p.V345I|SYNJ2_uc003qqz.1_Missense_Mutation_p.V249I|SYNJ2_uc003qra.1_5'Flank	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	632	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		GCTGGTGGGCGTCTGTCTTTA	0.453													16	49					0	0	0.004990	0	0	
TULP4	56995	broad.mit.edu	37	6	158834180	158834180	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:158834180C>T	uc003qrf.2	+	2	1693	c.336C>T	c.(334-336)TAC>TAT	p.Y112Y	TULP4_uc011efo.1_Silent_p.Y112Y|TULP4_uc003qrg.2_Silent_p.Y112Y	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	112	WD 1.				intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GGATTCAGTACGAGGGCAGGT	0.612													6	30					0	0	0.001984	0	0	
TULP4	56995	broad.mit.edu	37	6	158923412	158923412	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:158923412G>A	uc003qrf.2	+	13	4074	c.2717G>A	c.(2716-2718)CGG>CAG	p.R906Q	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	906					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CCCCGCACCCGGATGCTGTGC	0.652													14	39					0	0	0.003163	0	0	
PNLDC1	154197	broad.mit.edu	37	6	160227084	160227084	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:160227084A>G	uc003qsx.1	+	7	669	c.498A>G	c.(496-498)GAA>GAG	p.E166E	PNLDC1_uc003qsy.1_Silent_p.E177E	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain	166	Cytoplasmic (Potential).					integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TGGCCAAGGAAGGCGACTGGA	0.562													14	31					0	0	0.001855	0	0	
AGPAT4	56895	broad.mit.edu	37	6	161560485	161560485	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:161560485C>T	uc003qtr.1	-	8	1238	c.1011G>A	c.(1009-1011)ACG>ACA	p.T337T	AGPAT4_uc003qts.1_Silent_p.T197T|AGPAT4_uc011egb.1_Silent_p.T175T	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	337					phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		AGCTGGCCAGCGTCAGGGAAG	0.622													6	58					0	0	0.001168	0	0	
AGPAT4	56895	broad.mit.edu	37	6	161587387	161587387	+	Missense_Mutation	SNP	C	T	T	rs115923077	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:161587387C>T	uc003qtr.1	-	3	468	c.241G>A	c.(241-243)GCC>ACC	p.A81T	AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_RNA|AGPAT4_uc011egc.1_Missense_Mutation_p.A81T|AGPAT4_uc011egd.1_Missense_Mutation_p.A19T|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	81					phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		TTGAGGTAGGCGCGCGGGTCC	0.527													6	31					0	0	0.001168	0	0	
UNC93A	54346	broad.mit.edu	37	6	167721271	167721271	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:167721271G>A	uc003qvq.2	+	7	1156	c.981G>A	c.(979-981)GCG>GCA	p.A327A	UNC93A_uc003qvr.2_Silent_p.A285A	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	327	Helical; (Potential).					integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CCCCAGGCGCGGTGACCCACG	0.627													11	43					0	0	0.004990	0	0	
MLLT4	4301	broad.mit.edu	37	6	168315892	168315892	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:168315892C>T	uc003qwd.2	+	18	2462	c.2320C>T	c.(2320-2322)CGC>TGC	p.R774C	MLLT4_uc003qwb.1_Missense_Mutation_p.R759C|MLLT4_uc003qwc.1_Missense_Mutation_p.R775C|MLLT4_uc003qwg.1_Missense_Mutation_p.R84C	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	775	Dilute.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		CTTGCTACGACGCTGCAGAGT	0.527			T	MLL	AL								13	62					0	0	0.003163	0	0	
THBS2	7058	broad.mit.edu	37	6	169648753	169648753	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:169648753G>A	uc003qwt.2	-	4	616	c.368C>T	c.(367-369)ACG>ATG	p.T123M		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	123	TSP N-terminal.|Heparin-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GAGATCCAGCGTGTCCGCGGG	0.652													4	20					0	0	0.009096	0	0	
ADAP1	11033	broad.mit.edu	37	7	939112	939112	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:939112G>A	uc003sjo.3	-	9	987	c.811C>T	c.(811-813)CGG>TGG	p.R271W	ADAP1_uc003sjm.3_Missense_Mutation_p.R97W|ADAP1_uc011jvs.1_Missense_Mutation_p.R176W|ADAP1_uc003sjn.3_Missense_Mutation_p.R199W|ADAP1_uc010ksc.2_Missense_Mutation_p.R199W	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1	271	PH 2.				cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						CAGCGCTTCCGGAAGCCTTCC	0.652													5	13					0	0	0.001984	0	0	
ZDHHC4	55146	broad.mit.edu	37	7	6620233	6620233	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:6620233T>C	uc003sqi.2	+	4	399	c.41T>C	c.(40-42)GTG>GCG	p.V14A	ZDHHC4_uc003sqg.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sql.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqh.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqj.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqk.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqm.2_Missense_Mutation_p.V14A	NM_001134388	NP_001127860	Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	14	Helical; (Potential).					integral to membrane	acyltransferase activity|zinc ion binding			breast(1)|pancreas(1)	2		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		CTGGCTTCGGTGCTGATGGGT	0.498													21	131					0	0	0.010504	0	0	
ZNF12	7559	broad.mit.edu	37	7	6731401	6731401	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:6731401G>A	uc003sqt.1	-	5	1726	c.1172C>T	c.(1171-1173)TCG>TTG	p.S391L	ZNF12_uc011jxa.1_Missense_Mutation_p.S229L|ZNF12_uc003sqs.1_Missense_Mutation_p.S353L	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	391	C2H2-type 5.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		TGACTTCTGCGAGAAGGTTTT	0.438													13	51					0	0	0.001855	0	0	
TMEM195	392636	broad.mit.edu	37	7	15458233	15458233	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:15458233C>T	uc003stb.1	-	5	729	c.559G>A	c.(559-561)GCT>ACT	p.A187T		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	187					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						AGATGAACAGCATATACTGAA	0.313													4	38					0	0	0.009096	0	0	
RPL23P8	222901	broad.mit.edu	37	7	20867022	20867022	+	RNA	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:20867022C>A	uc011jyj.1	+	1		c.106C>A				NR_026673				Homo sapiens ribosomal protein L23 pseudogene 8 (RPL23P8), non-coding RNA.												0						GAGCTGTGATCAACTGTGCTG	0.532													12	33					1.52009e-12	1.6972e-12	0.003163	1	0	
MPP6	51678	broad.mit.edu	37	7	24681374	24681374	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:24681374A>G	uc003swx.2	+	4	456	c.157A>G	c.(157-159)AGT>GGT	p.S53G	MPP6_uc003swy.2_Missense_Mutation_p.S53G	NM_016447	NP_057531	Q9NZW5	MPP6_HUMAN	membrane protein, palmitoylated 6	53	L27 2.				protein complex assembly		protein binding				0						AGAAGCTGTCAGTGACAATAA	0.343													7	82					0	0	0.001984	0	0	
CCDC129	223075	broad.mit.edu	37	7	31592688	31592688	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:31592688A>G	uc003tcj.1	+	2	1043	c.50A>G	c.(49-51)GAA>GGA	p.E17G	CCDC129_uc011kad.1_Missense_Mutation_p.E27G|CCDC129_uc003tci.1_Missense_Mutation_p.E16G|CCDC129_uc011kae.1_Missense_Mutation_p.E43G|CCDC129_uc003tck.1_5'Flank	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	17											0						GAAGGCCAGGAAAAGAGCAAG	0.498													8	33					0	0	0.008291	0	0	
PDE1C	5137	broad.mit.edu	37	7	32109997	32109997	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:32109997C>T	uc003tcm.1	-	1	478	c.9G>A	c.(7-9)TCG>TCA	p.S3S	PDE1C_uc003tcn.1_Silent_p.S3S|PDE1C_uc003tco.1_Intron|PDE1C_uc003tcr.2_Silent_p.S3S|PDE1C_uc003tcs.2_Silent_p.S3S	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	3					activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			CCTTGGTTGGCGACTCCATAG	0.562													21	58					0	0	0.008871	0	0	
AVL9	23080	broad.mit.edu	37	7	33078502	33078502	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:33078502C>T	uc011kai.1	+	12	1524	c.1378C>T	c.(1378-1380)CGT>TGT	p.R460C	NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron|uc003tdl.1_5'Flank	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	Error:Variant_position_missing_in_Q8NBF6_after_alignment						integral to membrane					0						GTGTAGAAGACGTGTTCAAAA	0.358													4	7					0	0	0.000602	0	0	
BBS9	27241	broad.mit.edu	37	7	33427709	33427709	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:33427709G>A	uc003tdn.1	+	19	2581	c.2068G>A	c.(2068-2070)GCC>ACC	p.A690T	BBS9_uc003tdo.1_Missense_Mutation_p.A655T|BBS9_uc003tdp.1_Missense_Mutation_p.A685T|BBS9_uc003tdq.1_Missense_Mutation_p.A650T|BBS9_uc010kwn.1_RNA|BBS9_uc003tdr.1_Missense_Mutation_p.A214T|BBS9_uc003tds.1_Missense_Mutation_p.A113T|BBS9_uc003tdt.2_RNA	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	690					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TAAAACTCCTGCCCCTCTTCA	0.393									Bardet-Biedl_syndrome				19	156					0	0	0.012319	0	0	
ELMO1	9844	broad.mit.edu	37	7	37052934	37052934	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:37052934T>C	uc003tfk.1	-	16	1714	c.1407A>G	c.(1405-1407)GAA>GAG	p.E469E	ELMO1_uc011kbc.1_Silent_p.E373E|ELMO1_uc010kxg.1_Silent_p.E469E	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	469	ELMO.				actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						TTGCCCTCATTTCCTTCCATG	0.517													12	48					0	0	0.010729	0	0	
CDK13	8621	broad.mit.edu	37	7	40132832	40132832	+	Silent	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:40132832G>C	uc003thh.3	+	13	3966	c.3684G>C	c.(3682-3684)GTG>GTC	p.V1228V	CDK13_uc003thi.3_Silent_p.V1168V|CDK13_uc003thj.2_Silent_p.V279V|CDK13_uc003thk.2_Silent_p.V161V	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	1228					alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5						GCACTCCGGTGTCGGGTAAGT	0.453													11	48					0	0	0.008291	0	0	
GLI3	2737	broad.mit.edu	37	7	42005251	42005251	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:42005251G>T	uc011kbh.1	-	15	3511	c.3420C>A	c.(3418-3420)GGC>GGA	p.G1140G	GLI3_uc011kbg.1_Silent_p.G1081G	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1140					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						GGAACTGCTGGCCAGCGTGGC	0.677									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				7	40					0.000274275	0.000291298	0.004482	1	0	
DDX56	54606	broad.mit.edu	37	7	44612618	44612618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:44612618C>T	uc003tlg.2	-	3	897	c.254G>A	c.(253-255)GGC>GAC	p.G85D	DDX56_uc003tle.2_RNA|DDX56_uc003tlf.2_Missense_Mutation_p.G21D|DDX56_uc003tlh.2_RNA|DDX56_uc010kyg.2_Missense_Mutation_p.G85D|DDX56_uc010kyh.1_Intron	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 56	85	Helicase ATP-binding.				rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding			upper_aerodigestive_tract(1)	1						AAGAACAAGGCCTCTCACTGC	0.522													16	104					0	0	0.006122	0	0	
OGDH	4967	broad.mit.edu	37	7	44713473	44713473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:44713473C>T	uc003tln.2	+	6	830	c.721C>T	c.(721-723)CCT>TCT	p.P241S	OGDH_uc003tlm.2_Missense_Mutation_p.P241S|OGDH_uc011kbx.1_Missense_Mutation_p.P237S|OGDH_uc011kby.1_Intron|OGDH_uc003tlp.2_Missense_Mutation_p.P252S|OGDH_uc011kbz.1_Intron|OGDH_uc003tlo.1_Missense_Mutation_p.P74S	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	241					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)	GTTTGAGACCCCTGGGATCAT	0.562													20	83					0	0	0.008871	0	0	
IKZF1	10320	broad.mit.edu	37	7	50467674	50467674	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:50467674C>T	uc003tow.3	+	9	1077	c.909C>T	c.(907-909)AAC>AAT	p.N303N	IKZF1_uc003tox.3_Silent_p.N261N|IKZF1_uc003toy.3_Silent_p.N261N|IKZF1_uc011kck.1_Silent_p.N216N|IKZF1_uc003toz.3_Silent_p.N273N|IKZF1_uc010kyx.2_Silent_p.N43N|IKZF1_uc003tpa.3_Silent_p.N45N	NM_006060	NP_006051	Q13422	IKZF1_HUMAN	zinc finger protein, subfamily 1A, 1 (Ikaros)	303					cell cycle|chromatin modification|mesoderm development	cytoplasm|nucleus	zinc ion binding			haematopoietic_and_lymphoid_tissue(147)|lung(1)	148	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				AGAAGGAGAACGAAATGATGA	0.652			D		ALL								10	27					0	0	0.006214	0	0	
COBL	23242	broad.mit.edu	37	7	51096609	51096609	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:51096609G>A	uc003tpr.3	-	10	2369	c.2184C>T	c.(2182-2184)ACC>ACT	p.T728T	COBL_uc003tps.2_Silent_p.T785T|COBL_uc011kcl.1_Silent_p.T728T|COBL_uc003tpp.3_Silent_p.T514T|COBL_uc003tpq.3_Silent_p.T669T|COBL_uc003tpo.3_Silent_p.T270T	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	728										skin(3)|ovary(2)	5	Glioma(55;0.08)					TAATGGCTCCGGTGGAGAGGG	0.507													7	45					0	0	0.001984	0	0	
ZNF680	340252	broad.mit.edu	37	7	63981628	63981628	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:63981628A>T	uc003tta.2	-	4	1677	c.1504T>A	c.(1504-1506)TCC>ACC	p.S502T	ZNF680_uc010kzr.2_Missense_Mutation_p.S429T	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	502	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)				AGGTGTGAGGACCGGTTAAAA	0.348													4	73					0	0	0.009096	0	0	
VKORC1L1	154807	broad.mit.edu	37	7	65419074	65419074	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:65419074C>T	uc003tul.2	+	3	420	c.318C>T	c.(316-318)AGC>AGT	p.S106S	VKORC1L1_uc011kds.1_Missense_Mutation_p.R70C|VKORC1L1_uc003tum.1_5'Flank	NM_173517	NP_775788	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit	106	Helical; (Potential).					integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)	TGACAGCAAGCGCTGTGGCGG	0.537													5	50					0	0	0.013537	0	0	
TBL2	26608	broad.mit.edu	37	7	72988315	72988315	+	Silent	SNP	G	A	A	rs147754612		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:72988315G>A	uc003tyh.2	-	3	533	c.399C>T	c.(397-399)AAC>AAT	p.N133N	TBL2_uc011kex.1_Silent_p.N97N|TBL2_uc010lbg.2_Silent_p.N38N|TBL2_uc003tyi.2_Translation_Start_Site|TBL2_uc011key.1_Silent_p.N4N|TBL2_uc010lbh.2_Silent_p.N38N	NM_012453	NP_036585	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	133											0		Lung NSC(55;0.0659)|all_lung(88;0.152)				CCAGCTCCACGTTGGCTCTCA	0.607													5	39					0	0	0.001168	0	0	
CLIP2	7461	broad.mit.edu	37	7	73778608	73778608	+	Missense_Mutation	SNP	G	A	A	rs140333329		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:73778608G>A	uc003uam.2	+	8	1670	c.1343G>A	c.(1342-1344)CGC>CAC	p.R448H	CLIP2_uc003uan.2_Missense_Mutation_p.R448H	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	448	Potential.					microtubule associated complex				skin(3)	3						CTGCAGTTCCGCGTGGAGGAG	0.607													6	13					0	0	0.001984	0	0	
POM121C	100101267	broad.mit.edu	37	7	75053846	75053846	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:75053846T>C	uc003udk.3	-	11	1719	c.834A>G	c.(832-834)TCA>TCG	p.S278S		NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like	520	Pore side (Potential).				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						ACCACTGTAATGAAGCCTTCT	0.478													25	116					0	0	0.006320	0	0	
YWHAG	7532	broad.mit.edu	37	7	75959484	75959484	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:75959484C>T	uc011kgj.1	-	2	371	c.154G>A	c.(154-156)GTT>ATT	p.V52I		NM_012479	NP_036611	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan	52					G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity			ovary(1)|lung(1)	2						GCCCCCACAACGTTCTTGTAG	0.517													8	58					0	0	0.003080	0	0	
ZP3	7784	broad.mit.edu	37	7	76062907	76062907	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:76062907C>T	uc003ufd.3	+	4	666	c.656C>T	c.(655-657)GCC>GTC	p.A219V	ZP3_uc003ufc.3_Missense_Mutation_p.A168V|ZP3_uc003ufe.2_Missense_Mutation_p.A127V	NM_001110354	NP_001103824	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 isoform 1	219	Extracellular (Potential).|ZP.				binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0						CACTGCGTGGCCACACCGACA	0.592													15	57					0	0	0.003163	0	0	
CCDC146	57639	broad.mit.edu	37	7	76891552	76891552	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:76891552G>T	uc003uga.2	+	9	1228	c.1101G>T	c.(1099-1101)ATG>ATT	p.M367I	CCDC146_uc010ldp.2_Missense_Mutation_p.M113I	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	367										ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TAAGAAAGATGGAACTGCTCT	0.403													11	78					2.80697e-09	3.08473e-09	0.010729	1	0	
GNAI1	2770	broad.mit.edu	37	7	79818534	79818534	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:79818534A>G	uc003uhb.1	+	3	627	c.290A>G	c.(289-291)GAC>GGC	p.D97G	GNAI1_uc011kgt.1_Missense_Mutation_p.D45G	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	97					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						GACTTTGGTGACTCAGCCCGG	0.413													4	51					0	0	0.009096	0	0	
PCLO	27445	broad.mit.edu	37	7	82579728	82579728	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:82579728G>A	uc003uhx.2	-	6	10465	c.10176C>T	c.(10174-10176)AGC>AGT	p.S3392S	PCLO_uc003uhv.2_Silent_p.S3392S|PCLO_uc010lec.2_Silent_p.S357S	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3323					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						CTGAAACAGTGCTCAGGATAC	0.438													5	58					0	0	0.001984	0	0	
PCLO	27445	broad.mit.edu	37	7	82584025	82584025	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:82584025G>T	uc003uhx.2	-	5	6533	c.6244C>A	c.(6244-6246)CCA>ACA	p.P2082T	PCLO_uc003uhv.2_Missense_Mutation_p.P2082T	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2013					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						GCCTGGGTTGGGCTAGATCCA	0.468													14	71					1.3612e-06	1.47464e-06	0.003163	1	0	
SEMA3A	10371	broad.mit.edu	37	7	83764138	83764138	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:83764138T>A	uc003uhz.2	-	2	557	c.242A>T	c.(241-243)GAC>GTC	p.D81V		NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor	81	Sema.				axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4						ATTAACCAGGTCGAATGAAAA	0.358													14	67					0	0	0.002450	0	0	
ABCB1	5243	broad.mit.edu	37	7	87196110	87196110	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:87196110C>T	uc003uiz.1	-	7	939	c.521G>A	c.(520-522)CGA>CAA	p.R174Q	ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	174	ABC transmembrane type-1 1.				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	CTCTGTAAGTCGGGTGTTAAG	0.368													16	31					0	0	0.006122	0	0	
ZNF804B	219578	broad.mit.edu	37	7	88964957	88964957	+	Silent	SNP	G	A	A	rs138375583	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:88964957G>A	uc011khi.1	+	4	3199	c.2661G>A	c.(2659-2661)AGG>AGA	p.R887R		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	887						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GAAAAGTCAGGCCCATGAAGT	0.433										HNSCC(36;0.09)			11	119					0	0	0.008291	0	0	
STEAP1	26872	broad.mit.edu	37	7	89790129	89790129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:89790129C>T	uc003ujx.2	+	3	295	c.95C>T	c.(94-96)ACG>ATG	p.T32M	STEAP1_uc010lem.2_Missense_Mutation_p.T32M	NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the	32					electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)					CATAAGGACACGGGAGAGACC	0.388													11	122					0	0	0.008291	0	0	
PEX1	5189	broad.mit.edu	37	7	92146932	92146932	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:92146932G>A	uc003uly.2	-	5	993	c.897C>T	c.(895-897)AAC>AAT	p.N299N	PEX1_uc011khr.1_Silent_p.N91N|PEX1_uc010ley.2_Silent_p.N299N|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	299					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTGCTGACGCGTTATATATAC	0.368													13	36					0	0	0.001855	0	0	
C7orf64	84060	broad.mit.edu	37	7	92163897	92163897	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:92163897T>C	uc003ulz.2	+	4	671	c.630T>C	c.(628-630)TGT>TGC	p.C210C	C7orf64_uc011khu.1_3'UTR|C7orf64_uc003uma.2_Silent_p.C210C	NM_032120	NP_115496	Q5RL73	CG064_HUMAN	hypothetical protein LOC84060	210							nucleotide binding			ovary(2)	2						CCTCAAAATGTATGTGTTCAT	0.413													8	68					0	0	0.003080	0	0	
HEPACAM2	253012	broad.mit.edu	37	7	92848540	92848540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:92848540G>A	uc003umm.2	-	2	327	c.304C>T	c.(304-306)CCA>TCA	p.P102S	HEPACAM2_uc003uml.2_Missense_Mutation_p.P90S|HEPACAM2_uc010lff.2_Missense_Mutation_p.P90S|HEPACAM2_uc011khy.1_Missense_Mutation_p.P125S	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	102	Extracellular (Potential).					integral to membrane		p.F102L(1)		ovary(3)|breast(1)|kidney(1)	5						GCATTGGGTGGCATCATGGTG	0.463													15	62					0	0	0.002450	0	0	
CCDC132	55610	broad.mit.edu	37	7	92882054	92882054	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:92882054T>C	uc003umo.2	+	3	319	c.191T>C	c.(190-192)GTG>GCG	p.V64A	CCDC132_uc003umq.2_RNA|CCDC132_uc003ump.2_Missense_Mutation_p.V34A|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron|CCDC132_uc003umn.2_Missense_Mutation_p.V64A	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	64											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TATTTTTCTGTGGATTCATTT	0.323													10	55					0	0	0.008291	0	0	
CASD1	64921	broad.mit.edu	37	7	94184921	94184921	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:94184921G>A	uc003uni.3	+	18	2472	c.2245G>A	c.(2245-2247)GCA>ACA	p.A749T	CASD1_uc003unj.3_Missense_Mutation_p.A749T	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor	749						integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			TGTTTGTGTGGCACATGAAAT	0.393													9	76					0	0	0.006214	0	0	
SGCE	8910	broad.mit.edu	37	7	94252690	94252690	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:94252690C>T	uc003unl.2	-	4	521	c.410G>A	c.(409-411)CGC>CAC	p.R137H	SGCE_uc003unm.2_Missense_Mutation_p.R137H|SGCE_uc003unn.2_Missense_Mutation_p.R137H|SGCE_uc011kic.1_Missense_Mutation_p.R96H|SGCE_uc011kid.1_Missense_Mutation_p.R173H	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2	137	Extracellular (Potential).				cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CTCAAAGGTGCGCCTGTTGTA	0.274													6	28					0	0	0.003080	0	0	
LMTK2	22853	broad.mit.edu	37	7	97823050	97823050	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:97823050G>A	uc003upd.1	+	11	3566	c.3273G>A	c.(3271-3273)ACG>ACA	p.T1091T		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1091					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CCCCTGAGACGTTCACAGCTG	0.607													8	35					0	0	0.004482	0	0	
TECPR1	25851	broad.mit.edu	37	7	97872868	97872868	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:97872868G>A	uc003upg.2	-	6	773	c.568C>T	c.(568-570)CCC>TCC	p.P190S	TECPR1_uc003uph.1_Missense_Mutation_p.P111S	NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	190						integral to membrane	protein binding			pancreas(1)	1						TCGTTGAAGGGGTCGGGCAGC	0.622													10	26					0	0	0.006214	0	0	
AGFG2	3268	broad.mit.edu	37	7	100151089	100151089	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:100151089C>T	uc003uvf.2	+	4	687	c.551C>T	c.(550-552)CCG>CTG	p.P184L	AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_Missense_Mutation_p.R46C	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	184					regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1						GATCCTGCACCGTCTCTCTCA	0.557													9	51					0	0	0.010729	0	0	
ACTL6B	51412	broad.mit.edu	37	7	100247736	100247736	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:100247736T>A	uc003uvy.2	-	5	499	c.392A>T	c.(391-393)GAG>GTG	p.E131V	ACTL6B_uc003uvx.1_5'Flank|ACTL6B_uc003uvz.2_RNA	NM_016188	NP_057272	O94805	ACL6B_HUMAN	actin-like 6B	131					chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex|SWI/SNF complex	ATP binding|protein binding|structural constituent of cytoskeleton			ovary(1)	1	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TGTCAGCTTCTCCCGCTTGGC	0.463													9	31					0	0	0.004482	0	0	
TRIP6	7205	broad.mit.edu	37	7	100469244	100469244	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:100469244C>A	uc003uww.2	+	7	1249	c.1079C>A	c.(1078-1080)CCT>CAT	p.P360H		NM_003302	NP_003293	Q15654	TRIP6_HUMAN	thyroid receptor-interacting protein 6	360	LIM zinc-binding 2.				focal adhesion assembly|positive regulation of cell migration|regulation of transcription, DNA-dependent|release of cytoplasmic sequestered NF-kappaB|transcription, DNA-dependent	cytoplasm|cytoskeleton|focal adhesion|nucleus	identical protein binding|interleukin-1 receptor binding|kinase binding|thyroid hormone receptor binding|zinc ion binding			central_nervous_system(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					GCCTACCACCCTGGCTGCTTC	0.622													9	36					0.000978159	0.00103168	0.010729	1	0	
MUC17	140453	broad.mit.edu	37	7	100677874	100677874	+	Silent	SNP	G	A	A	rs147962629	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:100677874G>A	uc003uxp.1	+	3	3230	c.3177G>A	c.(3175-3177)ACG>ACA	p.T1059T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1059	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|15.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					GTTCTGAAACGAGCACACTTT	0.502													85	328					0	0	0.014410	0	0	
SERPINE1	5054	broad.mit.edu	37	7	100773872	100773872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:100773872G>A	uc003uxt.2	+	3	590	c.442G>A	c.(442-444)GAC>AAC	p.D148N	SERPINE1_uc011kkj.1_Missense_Mutation_p.D133N|SERPINE1_uc003uxu.1_5'Flank	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1	148					angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	CAAGCAAGTGGACTTTTCAGA	0.552													8	279					0	0	0.006214	0	0	
ORAI2	80228	broad.mit.edu	37	7	102086989	102086989	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:102086989G>A	uc010lhz.1	+	4	490	c.255G>A	c.(253-255)ACG>ACA	p.T85T	ORAI2_uc003uzj.2_Silent_p.T85T|ORAI2_uc003uzk.2_Silent_p.T85T|ORAI2_uc011kks.1_Silent_p.T8T	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	85						integral to membrane	protein binding			ovary(1)|kidney(1)	2						AGCTGGAGACGCAGTACCAGT	0.672													4	9					0	0	0.009096	0	0	
PSMC2	5701	broad.mit.edu	37	7	103002424	103002424	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:103002424C>T	uc003vbs.2	+	5	381	c.311C>T	c.(310-312)GCT>GTT	p.A104V	SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|PSMC2_uc011kln.1_Missense_Mutation_p.A104V|PSMC2_uc011klo.1_5'UTR	NM_002803	NP_002794	P35998	PRS7_HUMAN	proteasome 26S ATPase subunit 2	104					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|interspecies interaction between organisms|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	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0						ATAATCAATGCTGATTCGGAG	0.388													18	66					0	0	0.006122	0	0	
RELN	5649	broad.mit.edu	37	7	103138557	103138557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:103138557G>A	uc003vca.2	-	54	8970	c.8810C>T	c.(8809-8811)GCG>GTG	p.A2937V	RELN_uc010liz.2_Missense_Mutation_p.A2937V	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2937					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TTGTGTAACCGCTTGTCTCAC	0.428													19	108					0	0	0.007413	0	0	
COG5	10466	broad.mit.edu	37	7	106851578	106851578	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:106851578G>A	uc003ved.2	-	19	2816	c.2291C>T	c.(2290-2292)ACG>ATG	p.T764M	COG5_uc003vec.2_Missense_Mutation_p.T785M|COG5_uc003vee.2_Missense_Mutation_p.T785M	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform	764					intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						GGGTGCTCTCGTGAACAAAAA	0.468													14	55					0	0	0.004007	0	0	
FOXP2	93986	broad.mit.edu	37	7	114270000	114270000	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:114270000G>A	uc003vhb.2	+	5	911	c.537G>A	c.(535-537)CAG>CAA	p.Q179Q	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Silent_p.Q204Q|FOXP2_uc003vha.2_Silent_p.Q87Q|FOXP2_uc011kmu.1_Silent_p.Q196Q|FOXP2_uc011kmv.1_Silent_p.Q179Q|FOXP2_uc010ljz.1_Silent_p.Q87Q|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_Silent_p.Q179Q|FOXP2_uc003vgx.2_Silent_p.Q179Q|FOXP2_uc003vhd.2_Silent_p.Q179Q|FOXP2_uc003vhc.2_Silent_p.Q204Q	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	179	Gln-rich.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						agcaacaacagcagcagcagc	0.159													5	16					0	0	0.013537	0	0	
CFTR	1080	broad.mit.edu	37	7	117232480	117232480	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:117232480C>T	uc003vjd.2	+	14	2391	c.2259C>T	c.(2257-2259)AGC>AGT	p.S753S	CFTR_uc011knq.1_Silent_p.S159S	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	753	Cytoplasmic (Potential).				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	CTCGCATCAGCGTGATCAGCA	0.512									Cystic_Fibrosis				9	32					0	0	0.004482	0	0	
CTTNBP2	83992	broad.mit.edu	37	7	117407207	117407207	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:117407207C>T	uc003vjf.2	-	9	2894	c.2802G>A	c.(2800-2802)AGG>AGA	p.R934R		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	934	ANK 6.									ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GCCCTCCGTGCCTACACAAGA	0.443													4	87					0	0	0.009096	0	0	
C7orf58	79974	broad.mit.edu	37	7	120629693	120629693	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:120629693G>A	uc003vjq.3	+	2	465	c.18G>A	c.(16-18)GTG>GTA	p.V6V	C7orf58_uc003vjr.1_Silent_p.V6V|C7orf58_uc003vjs.3_Silent_p.V6V	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	6						endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					GTCGCCCAGTGTTCCCTTGTC	0.527													10	56					0	0	0.013537	0	0	
ASB15	142685	broad.mit.edu	37	7	123267253	123267253	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:123267253C>T	uc003vku.1	+	9	1079	c.787C>T	c.(787-789)CTG>TTG	p.L263L	ASB15_uc003vkv.1_Silent_p.L263L|ASB15_uc003vkw.1_Silent_p.L263L	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box-containing 15	263	ANK 5.				intracellular signal transduction					skin(2)|lung(1)	3						TTCCCTCCTGCTGGAATATGG	0.517													10	29					0	0	0.006214	0	0	
FLNC	2318	broad.mit.edu	37	7	128484899	128484899	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:128484899G>A	uc003vnz.3	+	21	3589	c.3380G>A	c.(3379-3381)GGC>GAC	p.G1127D	FLNC_uc003voa.3_Missense_Mutation_p.G1127D	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1127	Filamin 9.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						ACGGAGCCTGGCGAGTACACC	0.627													16	48					0	0	0.008871	0	0	
FLNC	2318	broad.mit.edu	37	7	128486107	128486107	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:128486107G>A	uc003vnz.3	+	22	4063	c.3854G>A	c.(3853-3855)GGC>GAC	p.G1285D	FLNC_uc003voa.3_Missense_Mutation_p.G1285D	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1285	Filamin 11.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						GCCACAGGCGGCAACCACGTG	0.632													7	21					0	0	0.010729	0	0	
AHCYL2	23382	broad.mit.edu	37	7	129019487	129019487	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:129019487G>C	uc011kov.1	+	2	426	c.372G>C	c.(370-372)CAG>CAC	p.Q124H	AHCYL2_uc003vot.2_Missense_Mutation_p.Q123H|AHCYL2_uc003vov.2_Missense_Mutation_p.Q21H|AHCYL2_uc011kow.1_Missense_Mutation_p.Q22H|AHCYL2_uc011kox.1_Missense_Mutation_p.Q21H	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform	124					one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						AGCAGATCCAGTTTGCTGACC	0.408													6	30					0	0	0.001984	0	0	
FAM40B	57464	broad.mit.edu	37	7	129096401	129096401	+	Missense_Mutation	SNP	C	T	T	rs150058386		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:129096401C>T	uc011koy.1	+	9	996	c.956C>T	c.(955-957)CCG>CTG	p.P319L	FAM40B_uc003vow.2_Missense_Mutation_p.P319L|FAM40B_uc011koz.1_5'Flank	NM_020704	NP_065755	Q9ULQ0	FA40B_HUMAN	hypothetical protein LOC57464 isoform a	319											0						GCTGCCTCCCCGCCCTCTTAC	0.602													14	44					0	0	0.003163	0	0	
TSGA13	114960	broad.mit.edu	37	7	130364019	130364019	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:130364019A>G	uc003vqi.2	-	5	818	c.361T>C	c.(361-363)TCC>CCC	p.S121P	TSGA13_uc003vqj.2_Missense_Mutation_p.S121P	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13	121										ovary(2)	2	Melanoma(18;0.0435)					AACTCCTTGGAAAAATATTTT	0.443													9	91					0	0	0.004482	0	0	
PLXNA4	91584	broad.mit.edu	37	7	131866287	131866287	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:131866287G>A	uc003vra.3	-	18	3574	c.3345C>T	c.(3343-3345)CCC>CCT	p.P1115P		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1115	Extracellular (Potential).|IPT/TIG 3.					integral to membrane|intracellular|plasma membrane				ovary(1)	1						CAAACTCCTCGGGCCTCTCGG	0.577													12	43					0	0	0.001855	0	0	
LRGUK	136332	broad.mit.edu	37	7	133906546	133906546	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:133906546A>G	uc003vrm.1	+	16	1875	c.1859A>G	c.(1858-1860)CAC>CGC	p.H620R		NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain	620							ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5						AAGACATCCCACCTGAAACCT	0.313													11	75					0	0	0.013537	0	0	
AKR1B1	231	broad.mit.edu	37	7	134135578	134135578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:134135578T>C	uc003vrp.1	-	3	385	c.311A>G	c.(310-312)TAC>TGC	p.Y104C	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	104					C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)	GAGGTCCAGGTAGTCCAGCTT	0.572													9	40					0	0	0.004482	0	0	
DGKI	9162	broad.mit.edu	37	7	137172408	137172408	+	Missense_Mutation	SNP	C	T	T	rs148779791		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:137172408C>T	uc003vtt.2	-	23	2331	c.2330G>A	c.(2329-2331)CGT>CAT	p.R777H	DGKI_uc003vtu.2_Missense_Mutation_p.R477H	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	777					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						ACAGTCTCCACGCACAACTAG	0.368													40	198					0	0	0.011902	0	0	
ATP6V0A4	50617	broad.mit.edu	37	7	138418958	138418958	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:138418958C>T	uc003vuf.2	-	15	1852	c.1614G>A	c.(1612-1614)TCG>TCA	p.S538S	ATP6V0A4_uc003vug.2_Silent_p.S538S|ATP6V0A4_uc003vuh.2_Silent_p.S538S	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	538	Cytoplasmic (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						TCATTTTATACGAGTTCAGAA	0.413													15	63					0	0	0.004007	0	0	
TTC26	79989	broad.mit.edu	37	7	138865925	138865925	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:138865925T>A	uc003vus.2	+	16	1514	c.1400T>A	c.(1399-1401)ATT>AAT	p.I467N	TTC26_uc011kqn.1_Missense_Mutation_p.I467N|TTC26_uc011kqo.1_Missense_Mutation_p.I436N|TTC26_uc011kqp.1_Missense_Mutation_p.I362N|TTC26_uc003vut.2_Missense_Mutation_p.I327N|TTC26_uc011kqq.1_Missense_Mutation_p.I336N	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1	467							binding			ovary(1)	1						TTACAGCTCATTGCTAATGAC	0.393													22	59					0	0	0.002780	0	0	
BRAF	673	broad.mit.edu	37	7	140453128	140453128	+	Nonsense_Mutation	SNP	G	A	A	rs104886015		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:140453128G>A	uc003vwc.3	-	15	1868	c.1807C>T	c.(1807-1809)CGA>TGA	p.R603*		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	603	Protein kinase.				activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.R603*(4)|p.T599_R603>I(2)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.V600_W604del(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	CCACTCCATCGAGATTTCACT	0.383		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				20	63					0	0	0.012319	0	0	
LOC93432	93432	broad.mit.edu	37	7	141843582	141843582	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:141843582C>T	uc003vwz.2	+	13	1390	c.1331C>T	c.(1330-1332)CCG>CTG	p.P444L		NR_003715				RecName: Full=Putative maltase-glucoamylase-like protein LOC93432;												0						TATCCGGGACCGACAGTCTTT	0.463													2	1					0	0	0.004672	0	0	
OR9A2	135924	broad.mit.edu	37	7	142723873	142723873	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:142723873A>G	uc003wcc.1	-	1	347	c.347T>C	c.(346-348)GTG>GCG	p.V116A		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	116					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.059)					ATAACGGTCCACAGCCATCAC	0.448													11	57					0	0	0.013537	0	0	
TPK1	27010	broad.mit.edu	37	7	144320278	144320278	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:144320278A>G	uc003weq.2	-	6	438	c.335T>C	c.(334-336)ATA>ACA	p.I112T	TPK1_uc003weo.2_Missense_Mutation_p.I107T|TPK1_uc003wep.2_RNA|TPK1_uc003wer.2_Missense_Mutation_p.I112T|TPK1_uc003wes.2_RNA	NM_022445	NP_071890	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1 isoform a	112					thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)	TTTTTCTTCTATCTTCTTTTG	0.323													37	141					0	0	0.004878	0	0	
ZNF398	57541	broad.mit.edu	37	7	148876693	148876693	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:148876693C>T	uc003wfl.2	+	6	2004	c.1729C>T	c.(1729-1731)CGC>TGC	p.R577C	ZNF398_uc011kul.1_Missense_Mutation_p.R406C|ZNF398_uc011kum.1_Missense_Mutation_p.R582C	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	577	C2H2-type 9.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			CAGGAGCTTCCGCTACAAACA	0.602													6	24					0	0	0.003080	0	0	
ZNF777	27153	broad.mit.edu	37	7	149129387	149129387	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:149129387G>A	uc003wfv.2	-	6	2139	c.1976C>T	c.(1975-1977)ACG>ATG	p.T659M		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	659					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CCGCTCACCCGTGTGCGTGAT	0.632													18	70					0	0	0.010504	0	0	
ZNF777	27153	broad.mit.edu	37	7	149133705	149133705	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:149133705C>T	uc003wfv.2	-	5	1463	c.1300G>A	c.(1300-1302)GAA>AAA	p.E434K		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	434	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TGCTTCAGTTCGCTGAACTCG	0.652													4	32					0	0	0.009096	0	0	
SSPO	23145	broad.mit.edu	37	7	149485990	149485990	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:149485990C>T	uc010lpk.2	+	29	4209	c.4209C>T	c.(4207-4209)GGC>GGT	p.G1403G		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	1403	LDL-receptor class A 1.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ACGACTGTGGCGATGGCTCTG	0.582													7	12					0	0	0.001984	0	0	
SSPO	23145	broad.mit.edu	37	7	149508064	149508064	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:149508064C>T	uc010lpk.2	+	67	9458	c.9458C>T	c.(9457-9459)CCG>CTG	p.P3153L		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	3153					cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTCTACCCCCCGGGCAGCACT	0.602													7	13					0	0	0.003080	0	0	
ZNF862	643641	broad.mit.edu	37	7	149547397	149547397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:149547397C>T	uc010lpn.2	+	5	1279	c.1087C>T	c.(1087-1089)CGG>TGG	p.R363W	ZNF862_uc003wgm.2_RNA	NM_001099220	NP_001092690	O60290	ZN862_HUMAN	zinc finger protein 862	363	KRAB 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|nucleic acid binding|protein dimerization activity			skin(1)	1						AGACGTGATGCGGATGAACTA	0.577													6	13					0	0	0.004482	0	0	
CHPF2	54480	broad.mit.edu	37	7	150935265	150935265	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:150935265G>A	uc003wjr.1	+	4	3330	c.1817G>A	c.(1816-1818)CGC>CAC	p.R606H	CHPF2_uc003wjq.1_Missense_Mutation_p.R598H|MIR671_hsa-mir-671|MI0003760_5'Flank	NM_019015	NP_061888	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	606	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(1)	1						GTCCTCAACCGCTGTCGCATG	0.587													4	44					0	0	0.009096	0	0	
HTR5A	3361	broad.mit.edu	37	7	154862889	154862889	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:154862889A>G	uc003wlu.1	+	1	344	c.280A>G	c.(280-282)ATG>GTG	p.M94V	uc011kvt.1_Missense_Mutation_p.M42T|uc003wlt.2_Missense_Mutation_p.M42T	NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	94	Helical; Name=2; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		CGCGCTGGTCATGCCGCTGAG	0.682													3	13					0	0	0.009096	0	0	
PTPRN2	5799	broad.mit.edu	37	7	157959878	157959878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:157959878G>A	uc003wno.2	-	6	776	c.655C>T	c.(655-657)CGG>TGG	p.R219W	PTPRN2_uc003wnp.2_Missense_Mutation_p.R202W|PTPRN2_uc003wnq.2_Missense_Mutation_p.R219W|PTPRN2_uc003wnr.2_Missense_Mutation_p.R181W|PTPRN2_uc011kwa.1_Missense_Mutation_p.R242W	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	219	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCGAGGGTCCGCGGCAGGAGG	0.657													4	21					0	0	0.000602	0	0	
WDR60	55112	broad.mit.edu	37	7	158734693	158734693	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:158734693G>A	uc003woe.3	+	24	3014	c.2856G>A	c.(2854-2856)ACG>ACA	p.T952T	WDR60_uc010lqv.2_RNA|WDR60_uc010lqw.2_Silent_p.T584T	NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	952	WD 4.									ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		ACAGCAGCACGGACAGCCATG	0.622													5	33					0	0	0.001168	0	0	
CSMD1	64478	broad.mit.edu	37	8	3008925	3008925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:3008925C>T	uc011kwk.1	-	40	6418	c.6028G>A	c.(6028-6030)GGC>AGC	p.G2010S	CSMD1_uc011kwj.1_Missense_Mutation_p.G1402S|CSMD1_uc003wqe.2_Missense_Mutation_p.G1166S|CSMD1_uc010lrg.2_Missense_Mutation_p.G78S	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2010	Extracellular (Potential).|CUB 12.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTACCATAGCCGATGGGTAAT	0.443													8	41					0	0	0.004482	0	0	
MCPH1	79648	broad.mit.edu	37	8	6302423	6302423	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:6302423C>T	uc003wqi.2	+	8	1248	c.1180C>T	c.(1180-1182)CTG>TTG	p.L394L	MCPH1_uc003wqh.2_Silent_p.L394L|MCPH1_uc011kwl.1_Silent_p.L346L	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	394						microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GGAAGACAGGCTGCAGCACGT	0.512													18	31					0	0	0.008871	0	0	
SOX7	83595	broad.mit.edu	37	8	10692279	10692279	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:10692279C>T	uc011kwz.1	-	2	59	c.26G>A	c.(25-27)CGG>CAG	p.R9Q	PINX1_uc003wth.2_Missense_Mutation_p.R9Q|PINX1_uc003wti.2_Missense_Mutation_p.R9Q	NM_031439	NP_113627	Q9BT81	SOX7_HUMAN	SRY-box 7	Error:Variant_position_missing_in_Q9BT81_after_alignment					endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)		CTTCTGCTTCCGCCGACCTGT	0.448													4	43					0	0	0.009096	0	0	
DLC1	10395	broad.mit.edu	37	8	12957788	12957788	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:12957788C>T	uc003wwm.2	-	9	2502	c.2058G>A	c.(2056-2058)GCG>GCA	p.A686A	DLC1_uc003wwk.1_Silent_p.A249A|DLC1_uc003wwl.1_Silent_p.A283A|DLC1_uc011kxx.1_Silent_p.A175A	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	686					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						GCTTTGAGGGCGCTTTGTGCT	0.557													34	94					0	0	0.004289	0	0	
MTUS1	57509	broad.mit.edu	37	8	17611860	17611860	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:17611860G>C	uc003wxv.2	-	2	1931	c.1457C>G	c.(1456-1458)ACG>AGG	p.T486R	MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_Missense_Mutation_p.T486R|MTUS1_uc010lsz.2_Missense_Mutation_p.T486R	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1	486						Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)		TGGGGTATTCGTTTTGATTGT	0.393													8	177					0	0	0.003080	0	0	
XPO7	23039	broad.mit.edu	37	8	21848376	21848376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:21848376C>T	uc003xaa.3	+	18	2089	c.1987C>T	c.(1987-1989)CGG>TGG	p.R663W	XPO7_uc010lti.2_Missense_Mutation_p.R672W|XPO7_uc010ltk.2_Missense_Mutation_p.R664W	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	663					mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		GACAGACATGCGGTGTCGGAC	0.418													46	234					0	0	0.014410	0	0	
XPO7	23039	broad.mit.edu	37	8	21857142	21857142	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:21857142C>T	uc003xaa.3	+	24	2841	c.2739C>T	c.(2737-2739)ATC>ATT	p.I913I	XPO7_uc010lti.2_Silent_p.I922I|XPO7_uc010ltk.2_Silent_p.I914I	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	913					mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		CTCACGTCATCATGTATATTC	0.448													35	72					0	0	0.003271	0	0	
REEP4	80346	broad.mit.edu	37	8	21996976	21996976	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:21996976G>A	uc003xau.1	-	5	823	c.370C>T	c.(370-372)CGG>TGG	p.R124W	REEP4_uc010ltt.1_Missense_Mutation_p.R124W|REEP4_uc011kyz.1_Missense_Mutation_p.R124W	NM_025232	NP_079508	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	124						integral to membrane				skin(1)	1				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		TTGAGGCCCCGCTTCCCGAAG	0.662													4	20					0	0	0.009096	0	0	
PIWIL2	55124	broad.mit.edu	37	8	22147407	22147407	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:22147407A>G	uc003xbn.2	+	9	1182	c.1034A>G	c.(1033-1035)GAC>GGC	p.D345G	PIWIL2_uc011kzf.1_Missense_Mutation_p.D345G|PIWIL2_uc010ltv.2_Missense_Mutation_p.D345G	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	345					DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		AACTTTTATGACCCTACAAGT	0.343													14	51					0	0	0.004007	0	0	
PIWIL2	55124	broad.mit.edu	37	8	22210726	22210726	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:22210726G>A	uc003xbn.2	+	21	2805	c.2657_splice	c.e21+1	p.W886_splice	PIWIL2_uc011kzf.1_Splice_Site_p.W886_splice|PIWIL2_uc010ltv.2_Splice_Site_p.W886_splice|PIWIL2_uc003xbo.2_Splice_Site_p.W40_splice	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		GCTGTGAGTGGTAAGTGAGCA	0.413													33	76					0	0	0.004289	0	0	
KIAA1967	57805	broad.mit.edu	37	8	22463333	22463333	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:22463333G>A	uc003xch.2	+	2	184	c.47G>A	c.(46-48)CGC>CAC	p.R16H	KIAA1967_uc003xci.2_Missense_Mutation_p.R16H|KIAA1967_uc003xcj.1_5'Flank	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	16					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		CCAGGGGGACGCAACTTCTCA	0.527													12	65					0	0	0.010729	0	0	
RHOBTB2	23221	broad.mit.edu	37	8	22864897	22864897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:22864897C>T	uc003xcq.2	+	5	1676	c.1139C>T	c.(1138-1140)CCG>CTG	p.P380L	RHOBTB2_uc003xcp.2_Missense_Mutation_p.P402L|RHOBTB2_uc011kzp.1_Missense_Mutation_p.P387L|uc003xcr.2_RNA	NM_015178	NP_055993	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2 isoform 3	380	BTB 1.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			ovary(1)|lung(1)	2		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		GGGTACCTACCGGGCAGGGGT	0.617													27	59					0	0	0.009535	0	0	
NEFL	4747	broad.mit.edu	37	8	24813156	24813156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:24813156C>T	uc003xee.2	-	1	976	c.874G>A	c.(874-876)GCC>ACC	p.A292T		NM_006158	NP_006149	P07196	NFL_HUMAN	neurofilament, light polypeptide 68kDa	292	Rod.|Coil 2B.				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		GTGTTCTTGGCGGCGCTCTCG	0.632													10	18					0	0	0.008291	0	0	
DPYSL2	1808	broad.mit.edu	37	8	26501484	26501484	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:26501484G>A	uc003xfb.1	+	10	1337	c.987G>A	c.(985-987)ACG>ACA	p.T329T	DPYSL2_uc003xfa.2_Silent_p.T434T|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_Silent_p.T293T	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	329					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		TCCAGGTCACGGGCAGTGCCC	0.542													8	21					0	0	0.006214	0	0	
DPYSL2	1808	broad.mit.edu	37	8	26501587	26501587	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:26501587G>A	uc003xfb.1	+	10	1440	c.1090G>A	c.(1090-1092)GTC>ATC	p.V364I	DPYSL2_uc003xfa.2_Missense_Mutation_p.V469I|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_Missense_Mutation_p.V328I	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	364					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		GCGGATGTCCGTCATCTGGGA	0.582													8	40					0	0	0.006214	0	0	
PTK2B	2185	broad.mit.edu	37	8	27303434	27303434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:27303434C>T	uc003xfn.1	+	29	3146	c.2338C>T	c.(2338-2340)CGG>TGG	p.R780W	PTK2B_uc003xfo.1_Missense_Mutation_p.R780W|PTK2B_uc003xfp.1_Missense_Mutation_p.R780W|PTK2B_uc003xfq.1_Intron	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	780				R -> G (in Ref. 2; AAB47217).	apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)		CCACAGCATGCGGGTAAGAGG	0.617													13	64					0	0	0.003163	0	0	
KIF13B	23303	broad.mit.edu	37	8	29005050	29005050	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:29005050C>T	uc003xhh.3	-	17	1942	c.1883G>A	c.(1882-1884)CGC>CAC	p.R628H	KIF13B_uc003xhj.2_Missense_Mutation_p.R525H	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	628	Potential.				microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		AAGCCTCTGGCGCTCCAGTGC	0.453													4	38					0	0	0.009096	0	0	
ADAM32	203102	broad.mit.edu	37	8	39068795	39068795	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:39068795C>T	uc003xmt.3	+	12	1430	c.1185C>T	c.(1183-1185)GGC>GGT	p.G395G	ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32	395	Disintegrin.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CAGTCTGTGGCAATGGCAGAT	0.338													8	14					0	0	0.006214	0	0	
ADAM18	8749	broad.mit.edu	37	8	39495209	39495209	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:39495209G>T	uc003xni.2	+	9	814	c.814G>T	c.(814-816)GCA>TCA	p.A272S	ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Missense_Mutation_p.A248S	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	272	Peptidase M12B.|Extracellular (Potential).				cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			CCATGACATAGCATACTTACT	0.338													18	58					1.01871e-10	1.12988e-10	0.008871	1	0	
ANK1	286	broad.mit.edu	37	8	41550195	41550195	+	Missense_Mutation	SNP	C	T	T	rs148942046	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:41550195C>T	uc003xok.2	-	31	3913	c.3829G>A	c.(3829-3831)GTG>ATG	p.V1277M	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Missense_Mutation_p.V593M|ANK1_uc003xoi.2_Missense_Mutation_p.V1277M|ANK1_uc003xoj.2_Missense_Mutation_p.V1277M|ANK1_uc003xol.2_Missense_Mutation_p.V1277M|ANK1_uc003xom.2_Missense_Mutation_p.V1318M	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1277					axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCCACCTCCACGAAGTTCTCA	0.577													39	197					0	0	0.013114	0	0	
AP3M2	10947	broad.mit.edu	37	8	42023047	42023047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:42023047C>T	uc003xop.2	+	7	1063	c.772C>T	c.(772-774)CGC>TGC	p.R258C	AP3M2_uc003xoo.2_Missense_Mutation_p.R258C|AP3M2_uc010lxe.2_RNA|AP3M2_uc003xoq.1_Missense_Mutation_p.R143C|AP3M2_uc003xor.1_Missense_Mutation_p.R258C	NM_001134296	NP_001127768	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	258	MHD.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			TGGAAACTTCCGCCTGCTGTC	0.453													39	85					0	0	0.006230	0	0	
PRKDC	5591	broad.mit.edu	37	8	48690324	48690324	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:48690324G>A	uc003xqi.2	-	85	12022	c.11965C>T	c.(11965-11967)CGG>TGG	p.R3989W	PRKDC_uc003xqj.2_Missense_Mutation_p.R3958W|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	3989	PI3K/PI4K.				cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				CGGAAGGCCCGGAGTGCGTGT	0.493								NHEJ					26	75					0	0	0.006320	0	0	
EFCAB1	79645	broad.mit.edu	37	8	49647682	49647682	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:49647682G>A	uc003xqo.2	-	1	189	c.29C>T	c.(28-30)ACG>ATG	p.T10M	EFCAB1_uc003xqn.3_RNA|EFCAB1_uc011ldj.1_Missense_Mutation_p.T10M|EFCAB1_uc010lxx.2_RNA|EFCAB1_uc011ldk.1_RNA	NM_024593	NP_078869	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1 isoform a	10							calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				TAAGGTGTCCGTCAGCTTCTG	0.612													10	87					0	0	0.013537	0	0	
PXDNL	137902	broad.mit.edu	37	8	52321554	52321554	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:52321554G>A	uc003xqu.3	-	17	2731	c.2630C>T	c.(2629-2631)ACG>ATG	p.T877M	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	877					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TGAATCCACCGTCGCAGAGGG	0.662													6	32					0	0	0.004482	0	0	
PXDNL	137902	broad.mit.edu	37	8	52321594	52321594	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:52321594G>A	uc003xqu.3	-	17	2691	c.2590C>T	c.(2590-2592)CGC>TGC	p.R864C	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	864					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GGGCTGGAGCGCGCGAAGAGC	0.662													10	21					0	0	0.001855	0	0	
NPBWR1	2831	broad.mit.edu	37	8	53853442	53853442	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:53853442C>T	uc011ldu.1	+	1	975	c.975C>T	c.(973-975)CGC>CGT	p.R325R		NM_005285	NP_005276	P48145	NPBW1_HUMAN	G protein-coupled receptor 7	325	Cytoplasmic (Potential).				synaptic transmission	plasma membrane	opioid receptor activity|protein binding			ovary(2)|breast(1)	3		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				TAACTTGCCGCGCGGCAGCCT	0.692													4	5					0	0	0.006214	0	0	
RP1	6101	broad.mit.edu	37	8	55533986	55533986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:55533986C>T	uc003xsd.1	+	2	608	c.460C>T	c.(460-462)CGG>TGG	p.R154W	RP1_uc011ldy.1_Missense_Mutation_p.R154W	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	154	Doublecortin 2.				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CCGCCCCCCACGGAGCCTAGT	0.692													10	47					0	0	0.002450	0	0	
CHD7	55636	broad.mit.edu	37	8	61765392	61765392	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:61765392G>A	uc003xue.2	+	31	6585	c.6108G>A	c.(6106-6108)CCG>CCA	p.P2036P		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2036					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TTACAGAACCGCCCGACCTCT	0.473													22	137					0	0	0.014323	0	0	
CYP7B1	9420	broad.mit.edu	37	8	65528376	65528376	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:65528376A>G	uc003xvj.2	-	3	926	c.722T>C	c.(721-723)ATT>ACT	p.I241T		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	241					bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				TTTCTCTCTAATAGACTTGAC	0.328													4	139					0	0	0.000602	0	0	
ADHFE1	137872	broad.mit.edu	37	8	67369347	67369347	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:67369347A>G	uc003xwb.3	+	12	1142	c.1108A>G	c.(1108-1110)ACT>GCT	p.T370A	ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Missense_Mutation_p.T322A|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_Missense_Mutation_p.T300A	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	370					2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			AGCGGTGTTCACTTTCACGGC	0.483													17	177					0	0	0.008871	0	0	
C8orf45	157777	broad.mit.edu	37	8	67789611	67789611	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:67789611T>G	uc003xwz.3	+	5	484	c.313T>G	c.(313-315)TTA>GTA	p.L105V	C8orf45_uc003xwv.2_Missense_Mutation_p.L105V|C8orf45_uc011lev.1_Missense_Mutation_p.L105V|C8orf45_uc011lew.1_Missense_Mutation_p.L36V|C8orf45_uc011lex.1_Intron|C8orf45_uc003xwy.3_Missense_Mutation_p.L105V	NM_173518	NP_775789	Q4G0Z9	CH045_HUMAN	minichromosome maintenance complex	105					DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)			ATTAACACATTTACCTCCCCT	0.299													4	47					0	0	0.000602	0	0	
NCOA2	10499	broad.mit.edu	37	8	71068296	71068296	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:71068296T>C	uc003xyn.1	-	11	2466	c.2304A>G	c.(2302-2304)AGA>AGG	p.R768R		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	768					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TACTGTCCAGTCTCTCAAGTT	0.398			T	RUNXBP2	AML								10	60					0	0	0.010729	0	0	
NCOA2	10499	broad.mit.edu	37	8	71068364	71068364	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:71068364G>A	uc003xyn.1	-	11	2398	c.2236C>T	c.(2236-2238)CGC>TGC	p.R746C		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	746	LXXLL motif 3.				cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			AGCAAATAGCGAAGTAGTGCA	0.448			T	RUNXBP2	AML								32	98					0	0	0.004878	0	0	
TRPA1	8989	broad.mit.edu	37	8	72946564	72946564	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:72946564T>C	uc003xza.2	-	22	2779	c.2604A>G	c.(2602-2604)AAA>AAG	p.K868K	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	868	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	TCAACAAAGTTTTCAAAATTA	0.294													6	92					0	0	0.001984	0	0	
JPH1	56704	broad.mit.edu	37	8	75171672	75171672	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:75171672G>A	uc003yae.2	-	3	1246	c.1206C>T	c.(1204-1206)TGC>TGT	p.C402C	JPH1_uc003yaf.2_Silent_p.C402C|JPH1_uc003yag.1_Silent_p.C266C	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	402	Ala-rich.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			TCGCGATGTCGCACTCCTGGC	0.617													7	64					0	0	0.003080	0	0	
ZFHX4	79776	broad.mit.edu	37	8	77768354	77768354	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:77768354G>A	uc003yav.2	+	10	9449	c.9062G>A	c.(9061-9063)CGT>CAT	p.R3021H	ZFHX4_uc003yau.1_Missense_Mutation_p.R3066H|ZFHX4_uc003yaw.1_Missense_Mutation_p.R3021H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3021						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GAACTTGATCGTATAAAGAAA	0.552										HNSCC(33;0.089)			49	101					0	0	0.014410	0	0	
PSKH2	85481	broad.mit.edu	37	8	87060712	87060712	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:87060712C>T	uc011lfy.1	-	3	1137	c.1137G>A	c.(1135-1137)TCG>TCA	p.S379S		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	379							ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)			CAGACAGTGGCGATTCTACTA	0.428													15	93					0	0	0.004990	0	0	
RUNX1T1	862	broad.mit.edu	37	8	93026963	93026963	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:93026963A>G	uc003yfd.2	-	3	396	c.312T>C	c.(310-312)TCT>TCC	p.S104S	RUNX1T1_uc003yfc.1_Silent_p.S77S|RUNX1T1_uc003yfe.1_Silent_p.S67S|RUNX1T1_uc010mao.2_Silent_p.S77S|RUNX1T1_uc011lgi.1_Silent_p.S115S|RUNX1T1_uc003yfh.1_Silent_p.S67S|RUNX1T1_uc003yfb.1_Silent_p.S67S|RUNX1T1_uc003yff.1_Silent_p.S67S|RUNX1T1_uc003yfg.1_Silent_p.S67S	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	104	Poly-Ser.				generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)			AGGAGGAGGAAGAAGAGGAAG	0.547													18	46					0	0	0.008871	0	0	
GEM	2669	broad.mit.edu	37	8	95272569	95272569	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:95272569G>A	uc003ygj.2	-	2	412	c.163C>T	c.(163-165)CGC>TGC	p.R55C	GEM_uc003ygi.2_Missense_Mutation_p.R55C	NM_005261	NP_005252	P55040	GEM_HUMAN	GTP-binding mitogen-induced T-cell protein	55					cell surface receptor linked signaling pathway|immune response|small GTPase mediated signal transduction	internal side of plasma membrane	calmodulin binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding			lung(1)	1	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			CAGCTTCGGCGGCAGTGGTCC	0.602													18	17					0	0	0.002780	0	0	
CCNE2	9134	broad.mit.edu	37	8	95900288	95900288	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:95900288T>C	uc003yhc.2	-	7	576	c.467A>G	c.(466-468)TAC>TGC	p.Y156C	CCNE2_uc003yhd.2_Missense_Mutation_p.Y156C	NM_057749	NP_477097	O96020	CCNE2_HUMAN	cyclin E2	156					cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	cytosol|nucleoplasm	protein kinase binding				0	Breast(36;8.75e-07)					ATGAAGTGTGTATACTTCACA	0.279													8	78					0	0	0.006214	0	0	
VPS13B	157680	broad.mit.edu	37	8	100568810	100568810	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:100568810C>T	uc003yiv.2	+	31	5064	c.4953C>T	c.(4951-4953)GTC>GTT	p.V1651V	VPS13B_uc003yiw.2_Silent_p.V1626V	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1651					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGGAAAGTGTCTCAGGAGGGG	0.433													10	62					0	0	0.010729	0	0	
RNF19A	25897	broad.mit.edu	37	8	101300355	101300355	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:101300355C>T	uc003yjj.1	-	3	365	c.48G>A	c.(46-48)CTG>CTA	p.L16L	RNF19A_uc003yjk.1_Silent_p.L16L|RNF19A_uc003yjl.1_Silent_p.L16L	NM_015435	NP_056250	Q9NV58	RN19A_HUMAN	ring finger protein 19	16					microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			TGTTTACACACAGCCCTTCAT	0.368													22	48					0	0	0.014323	0	0	
UBR5	51366	broad.mit.edu	37	8	103358524	103358524	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:103358524G>A	uc003ykr.1	-	7	709	c.676C>T	c.(676-678)CGG>TGG	p.R226W	UBR5_uc003yks.1_Missense_Mutation_p.R226W	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	226					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TCATCATCCCGGCTAAGTAAA	0.423													8	189					0	0	0.006214	0	0	
OXR1	55074	broad.mit.edu	37	8	107718844	107718844	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:107718844G>A	uc011lht.1	+	8	1197	c.1098G>A	c.(1096-1098)GCG>GCA	p.A366A	OXR1_uc003ymf.2_Silent_p.A365A|OXR1_uc011lhu.1_Silent_p.A358A|OXR1_uc010mcg.2_Intron|OXR1_uc010mch.2_Silent_p.A63A|OXR1_uc003ymg.1_Silent_p.A298A|OXR1_uc003ymi.1_Silent_p.A277A	NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1	366					cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			CTTCTGGTGCGTCATCAGAAT	0.418													20	72					0	0	0.014323	0	0	
PKHD1L1	93035	broad.mit.edu	37	8	110510979	110510979	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:110510979A>G	uc003yne.2	+	67	10911	c.10807A>G	c.(10807-10809)AGT>GGT	p.S3603G		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3603	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CAATGCCATCAGTGGCCTTTT	0.403										HNSCC(38;0.096)			4	46					0	0	0.009096	0	0	
CSMD3	114788	broad.mit.edu	37	8	113841970	113841970	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:113841970T>C	uc003ynu.2	-	12	1963	c.1804A>G	c.(1804-1806)ACC>GCC	p.T602A	CSMD3_uc003ynt.2_Missense_Mutation_p.T562A|CSMD3_uc011lhx.1_Missense_Mutation_p.T498A	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	602	Extracellular (Potential).|CUB 3.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ATTGTCAAGGTATCATAGCCA	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			8	69					0	0	0.004482	0	0	
TRPS1	7227	broad.mit.edu	37	8	116427198	116427198	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:116427198G>A	uc003ynz.2	-	6	3358	c.2899C>T	c.(2899-2901)CAG>TAG	p.Q967*	TRPS1_uc011lhy.1_Nonsense_Mutation_p.Q971*|TRPS1_uc003yny.2_Nonsense_Mutation_p.Q980*|TRPS1_uc010mcy.2_Nonsense_Mutation_p.Q967*	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	967					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTGCCCCTCTGCTGTTTGTTG	0.473									Langer-Giedion_syndrome				22	119					0	0	0.003330	0	0	
TRPS1	7227	broad.mit.edu	37	8	116599384	116599384	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:116599384G>A	uc003ynz.2	-	4	2964	c.2505C>T	c.(2503-2505)GCC>GCT	p.A835A	TRPS1_uc011lhy.1_Silent_p.A839A|TRPS1_uc003yny.2_Silent_p.A848A|TRPS1_uc010mcy.2_Silent_p.A835A	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	835					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CCAGATGGGCGGCCTCCACAT	0.617									Langer-Giedion_syndrome				16	71					0	0	0.004990	0	0	
EIF3H	8667	broad.mit.edu	37	8	117658816	117658816	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:117658816A>G	uc003yoa.2	-	7	881	c.855T>C	c.(853-855)AAT>AAC	p.N285N	EIF3H_uc003yob.2_Silent_p.N299N	NM_003756	NP_003747	O15372	EIF3H_HUMAN	eukaryotic translation initiation factor 3,	285					regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					GGCGCTGCATATTCTCCTGCT	0.522													42	122					0	0	0.010771	0	0	
SLC30A8	169026	broad.mit.edu	37	8	118170036	118170036	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:118170036G>A	uc003yoh.2	+	4	755	c.525G>A	c.(523-525)GCG>GCA	p.A175A	SLC30A8_uc010mcz.2_Silent_p.A126A|SLC30A8_uc011lia.1_Silent_p.A126A|SLC30A8_uc003yog.2_Silent_p.A126A	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	175	Extracellular (Potential).				insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AGATCCAGGCGACTGTGATGA	0.557													18	88					0	0	0.008871	0	0	
SLC30A8	169026	broad.mit.edu	37	8	118184853	118184853	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:118184853C>T	uc003yoh.2	+	8	1273	c.1043C>T	c.(1042-1044)ACC>ATC	p.T348I	SLC30A8_uc010mcz.2_Missense_Mutation_p.T299I|SLC30A8_uc011lia.1_Missense_Mutation_p.T299I|SLC30A8_uc003yog.2_Missense_Mutation_p.T299I	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	348	Cytoplasmic (Potential).				insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			CACTCACTCACCATTCAGATG	0.502													47	106					0	0	0.014410	0	0	
EXT1	2131	broad.mit.edu	37	8	118817060	118817060	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:118817060A>G	uc003yok.1	-	10	2729	c.1956T>C	c.(1954-1956)TGT>TGC	p.C652C		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	652	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			GAATGTCCTCACAATTGGCCA	0.443			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				34	76					0	0	0.004289	0	0	
DEPDC6	64798	broad.mit.edu	37	8	120886177	120886177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:120886177G>A	uc003yow.3	+	1	278	c.91G>A	c.(91-93)GCT>ACT	p.A31T	DEPDC6_uc011lid.1_Missense_Mutation_p.A31T	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6	31					intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GGAGCGCATGGCTGAGGTCTT	0.657													4	29					0	0	0.009096	0	0	
COL14A1	7373	broad.mit.edu	37	8	121256225	121256225	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:121256225C>T	uc003yox.2	+	20	2722	c.2457C>T	c.(2455-2457)AGC>AGT	p.S819S	COL14A1_uc003yoy.2_Silent_p.S497S	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	819	Fibronectin type-III 6.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			AAGGCGTCAGCGTCTCCGCTC	0.488													26	116					0	0	0.003330	0	0	
HAS2	3037	broad.mit.edu	37	8	122627011	122627011	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:122627011G>A	uc003yph.2	-	4	1535	c.997C>T	c.(997-999)CGA>TGA	p.R333*		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	333	Cytoplasmic (Potential).					integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			CACTTAGATCGAGCTGTGTAT	0.468													15	128					0	0	0.004007	0	0	
KLHL38	340359	broad.mit.edu	37	8	124663889	124663889	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:124663889G>A	uc003yqs.1	-	1	1302	c.1278C>T	c.(1276-1278)GTC>GTT	p.V426V		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	426	Kelch 3.										0						CTTTCACAGCGACTGCGGGGT	0.552													11	77					0	0	0.008291	0	0	
FAM91A1	157769	broad.mit.edu	37	8	124824810	124824810	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:124824810C>A	uc003yqv.2	+	24	2444	c.2383C>A	c.(2383-2385)CTT>ATT	p.L795I	FAM91A1_uc011lil.1_Missense_Mutation_p.L553I	NM_144963	NP_659400	Q658Y4	F91A1_HUMAN	hypothetical protein LOC157769	795										ovary(1)|central_nervous_system(1)	2	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TTCAAGTTTGCTTTCACAGTC	0.383													29	102					5.8336e-16	6.55255e-16	0.003271	1	0	
FER1L6	654463	broad.mit.edu	37	8	125074138	125074138	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:125074138G>A	uc003yqw.2	+	25	3399	c.3193G>A	c.(3193-3195)GTG>ATG	p.V1065M	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1065	Cytoplasmic (Potential).|C2 4.					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)			GAGCATCTGCGTGGTGGACTG	0.557													8	74					0	0	0.008291	0	0	
TG	7038	broad.mit.edu	37	8	133899619	133899619	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:133899619C>T	uc003ytw.2	+	9	2043	c.2002C>T	c.(2002-2004)CGC>TGC	p.R668C		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	668	Thyroglobulin type-1 6.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GCAAAGGGCTCGCATGCAAAG	0.557													7	47					0	0	0.003080	0	0	
ZFAT	57623	broad.mit.edu	37	8	135649947	135649947	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:135649947C>T	uc003yup.2	-	3	380	c.205G>A	c.(205-207)GTC>ATC	p.V69I	ZFAT_uc003yun.2_Missense_Mutation_p.V57I|ZFAT_uc003yuo.2_Missense_Mutation_p.V57I|ZFAT_uc010meh.2_Missense_Mutation_p.V57I|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.V57I|ZFAT_uc010mej.2_Missense_Mutation_p.V69I|ZFAT_uc003yur.2_Missense_Mutation_p.V57I	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	69					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CTCTTCATGACCAAAAACTCT	0.522													24	59					0	0	0.003330	0	0	
KHDRBS3	10656	broad.mit.edu	37	8	136594174	136594174	+	Missense_Mutation	SNP	C	T	T	rs150971318		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:136594174C>T	uc003yuv.2	+	6	1059	c.665C>T	c.(664-666)ACG>ATG	p.T222M	KHDRBS3_uc003yuw.2_Missense_Mutation_p.T222M|KHDRBS3_uc010mek.2_RNA	NM_006558	NP_006549	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal	222	Interaction with SIAH1.			Missing: Complete loss of SIAH1-mediated degradation.	regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			CCACGAGGGACGCCAACTCCC	0.557													14	54					0	0	0.002450	0	0	
EIF2C2	27161	broad.mit.edu	37	8	141567204	141567204	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:141567204G>C	uc003yvn.2	-	8	1050	c.1010C>G	c.(1009-1011)ACC>AGC	p.T337S	EIF2C2_uc010men.2_Missense_Mutation_p.T260S|EIF2C2_uc010meo.2_Missense_Mutation_p.T337S	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	337	PAZ.				mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			GGGAAGGTAGGTGTGTTTCTG	0.607													29	82					0	0	0.010818	0	0	
DENND3	22898	broad.mit.edu	37	8	142186732	142186732	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:142186732C>T	uc003yvy.2	+	15	2616	c.2338C>T	c.(2338-2340)CCC>TCC	p.P780S	DENND3_uc010mep.2_Missense_Mutation_p.P741S	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	780										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TCGGAGAATACCCACTTTAAA	0.468													12	55					0	0	0.001855	0	0	
EPPK1	83481	broad.mit.edu	37	8	144942358	144942358	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:144942358G>A	uc003zaa.1	-	1	5077	c.5064C>T	c.(5062-5064)GGC>GGT	p.G1688G		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1688	Plectin 29.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGATGATGCCGCCCGTGGCGA	0.672													22	28					0	0	0.004656	0	0	
LRRC14	9684	broad.mit.edu	37	8	145745377	145745377	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:145745377C>A	uc003zdk.1	+	2	414	c.268C>A	c.(268-270)CTG>ATG	p.L90M	RECQL4_uc003zdj.2_5'Flank|LRRC14_uc003zdl.1_Missense_Mutation_p.L90M|LRRC14_uc003zdo.2_5'Flank	NM_014665	NP_055480	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	90											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)			GGCTGTTATCCTGGGGCTGAC	0.647													6	33					0.00116845	0.00122775	0.001168	1	0	
ARHGAP39	80728	broad.mit.edu	37	8	145771022	145771022	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:145771022C>T	uc003zdt.1	-	7	2687	c.2132G>A	c.(2131-2133)CGG>CAG	p.R711Q	ARHGAP39_uc011llk.1_Missense_Mutation_p.R711Q|ARHGAP39_uc003zds.1_Missense_Mutation_p.R711Q	NM_025251	NP_079527	Q9C0H5	RHG39_HUMAN	KIAA1688 protein	711					axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0						CACCTTCCGCCGGAAGAGGCC	0.612													5	26					0	0	0.000602	0	0	
FOXD4	2298	broad.mit.edu	37	9	117619	117619	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:117619G>A	uc003zfz.2	-	1	799	c.501C>T	c.(499-501)CGC>CGT	p.R167R		NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4	167	Fork-head.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GGCCCGGCTCGCGGGGGATCT	0.632													23	224					0	0	0.003954	0	0	
KANK1	23189	broad.mit.edu	37	9	711849	711849	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:711849G>A	uc003zgl.1	+	7	1732	c.1083G>A	c.(1081-1083)ACG>ACA	p.T361T	KANK1_uc003zgm.2_Silent_p.T361T|KANK1_uc003zgn.1_Silent_p.T361T|KANK1_uc003zgo.1_Silent_p.T361T|KANK1_uc003zgp.1_Silent_p.T361T|KANK1_uc003zgq.2_Silent_p.T203T|KANK1_uc003zgr.1_Silent_p.T203T|KANK1_uc003zgs.1_Silent_p.T203T	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	361	Potential.				negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		AACAGAGCACGCAGAGGATAA	0.557													5	41					0	0	0.001168	0	0	
DMRT3	58524	broad.mit.edu	37	9	990216	990216	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:990216C>T	uc003zgw.1	+	2	668	c.630C>T	c.(628-630)AAC>AAT	p.N210N		NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor	210					cell differentiation|multicellular organismal development|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		TCCAGAAAAACGGAGGCAACC	0.597													15	39					0	0	0.003163	0	0	
PTPRD	5789	broad.mit.edu	37	9	8518269	8518269	+	Silent	SNP	C	T	T	rs137892356		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:8518269C>T	uc003zkk.2	-	20	1833	c.1122G>A	c.(1120-1122)GCG>GCA	p.A374A	PTPRD_uc003zkp.2_Silent_p.A374A|PTPRD_uc003zkq.2_Silent_p.A374A|PTPRD_uc003zkr.2_Silent_p.A368A|PTPRD_uc003zks.2_Silent_p.A364A|PTPRD_uc003zkl.2_Silent_p.A374A|PTPRD_uc003zkm.2_Silent_p.A361A|PTPRD_uc003zkn.2_Silent_p.A374A|PTPRD_uc003zko.2_Silent_p.A371A	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	374	Fibronectin type-III 1.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		AGCGTGTGGTCGCCACCCCAT	0.483										TSP Lung(15;0.13)			20	102					0	0	0.010504	0	0	
CNTLN	54875	broad.mit.edu	37	9	17394855	17394855	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:17394855A>G	uc003zmz.2	+	15	2429	c.2403A>G	c.(2401-2403)TCA>TCG	p.S801S	CNTLN_uc003zmy.2_Silent_p.S801S|CNTLN_uc010mio.2_Silent_p.S480S	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	801						centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		CACACCAGTCAGCAGACAGAG	0.428													19	82					0	0	0.007413	0	0	
ACO1	48	broad.mit.edu	37	9	32431791	32431791	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:32431791C>T	uc003zqw.3	+	15	1956	c.1801C>T	c.(1801-1803)CGT>TGT	p.R601C	ACO1_uc010mjh.1_Missense_Mutation_p.R435C|ACO1_uc003zqx.3_Missense_Mutation_p.R601C|ACO1_uc003zqy.3_RNA	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1	601					citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GGCAGTGGAGCGTCAGTATGT	0.488											OREG0019130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	81					0	0	0.006122	0	0	
UBAP2	55833	broad.mit.edu	37	9	33927811	33927811	+	Silent	SNP	C	T	T	rs144703983	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:33927811C>T	uc003ztq.1	-	20	2468	c.2355G>A	c.(2353-2355)GCG>GCA	p.A785A	UBAP2_uc011loc.1_Silent_p.A694A|UBAP2_uc011lod.1_Silent_p.A518A|UBAP2_uc011loe.1_Silent_p.A540A|UBAP2_uc011lof.1_Silent_p.A710A|UBAP2_uc011log.1_3'UTR|UBAP2_uc003ztn.1_Silent_p.A24A|UBAP2_uc003zto.1_Silent_p.A24A|UBAP2_uc003ztp.1_Silent_p.A24A	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2	785										ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		TCACCAAGGGCGCGGCCCTGC	0.642													4	27					0	0	0.009096	0	0	
PIGO	84720	broad.mit.edu	37	9	35089116	35089116	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:35089116C>T	uc003zwd.2	-	11	3639	c.3243G>A	c.(3241-3243)AGG>AGA	p.R1081R	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.2_Silent_p.R664R|PIGO_uc003zwf.2_Silent_p.R664R|PIGO_uc003zwg.1_3'UTR	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	1081					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GAAATAGCTGCCTGAACCAGG	0.527													28	99					0	0	0.006320	0	0	
PIGO	84720	broad.mit.edu	37	9	35095095	35095095	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:35095095G>A	uc003zwd.2	-	2	864	c.468C>T	c.(466-468)CAC>CAT	p.H156H	PIGO_uc003zwc.1_Silent_p.H156H|PIGO_uc003zwe.2_Silent_p.H156H|PIGO_uc003zwf.2_Silent_p.H156H|PIGO_uc003zwg.1_Translation_Start_Site	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	156					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CCACTATGGCGTGGCTGGCGA	0.517													10	45					0	0	0.004007	0	0	
TMEM8B	51754	broad.mit.edu	37	9	35842713	35842713	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:35842713C>T	uc003zym.2	+	7	1293	c.278C>T	c.(277-279)GCG>GTG	p.A93V	TMEM8B_uc003zyk.2_Missense_Mutation_p.A93V|TMEM8B_uc003zyl.2_Missense_Mutation_p.A260V|TMEM8B_uc003zyn.2_Intron|TMEM8B_uc003zyo.2_Missense_Mutation_p.A93V	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a	93	Extracellular (Potential).				cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1						CAGCTCAATGCGGTACTCTTT	0.617													4	13					0	0	0.000602	0	0	
FBXO10	26267	broad.mit.edu	37	9	37537214	37537214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:37537214G>A	uc004aab.2	-	3	1361	c.1312C>T	c.(1312-1314)CGG>TGG	p.R438W	FBXO10_uc004aac.2_Missense_Mutation_p.R454W|FBXO10_uc004aad.2_Intron	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10	438	PbH1 3.					ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(5)	5				GBM - Glioblastoma multiforme(29;0.0107)		TTCCCGTCCCGGAAGAGGCAC	0.582													8	34					0	0	0.010729	0	0	
Unknown	0	broad.mit.edu	37	9	66466537	66466537	+	RNA	SNP	G	A	A	rs148360097	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:66466537G>A	uc004aec.2	+	3		c.1170G>A								Homo sapiens, clone IMAGE:5213378, mRNA.																		acttgtttcagctaaactccc	0													3	15					0	0	0.004672	0	0	
Unknown	0	broad.mit.edu	37	9	68414574	68414574	+	RNA	SNP	T	C	C	rs148221466		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:68414574T>C	uc004aex.2	+	1		c.1129T>C								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		catggtttactgaatatttta	0.005													6	41					0	0	0.001168	0	0	
PGM5	5239	broad.mit.edu	37	9	70993145	70993145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:70993145A>G	uc004agr.2	+	2	521	c.292A>G	c.(292-294)ATC>GTC	p.I98V		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	98					cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2						ACAGAATGGCATCTTGTCGAC	0.478													6	55					0	0	0.001168	0	0	
TMEM2	23670	broad.mit.edu	37	9	74309467	74309467	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:74309467A>G	uc011lsa.1	-	21	4194	c.3654T>C	c.(3652-3654)CCT>CCC	p.P1218P	TMEM2_uc011lrz.1_Silent_p.P211P|TMEM2_uc010mos.2_Silent_p.P1155P|TMEM2_uc011lsb.1_RNA|TMEM2_uc004aik.2_Silent_p.P52P	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	1218						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)		CTGCTTTATCAGGTGACTGGA	0.348													10	38					0	0	0.010729	0	0	
C9orf79	286234	broad.mit.edu	37	9	90502650	90502650	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:90502650T>C	uc004app.3	+	4	3283	c.3248T>C	c.(3247-3249)GTT>GCT	p.V1083A		NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	1083						integral to membrane				ovary(3)	3						TCAGTCTGTGTTGCTCAGGAT	0.602													7	47					0	0	0.006214	0	0	
S1PR3	1903	broad.mit.edu	37	9	91616512	91616512	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:91616512G>A	uc004aqe.2	+	2	793	c.397G>A	c.(397-399)GCC>ACC	p.A133T		NM_005226	NP_005217	Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	133	Helical; Name=3; (By similarity).				anatomical structure morphogenesis|elevation of cytosolic calcium ion concentration|inflammatory response|positive regulation of cell proliferation	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|lung(1)|central_nervous_system(1)|skin(1)	5						ACTGGCCATCGCCATCGAGCG	0.582											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	36					0	0	0.012319	0	0	
C9orf129	445577	broad.mit.edu	37	9	96097723	96097723	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:96097723C>T	uc010mre.2	-	3	662	c.298G>A	c.(298-300)GCC>ACC	p.A100T		NM_001098808	NP_001092278	Q5T035	CI129_HUMAN	hypothetical protein LOC445577	100										ovary(1)	1						GGGAAGTAGGCGGAATCCACG	0.617													9	17					0	0	0.013537	0	0	
FANCC	2176	broad.mit.edu	37	9	97869413	97869413	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:97869413G>A	uc004avh.2	-	14	1730	c.1468C>T	c.(1468-1470)CTT>TTT	p.L490F		NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	490					protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)				TTGAGGAGAAGGTGCCTGATC	0.592			D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				6	30					0	0	0.001984	0	0	
ZNF782	158431	broad.mit.edu	37	9	99581109	99581109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:99581109C>T	uc004awp.1	-	6	1477	c.1196G>A	c.(1195-1197)TGC>TAC	p.C399Y	ZNF782_uc011lup.1_Missense_Mutation_p.C267Y	NM_001001662	NP_001001662	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	399	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				GGCTTTCCCGCACTCAGGACA	0.428													20	98					0	0	0.007413	0	0	
TRIM14	9830	broad.mit.edu	37	9	100854204	100854204	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:100854204C>T	uc004ayd.2	-	5	798	c.780G>A	c.(778-780)TCG>TCA	p.S260S	TRIM14_uc004ayf.1_Silent_p.S167S|TRIM14_uc011luz.1_Silent_p.S38S|TRIM14_uc011lva.1_Silent_p.S41S|TRIM14_uc004ayg.1_Silent_p.S260S|TRIM14_uc004ayh.1_Silent_p.S260S|TRIM14_uc004ayi.1_Intron|TRIM14_uc004ayj.1_Silent_p.S167S	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha	260	B30.2/SPRY.					cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TCAGCAATAGCGATCGCTCTG	0.537													9	63					0	0	0.006214	0	0	
CORO2A	7464	broad.mit.edu	37	9	100887136	100887136	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:100887136G>A	uc004ayl.2	-	12	1764	c.1498C>T	c.(1498-1500)CTG>TTG	p.L500L	CORO2A_uc004aym.2_Silent_p.L500L|CORO2A_uc004ayk.2_Silent_p.L147L	NM_003389	NP_003380	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	500	Potential.				actin cytoskeleton organization|intracellular signal transduction	actin cytoskeleton|transcriptional repressor complex	actin filament binding			skin(2)|ovary(1)|pancreas(1)	4		Acute lymphoblastic leukemia(62;0.0559)				TGGGTCAACAGCTCCCGGAGC	0.567													4	7					0	0	0.000602	0	0	
INVS	27130	broad.mit.edu	37	9	103035322	103035322	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:103035322T>C	uc004bap.1	+	12	1960	c.1748T>C	c.(1747-1749)ATG>ACG	p.M583T	INVS_uc010mta.1_Missense_Mutation_p.M487T|INVS_uc011lve.1_Missense_Mutation_p.M487T|INVS_uc004bao.1_Missense_Mutation_p.M583T|INVS_uc004baq.1_Missense_Mutation_p.M487T|INVS_uc004bar.1_Missense_Mutation_p.M487T|INVS_uc010mtb.1_Missense_Mutation_p.M257T	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	583	IQ 1.				negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)				AATCTCCTCATGAAGCATGAA	0.493													18	148					0	0	0.007413	0	0	
RNF20	56254	broad.mit.edu	37	9	104312994	104312994	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:104312994C>T	uc004bbn.2	+	10	1289	c.1199C>T	c.(1198-1200)GCA>GTA	p.A400V		NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20	400					histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		CAGTTGAAAGCACACTTGGAT	0.493													30	150					0	0	0.005524	0	0	
CYLC2	1539	broad.mit.edu	37	9	105767799	105767799	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:105767799G>A	uc004bbs.2	+	5	956	c.886G>A	c.(886-888)GCC>ACC	p.A296T		NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2	296	31 X 3 AA repeats of K-K-X.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)				taagaaggacgccacgaaaga	0.174													8	52					0	0	0.003080	0	0	
ABCA1	19	broad.mit.edu	37	9	107645350	107645350	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:107645350T>A	uc004bcl.2	-	5	704	c.391A>T	c.(391-393)ACA>TCA	p.T131S	ABCA1_uc004bcm.2_Missense_Mutation_p.T71S	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	131	Extracellular.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TGCTGTAATGTTCTCAGAACT	0.458													15	99					0	0	0.004007	0	0	
CTNNAL1	8727	broad.mit.edu	37	9	111741587	111741587	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:111741587G>A	uc004bdo.1	-	7	1117	c.1075C>T	c.(1075-1077)CAG>TAG	p.Q359*	CTNNAL1_uc010mts.1_Nonsense_Mutation_p.Q95*|CTNNAL1_uc010mtt.1_Nonsense_Mutation_p.Q359*|CTNNAL1_uc004bdp.1_Nonsense_Mutation_p.Q359*	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	359					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		GAAATTAACTGCTGCAGTTCC	0.398													8	59					0	0	0.006214	0	0	
WDR31	114987	broad.mit.edu	37	9	116079127	116079127	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:116079127C>T	uc004bhe.2	-	11	1258	c.1006G>A	c.(1006-1008)GCC>ACC	p.A336T	uc004bhb.2_5'Flank|WDR31_uc004bhc.2_Missense_Mutation_p.A335T|WDR31_uc004bhd.2_Missense_Mutation_p.A211T|WDR31_uc004bhf.2_RNA	NM_001012361	NP_001012361	Q8NA23	WDR31_HUMAN	WD repeat domain 31 isoform 1	336											0						AAGGAGATGGCGTCACCAACA	0.527													9	47					0	0	0.006214	0	0	
RGS3	5998	broad.mit.edu	37	9	116241776	116241776	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:116241776C>A	uc004bhq.2	+	5	630	c.421C>A	c.(421-423)CTG>ATG	p.L141M	RGS3_uc004bhr.2_Missense_Mutation_p.L29M|RGS3_uc004bhs.2_Translation_Start_Site	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	141	C2.				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						CTTAGGTCAGCTGAGGCTGTC	0.537													12	97					4.14922e-12	4.62034e-12	0.004007	1	0	
TNC	3371	broad.mit.edu	37	9	117848173	117848173	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:117848173C>T	uc004bjj.3	-	3	2199	c.1837G>A	c.(1837-1839)GAG>AAG	p.E613K	TNC_uc010mvf.2_Missense_Mutation_p.E613K	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	613	EGF-like 15.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						CTGTAGCCCTCGTTGCAGATG	0.587													6	21					0	0	0.003080	0	0	
PTGS1	5742	broad.mit.edu	37	9	125140783	125140783	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:125140783G>A	uc004bmg.1	+	4	418	c.283G>A	c.(283-285)GGG>AGG	p.G95R	PTGS1_uc011lys.1_Missense_Mutation_p.G70R|PTGS1_uc010mwb.1_5'UTR|PTGS1_uc004bmf.1_Missense_Mutation_p.G95R|PTGS1_uc004bmh.1_5'UTR|PTGS1_uc011lyt.1_5'UTR	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1	95					cyclooxygenase pathway|hormone biosynthetic process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)|skin(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)	GCTCACTCACGGGCGCTGGTT	0.627													9	53					0	0	0.010729	0	0	
ZBTB26	57684	broad.mit.edu	37	9	125681367	125681367	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:125681367G>A	uc004bnj.2	-	2	1059	c.847C>T	c.(847-849)CGT>TGT	p.R283C	ZBTB26_uc004bnk.2_Missense_Mutation_p.R283C	NM_020924	NP_065975	Q9HCK0	ZBT26_HUMAN	zinc finger and BTB domain containing 26	283	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCCAGGTGACGAAACACCCTG	0.463													21	107					0	0	0.004656	0	0	
LHX2	9355	broad.mit.edu	37	9	126777589	126777589	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:126777589C>T	uc004boe.1	+	3	1251	c.512C>T	c.(511-513)GCG>GTG	p.A171V	LHX2_uc010mwi.1_Missense_Mutation_p.A179V	NM_004789	NP_004780	P50458	LHX2_HUMAN	LIM homeobox protein 2	171						nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CACTTCGAGGCGCTGCTGCAG	0.667													8	33					0	0	0.006214	0	0	
ARPC5L	81873	broad.mit.edu	37	9	127637424	127637424	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:127637424C>T	uc004bpa.3	+	3	479	c.393C>T	c.(391-393)CAC>CAT	p.H131H	ARPC5L_uc011lzq.1_Silent_p.H79H	NM_030978	NP_112240	Q9BPX5	ARP5L_HUMAN	actin related protein 2/3 complex, subunit	131					regulation of actin filament polymerization	cytoplasm|cytoskeleton	actin binding				0						TCCAGTGGCACGAAAAGGTAT	0.507													15	64					0	0	0.006122	0	0	
FAM125B	89853	broad.mit.edu	37	9	129154437	129154437	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:129154437C>T	uc004bqh.1	+	5	583	c.502C>T	c.(502-504)CGG>TGG	p.R168W	FAM125B_uc004bqg.1_Missense_Mutation_p.R168W|FAM125B_uc011lzy.1_Missense_Mutation_p.R153W|FAM125B_uc010mxd.2_Missense_Mutation_p.R161W|FAM125B_uc011lzz.1_Missense_Mutation_p.R161W	NM_033446	NP_258257	Q9H7P6	F125B_HUMAN	hypothetical protein LOC89853 isoform 1	168	MABP.				protein transport	late endosome membrane					0						GATCATGGGCCGGACCAAGCA	0.507													25	76					0	0	0.003954	0	0	
ZBTB34	403341	broad.mit.edu	37	9	129642791	129642791	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:129642791G>A	uc004bqm.3	+	2	1198	c.1101G>A	c.(1099-1101)CCG>CCA	p.P367P		NM_001099270	NP_001092740	Q8NCN2	ZBT34_HUMAN	zinc finger and BTB domain containing 34	367					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						ATTGGTACCCGTACAATGAGA	0.537													15	30					0	0	0.003163	0	0	
FAM129B	64855	broad.mit.edu	37	9	130271277	130271277	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:130271277C>T	uc004brh.2	-	10	1497	c.1295G>A	c.(1294-1296)CGA>CAA	p.R432Q	FAM129B_uc004bri.2_Missense_Mutation_p.R419Q|FAM129B_uc004brj.3_Missense_Mutation_p.R432Q	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	432							protein binding				0						GATCTGGGCTCGCTGCTTGAA	0.637													4	18					0	0	0.009096	0	0	
ODF2	4957	broad.mit.edu	37	9	131221920	131221920	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:131221920C>A	uc011mbd.1	+	3	418	c.107C>A	c.(106-108)CCC>CAC	p.P36H	ODF2_uc011maz.1_Missense_Mutation_p.P36H|ODF2_uc011mba.1_5'UTR|ODF2_uc010myb.2_5'UTR|ODF2_uc011mbb.1_5'UTR|ODF2_uc011mbc.1_5'UTR|ODF2_uc004bva.2_5'UTR|ODF2_uc004bvb.2_5'UTR|ODF2_uc011mbe.1_5'UTR|ODF2_uc004bvc.2_5'UTR|ODF2_uc010myc.2_Missense_Mutation_p.P36H|ODF2_uc011mbf.1_Missense_Mutation_p.P36H|ODF2_uc004bvd.3_Missense_Mutation_p.P36H|ODF2_uc004bve.2_Missense_Mutation_p.P36H	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1	36					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1						TGTGGCGCACCCAGTGTAACT	0.517													7	38					2.0095e-06	2.17555e-06	0.001984	1	0	
WDR34	89891	broad.mit.edu	37	9	131396155	131396155	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:131396155C>T	uc004bvq.1	-	9	1603	c.1479G>A	c.(1477-1479)CAG>CAA	p.Q493Q	WDR34_uc004bvs.1_Silent_p.Q484Q|WDR34_uc004bvr.1_Silent_p.Q465Q	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34	493	WD 5.					cytoplasm				central_nervous_system(2)|skin(1)	3						GCTGAGTCTGCTGGCTGTTGA	0.562													6	36					0	0	0.006214	0	0	
DOLK	22845	broad.mit.edu	37	9	131708027	131708027	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:131708027T>C	uc004bwr.2	-	1	1986	c.1556A>G	c.(1555-1557)TAC>TGC	p.Y519C	NUP188_uc004bws.1_5'Flank|NUP188_uc004bwq.1_Intron	NM_014908	NP_055723	Q9UPQ8	DOLK_HUMAN	dolichol kinase	519	Cytoplasmic (Potential).				dolichyl diphosphate biosynthetic process|dolichyl monophosphate biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to endoplasmic reticulum membrane|membrane fraction	dolichol kinase activity				0						CTGTGTAGTGTATGCTTCCAG	0.473													19	72					0	0	0.010504	0	0	
SH3GLB2	56904	broad.mit.edu	37	9	131771036	131771036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:131771036G>A	uc004bwv.2	-	11	1261	c.1115C>T	c.(1114-1116)CCT>CTT	p.P372L	SH3GLB2_uc004bww.2_Missense_Mutation_p.P381L|SH3GLB2_uc004bwx.1_Missense_Mutation_p.P372L|SH3GLB2_uc011mbm.1_Missense_Mutation_p.P381L	NM_020145	NP_064530	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	372	SH3.				filopodium assembly|signal transduction	cytoplasm|nucleus	cytoskeletal adaptor activity|SH3 domain binding				0						GAGCCAGTCAGGGTCCATGCC	0.602											OREG0003926	type=REGULATORY REGION|Gene=SH3GLB2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	3	30					0	0	0.009096	0	0	
SH3GLB2	56904	broad.mit.edu	37	9	131777085	131777085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:131777085G>A	uc004bwv.2	-	4	579	c.433C>T	c.(433-435)CGC>TGC	p.R145C	SH3GLB2_uc004bww.2_Missense_Mutation_p.R145C|SH3GLB2_uc004bwx.1_Missense_Mutation_p.R145C|SH3GLB2_uc011mbm.1_Missense_Mutation_p.R145C	NM_020145	NP_064530	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	145	BAR.				filopodium assembly|signal transduction	cytoplasm|nucleus	cytoskeletal adaptor activity|SH3 domain binding				0						AGGAAGTTGCGCAAGGGTGTG	0.572													14	49					0	0	0.001855	0	0	
USP20	10868	broad.mit.edu	37	9	132630629	132630629	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:132630629G>A	uc004bys.2	+	11	1247	c.1036G>A	c.(1036-1038)GAG>AAG	p.E346K	USP20_uc004byr.2_Missense_Mutation_p.E346K|USP20_uc004byt.1_Missense_Mutation_p.E346K	NM_001110303	NP_001103773	Q9Y2K6	UBP20_HUMAN	ubiquitin specific protease 20	346					endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|ubiquitin thiolesterase activity|zinc ion binding			lung(1)|breast(1)	2		Ovarian(14;0.00556)				GCAAGTGGACGAGGACGCTGA	0.667													4	37					0	0	0.001984	0	0	
LAMC3	10319	broad.mit.edu	37	9	133951290	133951290	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:133951290G>A	uc004caa.1	+	21	3665	c.3567G>A	c.(3565-3567)GCG>GCA	p.A1189A		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	1189	Domain II and I.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCAGCTACGCGCTTCTCTGGA	0.617													4	9					0	0	0.000602	0	0	
NUP214	8021	broad.mit.edu	37	9	134074323	134074323	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:134074323G>A	uc004cag.2	+	29	5553	c.5442G>A	c.(5440-5442)CAG>CAA	p.Q1814Q	NUP214_uc004cah.2_Silent_p.Q1804Q|NUP214_uc004cai.2_Silent_p.Q1244Q|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Silent_p.Q640Q|NUP214_uc011mcf.1_Silent_p.Q591Q|NUP214_uc010mzh.1_Silent_p.Q328Q|NUP214_uc010mzi.1_Silent_p.Q328Q	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1814	Pro/Ser/Thr-rich.|11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GCTTTGGACAGGGAGGCTCTG	0.532			T	DEK|SET|ABL1	AML|T-ALL								11	33					0	0	0.008291	0	0	
RAPGEF1	2889	broad.mit.edu	37	9	134459910	134459910	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:134459910T>C	uc004cbc.2	-	20	2879	c.2749A>G	c.(2749-2751)ATG>GTG	p.M917V	RAPGEF1_uc004cbb.2_Missense_Mutation_p.M935V	NM_005312	NP_005303	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform a	917	Ras-GEF.				activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		ATTACCTTCATGATCTTGATG	0.582													17	54					0	0	0.004990	0	0	
SETX	23064	broad.mit.edu	37	9	135201786	135201786	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:135201786C>T	uc004cbk.2	-	10	5382	c.5199G>A	c.(5197-5199)GTG>GTA	p.V1733V	SETX_uc004cbj.2_Silent_p.V1352V|SETX_uc010mzt.2_Silent_p.V1352V	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1733					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ATCTGACAGGCACAGGTCTTG	0.358													9	48					0	0	0.006214	0	0	
TTF1	7270	broad.mit.edu	37	9	135251410	135251410	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:135251410G>A	uc004cbl.2	-	11	2662	c.2610C>T	c.(2608-2610)GAC>GAT	p.D870D	TTF1_uc011mcp.1_RNA|TTF1_uc004cbm.2_Silent_p.D355D	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	870					negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		CTTCACTATCGTCTTCATAAT	0.254													13	57					0	0	0.003163	0	0	
DDX31	64794	broad.mit.edu	37	9	135487481	135487481	+	Missense_Mutation	SNP	C	T	T	rs148432033		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:135487481C>T	uc004cbq.1	-	19	2454	c.2302G>A	c.(2302-2304)GTG>ATG	p.V768M	DDX31_uc010mzu.1_Missense_Mutation_p.V695M	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	768						nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		TACCTTTTCACGTGTGCTTTC	0.532													29	109					0	0	0.008361	0	0	
C9orf96	169436	broad.mit.edu	37	9	136268949	136268949	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:136268949C>T	uc004cdk.2	+	15	1661	c.1600C>T	c.(1600-1602)CTG>TTG	p.L534L	C9orf96_uc004cdl.2_RNA	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	534							ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GCTGTCCCTGCTGGGTGAGCT	0.682													5	18					0	0	0.000602	0	0	
ADAMTS13	11093	broad.mit.edu	37	9	136320407	136320407	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:136320407T>G	uc004cdv.3	+	25	3694	c.3250T>G	c.(3250-3252)TGC>GGC	p.C1084G	ADAMTS13_uc004cdp.3_Missense_Mutation_p.C311G|ADAMTS13_uc004cdt.1_Missense_Mutation_p.C1084G|ADAMTS13_uc004cdu.1_Missense_Mutation_p.C1053G|ADAMTS13_uc004cdw.3_Missense_Mutation_p.C1084G|ADAMTS13_uc004cdx.3_Missense_Mutation_p.C1053G|ADAMTS13_uc004cdz.3_Missense_Mutation_p.C754G|ADAMTS13_uc004cea.1_5'Flank|ADAMTS13_uc004ceb.3_5'Flank	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1084	TSP type-1 8.				cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CTCTTGGCAGTGCTCTGTTTC	0.473													14	79					0	0	0.002450	0	0	
ADAMTSL2	9719	broad.mit.edu	37	9	136403509	136403509	+	Missense_Mutation	SNP	C	T	T	rs139661631		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:136403509C>T	uc011mdl.1	+	4	829	c.272C>T	c.(271-273)ACG>ATG	p.T91M	ADAMTSL2_uc004cei.2_Missense_Mutation_p.T91M	NM_001145320	NP_001138792	Q86TH1	ATL2_HUMAN	ADAMTS-like 2 precursor	91	TSP type-1 1.				negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)		AGGACCTGCACGGGCACGTCC	0.652													8	40					0	0	0.006214	0	0	
VAV2	7410	broad.mit.edu	37	9	136637093	136637093	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:136637093G>A	uc004ces.2	-	26	2257	c.2211C>T	c.(2209-2211)TTC>TTT	p.F737F	VAV2_uc004cer.2_Silent_p.F727F|VAV2_uc004cet.1_Silent_p.F276F	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform	737	SH2.				angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GGAGGCTGTCGAATTTCTTGG	0.602													11	65					0	0	0.013537	0	0	
CAMSAP1	157922	broad.mit.edu	37	9	138713422	138713422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:138713422C>T	uc004cgr.3	-	11	3085	c.3085G>A	c.(3085-3087)GAA>AAA	p.E1029K	CAMSAP1_uc004cgq.3_Missense_Mutation_p.E919K|CAMSAP1_uc010nbg.2_Missense_Mutation_p.E751K	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	1029						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CTGATGGTTTCGTTAAGCTTC	0.527													5	44					0	0	0.001168	0	0	
SNAPC4	6621	broad.mit.edu	37	9	139276396	139276396	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:139276396G>A	uc004chh.2	-	17	2206	c.2197C>T	c.(2197-2199)CAC>TAC	p.H733Y		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	733					snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		TGCAGAGCGTGTCTCCAGCGC	0.667													3	7					0	0	0.004672	0	0	
NOTCH1	4851	broad.mit.edu	37	9	139391870	139391870	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:139391870G>A	uc004chz.2	-	34	6321	c.6321C>T	c.(6319-6321)CAC>CAT	p.H2107H		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2107	Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TCACGATGTCGTGATGCATGC	0.672			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			5	30					0	0	0.001168	0	0	
TRAF2	7186	broad.mit.edu	37	9	139820309	139820309	+	Missense_Mutation	SNP	G	A	A	rs142412558	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:139820309G>A	uc010nbu.2	+	12	1635	c.1462G>A	c.(1462-1464)GAT>AAT	p.D488N	TRAF2_uc004cjv.2_Missense_Mutation_p.D488N|TRAF2_uc011mek.1_Missense_Mutation_p.D477N|TRAF2_uc010nbw.2_Missense_Mutation_p.D463N	NM_021138	NP_066961	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	488	MATH.				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane	CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		CGTGCGGGACGATGCCATCTT	0.597													9	43					0	0	0.008291	0	0	
Unknown	0	broad.mit.edu	37	MT	9866	9866	+	RNA	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrM:9866C>G	uc011mfi.1	+	1		c.1204C>G			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		ATCTGCTTCATCCGCCAACTA	0.443													306	500					0	0	0.014410	0	0	
Unknown	0	broad.mit.edu	37	MT	13758	13758	+	RNA	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrM:13758C>A	uc004cox.3	+	1		c.1422C>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		AACATTTCCCCCGCATCCCCC	0.478													7	648					0.00448238	0.00469516	0.004482	1	0	
PPP2R3B	28227	broad.mit.edu	37	X	306335	306335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:306335C>T	uc004cpg.2	-	7	1153	c.952G>A	c.(952-954)GTC>ATC	p.V318I	PPP2R3B_uc011mha.1_Missense_Mutation_p.V157I	NM_013239	NP_037371	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'',	318					cell cycle arrest|protein dephosphorylation	nucleus|protein phosphatase type 2A complex	calcium ion binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CAGTAGATGACGTAGAAATGC	0.617													16	41					0	0	0.008871	0	0	
ZBED1	9189	broad.mit.edu	37	X	2407303	2407303	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:2407303G>A	uc004cqg.2	-	2	1659	c.1458C>T	c.(1456-1458)TCC>TCT	p.S486S	DHRSX_uc004cqf.3_Intron|ZBED1_uc004cqh.1_Silent_p.S486S	NM_004729	NP_004720	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	486						nuclear chromosome	DNA binding|metal ion binding|protein dimerization activity|transposase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GCTCGAAGGCGGAGAGGAAGG	0.622													4	30					0	0	0.001984	0	0	
TLR8	51311	broad.mit.edu	37	X	12939516	12939516	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:12939516G>T	uc004cve.2	+	2	2425	c.2357G>T	c.(2356-2358)TGG>TTG	p.W786L	TLR8_uc004cvd.2_Missense_Mutation_p.W804L	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	786	Extracellular (Potential).|LRRCT.				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|lung(2)|large_intestine(1)	7						TTCCGAAGATGGATGGATGAA	0.438													25	80					3.96558e-24	4.4783e-24	0.004656	1	0	
BMX	660	broad.mit.edu	37	X	15543416	15543416	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:15543416G>A	uc004cww.2	+	8	946	c.758G>A	c.(757-759)AGC>AAC	p.S253N	BMX_uc004cwx.3_Missense_Mutation_p.S253N|BMX_uc004cwy.3_Missense_Mutation_p.S253N	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	253	Poly-Ser.				cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					TGCAGTAGCAGCAGCAGTGAA	0.294													11	95					0	0	0.008291	0	0	
ACE2	59272	broad.mit.edu	37	X	15585915	15585915	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:15585915C>T	uc004cxa.1	-	15	2099	c.1931G>A	c.(1930-1932)CGA>CAA	p.R644Q	ACE2_uc004cxb.2_Missense_Mutation_p.R644Q	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor	644	Extracellular (Potential).				angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)	AACAGATGATCGGAACAGGTA	0.373													13	64					0	0	0.013537	0	0	
NHS	4810	broad.mit.edu	37	X	17705908	17705908	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:17705908C>T	uc004cxx.2	+	2	950	c.612C>T	c.(610-612)CGC>CGT	p.R204R	NHS_uc011mix.1_Silent_p.R204R|NHS_uc004cxy.2_Silent_p.R27R|NHS_uc004cxz.2_Silent_p.R27R|NHS_uc004cya.2_5'UTR	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	204						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					TGTACTACCGCGCCCCGTGGC	0.602													13	41					0	0	0.001855	0	0	
PHEX	5251	broad.mit.edu	37	X	22117151	22117151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:22117151G>A	uc004dah.2	+	9	1164	c.961G>A	c.(961-963)GTC>ATC	p.V321I	PHEX_uc011mjr.1_Missense_Mutation_p.V321I|PHEX_uc011mjs.1_Missense_Mutation_p.V224I	NM_000444	NP_000435	P78562	PHEX_HUMAN	phosphate-regulating neutral endopeptidase	321	Extracellular (Potential).				biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3						CATCAAGAAGGTCATTGACAC	0.473													21	78					0	0	0.003954	0	0	
DCAF8L1	139425	broad.mit.edu	37	X	27997798	27997798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:27997798C>T	uc004dbx.1	-	1	1769	c.1654G>A	c.(1654-1656)GTG>ATG	p.V552M		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	552										ovary(3)|skin(1)	4						AGGTGACGCACGAAGAACCGA	0.478													16	89					0	0	0.006122	0	0	
DMD	1756	broad.mit.edu	37	X	31676228	31676228	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:31676228T>G	uc004dda.1	-	54	8150	c.7906A>C	c.(7906-7908)AAT>CAT	p.N2636H	DMD_uc004dcr.1_Missense_Mutation_p.N176H|DMD_uc004dcs.1_Missense_Mutation_p.N176H|DMD_uc004dct.1_Missense_Mutation_p.N176H|DMD_uc004dcu.1_Missense_Mutation_p.N176H|DMD_uc004dcv.1_Missense_Mutation_p.N176H|DMD_uc004dcw.2_Missense_Mutation_p.N1292H|DMD_uc004dcx.2_Missense_Mutation_p.N1295H|DMD_uc004dcz.2_Missense_Mutation_p.N2513H|DMD_uc004dcy.1_Missense_Mutation_p.N2632H|DMD_uc004ddb.1_Missense_Mutation_p.N2628H	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2636	Spectrin 18.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ACATCTACATTTGTCTGCCAC	0.403													14	56					0	0	0.007413	0	0	
DMD	1756	broad.mit.edu	37	X	31792185	31792185	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:31792185A>G	uc004dda.1	-	51	7678	c.7434T>C	c.(7432-7434)GCT>GCC	p.A2478A	DMD_uc004dcr.1_Silent_p.A18A|DMD_uc004dcs.1_Silent_p.A18A|DMD_uc004dct.1_Silent_p.A18A|DMD_uc004dcu.1_Silent_p.A18A|DMD_uc004dcv.1_Silent_p.A18A|DMD_uc004dcw.2_Silent_p.A1134A|DMD_uc004dcx.2_Silent_p.A1137A|DMD_uc004dcz.2_Silent_p.A2355A|DMD_uc004dcy.1_Silent_p.A2474A|DMD_uc004ddb.1_Silent_p.A2470A|DMD_uc004ddd.1_Silent_p.A18A	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2478	Spectrin 17.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTTCTGTCCAAGCCCGGTTGA	0.458													9	88					0	0	0.006214	0	0	
USP11	8237	broad.mit.edu	37	X	47098875	47098875	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:47098875C>T	uc004dhp.2	+	3	541	c.541C>T	c.(541-543)CGC>TGC	p.R181C	USP11_uc004dhq.2_Translation_Start_Site	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	181	DUSP.				protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|lung(1)|central_nervous_system(1)	3						ACCCATTGAACGCAAGGTATA	0.557													6	22					0	0	0.003080	0	0	
SSX6	280657	broad.mit.edu	37	X	47970652	47970652	+	Missense_Mutation	SNP	G	A	A	rs149866259	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:47970652G>A	uc004dix.1	+	4	315	c.193G>A	c.(193-195)GTC>ATC	p.V65I	SSX6_uc011mlv.1_Missense_Mutation_p.V65I	NM_173357	NP_775493			SubName: Full=Putative uncharacterized protein SSX1;												0						AGGTTTCAACGTCACCCTCTC	0.323													5	32					0	0	0.001168	0	0	
PAGE1	8712	broad.mit.edu	37	X	49459349	49459349	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:49459349A>G	uc004dom.2	-	2	158	c.25T>C	c.(25-27)TAT>CAT	p.Y9H		NM_003785	NP_003776	O75459	GAGB1_HUMAN	P antigen family, member 1	9					cellular defense response					skin(1)	1	Ovarian(276;0.236)					CTACGCCGATAGATTAATCTT	0.373													9	32					0	0	0.006214	0	0	
KDM5C	8242	broad.mit.edu	37	X	53228052	53228052	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:53228052A>G	uc004drz.2	-	16	2795	c.2262T>C	c.(2260-2262)GAT>GAC	p.D754D	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Silent_p.D687D|KDM5C_uc004dsa.2_Silent_p.D753D	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	754					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						CAGGAAGCTCATCCAAGGTAT	0.582			N|F|S		clear cell renal carcinoma								7	56					0	0	0.003080	0	0	
XKRX	402415	broad.mit.edu	37	X	100169759	100169759	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:100169759G>A	uc004egn.2	-	3	1523	c.918C>T	c.(916-918)GTC>GTT	p.V306V	XKRX_uc011mre.1_Silent_p.V102V	NM_212559	NP_997724	Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related,	306	Helical; (Potential).					integral to membrane|plasma membrane				breast(1)	1						CCAGAGTGCCGACCCGGCTGA	0.498													36	115					0	0	0.003271	0	0	
AMOT	154796	broad.mit.edu	37	X	112035060	112035060	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:112035060C>A	uc004epr.2	-	6	1926	c.1926G>T	c.(1924-1926)CAG>CAT	p.Q642H	AMOT_uc004eps.2_Missense_Mutation_p.Q233H	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	642	Potential.				actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1						TTCTCCATACCTGCTGGATTC	0.443													20	103					1.22574e-08	1.34438e-08	0.014323	1	0	
DOCK11	139818	broad.mit.edu	37	X	117722266	117722266	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:117722266C>T	uc004eqp.2	+	17	2025	c.1962C>T	c.(1960-1962)AGC>AGT	p.S654S	DOCK11_uc004eqq.2_Silent_p.S420S	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	654	DHR-1.				blood coagulation	cytosol	GTP binding			ovary(3)	3						AATACGATAGCCAGAAAACAT	0.294													15	71					0	0	0.002450	0	0	
THOC2	57187	broad.mit.edu	37	X	122805587	122805587	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:122805587G>C	uc004etu.2	-	9	826	c.794C>G	c.(793-795)TCT>TGT	p.S265C	THOC2_uc011muh.1_Missense_Mutation_p.S186C|THOC2_uc011mui.1_Missense_Mutation_p.S150C	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2	265					intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3						TCTGTATAAAGATGATGGTGT	0.323													22	64					0	0	0.003330	0	0	
MAMLD1	10046	broad.mit.edu	37	X	149639052	149639052	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:149639052A>G	uc004fee.1	+	3	1283	c.1207A>G	c.(1207-1209)ATG>GTG	p.M403V	MAMLD1_uc011mxt.1_Missense_Mutation_p.M365V|MAMLD1_uc011mxu.1_Missense_Mutation_p.M378V|MAMLD1_uc011mxv.1_Missense_Mutation_p.M378V|MAMLD1_uc011mxw.1_Missense_Mutation_p.M330V	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	403					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGCCCGCCATGCCCTATGC	0.587													20	56					0	0	0.002780	0	0	
SRPK3	26576	broad.mit.edu	37	X	153050422	153050422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:153050422G>A	uc004fil.2	+	13	1422	c.1390G>A	c.(1390-1392)GAG>AAG	p.E464K	SRPK3_uc004fik.2_Missense_Mutation_p.E530K|SRPK3_uc010nul.2_Missense_Mutation_p.E388K|SRPK3_uc004fin.2_Missense_Mutation_p.E463K|SRPK3_uc004fim.2_Missense_Mutation_p.E430K	NM_014370	NP_055185	Q9UPE1	SRPK3_HUMAN	serine arginine rich protein-specific kinase 3	464	Protein kinase.				cell differentiation|muscle organ development|muscle tissue development		ATP binding|protein serine/threonine kinase activity			pancreas(2)|lung(1)	3	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CTACCTGTTCGAGCCGCATTC	0.682													3	12					0	0	0.000602	0	0	
MECP2	4204	broad.mit.edu	37	X	153296471	153296471	+	Nonsense_Mutation	SNP	G	A	A	rs62931162		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chrX:153296471G>A	uc004fjv.2	-	4	1034	c.808C>T	c.(808-810)CGA>TGA	p.R270*	MECP2_uc004fjw.2_Nonsense_Mutation_p.R282*	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1	270	A.T hook 2.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCGGCTTTCGGCCCCGTTTC	0.622													8	30					0	0	0.001855	0	0	
C1orf127	148345	broad.mit.edu	37	1	11007833	11007833	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr1:11007833delC	uc010oao.1	-	8	1917	c.1912delG	c.(1912-1914)GCCfs	p.A638fs	C1orf127_uc001arr.1_Frame_Shift_Del_p.A620fs|C1orf127_uc001ars.1_Frame_Shift_Del_p.A612fs	NM_173507	NP_775778	B7ZLG7	B7ZLG7_HUMAN	hypothetical protein LOC148345	638										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGGAGTGAGGCCCCCCGGCCA	0.627													4	7	---	---	---	---						.
CDHR5	53841	broad.mit.edu	37	11	617603	617603	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:617603delG	uc001lqj.2	-	15	2391	c.2286delC	c.(2284-2286)CCCfs	p.P762fs	IRF7_uc009ycb.2_5'Flank|IRF7_uc010qwf.1_5'Flank|IRF7_uc001lqf.2_5'Flank|IRF7_uc010qwg.1_5'Flank|IRF7_uc001lqg.2_5'Flank|IRF7_uc001lqh.2_5'Flank|IRF7_uc001lqi.2_5'Flank|IRF7_uc010qwh.1_5'Flank|CDHR5_uc001lqk.2_Frame_Shift_Del_p.P568fs|CDHR5_uc009ycc.2_Frame_Shift_Del_p.P596fs|CDHR5_uc009ycd.2_Frame_Shift_Del_p.P756fs|CDHR5_uc001lql.2_Frame_Shift_Del_p.P762fs	NM_021924	NP_068743	Q9HBB8	CDHR5_HUMAN	mucin and cadherin-like isoform 1	762	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0						GGGCCGCTGCGGGGGGCTCAG	0.761													6	8	---	---	---	---						.
FNBP4	23360	broad.mit.edu	37	11	47744543	47744543	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:47744543delT	uc009ylv.2	-	15	2943	c.2790delA	c.(2788-2790)AAAfs	p.K930fs	FNBP4_uc001ngi.2_Frame_Shift_Del_p.K244fs|FNBP4_uc001ngj.2_Frame_Shift_Del_p.K837fs	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	930										ovary(1)	1						CTTTCCTTCCTTTTTTTGTCT	0.184													5	10	---	---	---	---						.
INPPL1	3636	broad.mit.edu	37	11	71948748	71948748	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr11:71948748delC	uc001osf.2	+	26	3607	c.3460delC	c.(3460-3462)CCCfs	p.P1154fs	INPPL1_uc001osg.2_Frame_Shift_Del_p.P912fs	NM_001567	NP_001558	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1154					actin filament organization|cell adhesion|endocytosis	actin cortical patch|cytosol	actin binding|SH2 domain binding|SH3 domain binding			skin(2)|ovary(1)|breast(1)	4						GGAGCTGCAGCCCCCCCGGGG	0.697													3	6	---	---	---	---						.
Unknown	0	broad.mit.edu	37	12	70825572	70825572	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr12:70825572delT	uc001svy.1	+	1		c.56delT								Homo sapiens cDNA FLJ30122 fis, clone BRACE1000087.																		ATCAAACCTATTTACTACATA	0.318													2	4	---	---	---	---						.
SUCLA2	8803	broad.mit.edu	37	13	48570982	48570982	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:48570982delT	uc001vbs.2	-	2	324	c.267delA	c.(265-267)AAAfs	p.K89fs	SUCLA2_uc010tgb.1_Frame_Shift_Del_p.K29fs|SUCLA2_uc010tgc.1_5'UTR|SUCLA2_uc010tgd.1_Frame_Shift_Del_p.K29fs|SUCLA2_uc001vbt.1_RNA|SUCLA2_uc001vbu.1_Frame_Shift_Del_p.K89fs	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	89	ATP-grasp.				succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|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;2.1e-06)	Succinic acid(DB00139)	TAGTACCTAATTTTTTGGCAA	0.353													19	41	---	---	---	---						.
BTF3L1	690	broad.mit.edu	37	13	77503127	77503127	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr13:77503127delT	uc001vkb.3	+	1		c.543delT				NR_026983				Homo sapiens basic transcription factor 3, like 1, mRNA (cDNA clone IMAGE:40013884).												0						CTCTTTTCAGTTTTTGCTTAT	0.308													4	5	---	---	---	---						.
TMED8	283578	broad.mit.edu	37	14	77802683	77802683	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr14:77802683delA	uc010ast.1	-	7		c.2185delT				NM_213601		Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain						transport	integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		CCTGGGGCCTAAAAAAATCAG	0.378													2	4	---	---	---	---						.
SCAND2	54581	broad.mit.edu	37	15	85184705	85184705	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr15:85184705delA	uc002bku.2	+	5		c.3520delA			SCAND2_uc002bkt.2_RNA|uc002bky.1_5'Flank	NR_004859				Homo sapiens SCAND2 mRNA, complete cds.												0						TAGTTACTTGAAAAAAGGTAT	0.269													4	2	---	---	---	---						.
Unknown	0	broad.mit.edu	37	16	89981047	89981048	+	RNA	INS	-	TT	TT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr16:89981047_89981048insTT	uc010ciy.1	+	2		c.1550_1551insTT								Homo sapiens cDNA clone IMAGE:40002380.																		gcacatttgtgtgtgtgcctgt	0.000													2	4	---	---	---	---						.
Unknown	0	broad.mit.edu	37	17	78977272	78977273	+	RNA	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr17:78977272_78977273insA	uc002jyx.1	+	1		c.138_139insA								Homo sapiens clone PP552 unknown mRNA.																		gactccatctgaaaaaaaaaag	0.050													3	3	---	---	---	---						.
PTPRS	5802	broad.mit.edu	37	19	5231449	5231449	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:5231449delG	uc002mbv.2	-	14	2261	c.2027delC	c.(2026-2028)CCGfs	p.P676fs	PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Frame_Shift_Del_p.P663fs|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	676	Extracellular (Potential).|Fibronectin type-III 4.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		AGTGGTGGTCGGGGGGATGCC	0.667													8	18	---	---	---	---						.
NTN5	126147	broad.mit.edu	37	19	49173894	49173894	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr19:49173894delC	uc002pkb.2	-	2	446	c.350delG	c.(349-351)GGCfs	p.G117fs	SEC1_uc010xzv.1_Intron|SEC1_uc002pka.2_Intron|SEC1_uc010xzw.1_Intron|SEC1_uc010ema.2_Intron|NTN5_uc002pkc.2_Frame_Shift_Del_p.G117fs	NM_145807	NP_665806	Q8WTR8	NET5_HUMAN	netrin 5 precursor	117						extracellular region				large_intestine(1)|pancreas(1)	2						CCTTTCAGGGCCCCCTAAGGC	0.701													2	4	---	---	---	---						.
FAHD2B	151313	broad.mit.edu	37	2	97749725	97749725	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:97749725delG	uc002sxm.2	-	7	993	c.842delC	c.(841-843)CCAfs	p.P281fs		NM_199336	NP_955368	Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing	281							hydrolase activity|metal ion binding				0						ACCGACACCTGGGGGGGTCCC	0.552													7	14	---	---	---	---						.
Unknown	0	broad.mit.edu	37	2	186659894	186659894	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr2:186659894delA	uc002upm.2	+	1		c.550delA								Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																		CTAAATTTACAAAAAAAACAC	0.403													3	6	---	---	---	---						.
Unknown	0	broad.mit.edu	37	20	11248228	11248228	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr20:11248228delT	uc002wnx.2	-	2		c.1350delA								Homo sapiens hypothetical protein LOC339593, mRNA (cDNA clone IMAGE:5166493), partial cds.																		GCTGCAGTGGTTTTTTTTTCC	0.433													3	5	---	---	---	---						.
Unknown	0	broad.mit.edu	37	21	47875063	47875063	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr21:47875063delT	uc002zjk.2	-	2		c.1366delA								full-length cDNA clone CS0DC003YA14 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																		gcttcttgggtttttttcttt	0.000													4	9	---	---	---	---						.
PSD2	84249	broad.mit.edu	37	5	139193288	139193288	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr5:139193288delG	uc003leu.1	+	3	971	c.766delG	c.(766-768)GGGfs	p.G256fs		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	256					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGGGCCCAGGGGGGGATGA	0.587													5	11	---	---	---	---						.
Unknown	0	broad.mit.edu	37	6	43813354	43813354	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr6:43813354delA	uc003owl.1	-	4		c.628delT								Homo sapiens cDNA FLJ40534 fis, clone TESTI2047824.																		CACAAGCCCTAAAAAACACTT	0.358													4	4	---	---	---	---						.
PTN	5764	broad.mit.edu	37	7	136938377	136938377	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr7:136938377delT	uc003vtq.2	-	3	486	c.123delA	c.(121-123)AAAfs	p.K41fs	PTN_uc010lmx.2_Frame_Shift_Del_p.K41fs|PTN_uc003vtr.1_Frame_Shift_Del_p.K41fs	NM_002825	NP_002816	P21246	PTN_HUMAN	pleiotrophin	41					nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2						ACTTCTTCACTTTTTTTTCTG	0.433													8	15	---	---	---	---						.
RP1L1	94137	broad.mit.edu	37	8	10470757	10470757	+	Frame_Shift_Del	DEL	G	-	-	rs74594406	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:10470757delG	uc003wtc.2	-	4	1080	c.851delC	c.(850-852)CCGfs	p.P284fs		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	284					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)		AGGGCCCACCGGGGGGTTGCT	0.662													21	39	---	---	---	---						.
CYP7B1	9420	broad.mit.edu	37	8	65528706	65528706	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:65528706delT	uc003xvj.2	-	3	596	c.392delA	c.(391-393)AATfs	p.N131fs		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	131					bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				CATGTCATGATTTTTTTGCAA	0.323													29	52	---	---	---	---						.
MIR1208	100302281	broad.mit.edu	37	8	129162432	129162433	+	RNA	INS	-	G	G	rs2648841	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:129162432_129162433insG	hsa-mir-1208|MI0006341	+			c.71_72insG																				0						ACCACTGTGGTGGGGGGGAGTG	0.564													19	42	---	---	---	---						.
WISP1	8840	broad.mit.edu	37	8	134237718	134237718	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr8:134237718delG	uc003yub.2	+	4	772	c.696delG	c.(694-696)CTGfs	p.L232fs	WISP1_uc003yuc.2_Frame_Shift_Del_p.L145fs|WISP1_uc010meb.2_Frame_Shift_Del_p.L60fs|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron|WISP1_uc003yud.2_Intron	NM_003882	NP_003873	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	232	TSP type-1.				cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GCTGCGGCCTGGGGGTCTCCA	0.607													30	44	---	---	---	---						.
FREM1	158326	broad.mit.edu	37	9	14789027	14789028	+	Frame_Shift_Del	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:14789027_14789028delGT	uc003zlm.2	-	23	4656_4657	c.4066_4067delAC	c.(4066-4068)ACCfs	p.T1356fs	FREM1_uc010mic.2_Intron	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	1356	CSPG 9.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		CATTGCCCCGGTGTGTGTGTAT	0.520													16	28	---	---	---	---						.
LOC442421	442421	broad.mit.edu	37	9	66502886	66502886	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:66502886delT	uc004aed.1	+	3		c.2979delT								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						GTGGCAAATATTTTTTTTTTG	0.313													4	3	---	---	---	---						.
COL27A1	85301	broad.mit.edu	37	9	117038016	117038016	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	cf40f330-fe61-46ba-9b96-ad011d85bb21	7966b3b9-707d-40ce-9895-151824d97ea7	g.chr9:117038016delC	uc011lxl.1	+	37	3685	c.3685delC	c.(3685-3687)CCCfs	p.P1229fs	COL27A1_uc004bii.2_RNA	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	1229	Collagen-like 10.|Pro-rich.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						TGAGGACGGGCCCCCCGGCCC	0.682													3	6	---	---	---	---						.
